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BRAIN 2025

A SCIENTIFIC VISION

BrainResearchthroughAdvancingInnovative
Neurotechnologies(BRAIN)WorkingGroup
ReporttotheAdvisoryCommitteetothe
Director,NIH

June5,2014

R O S T E R

CorneliaBargmann,PhD(cochair)
TheRockefellerUniversity

WilliamNewsome,PhD(cochair)
StanfordUniversity

DavidAnderson,PhD
CaliforniaInstituteofTechnology

EmeryBrown,MD,PhD
MassachusettsInstituteofTechnology
andMassachusettsGeneralHospital

KarlDeisseroth,MD,PhD
StanfordUniversity

JohnDonoghue,PhD
BrownUniversity

PeterMacLeish,PhD
MorehouseSchoolofMedicine

EXOFFICIOMEMBERS

KathyHudson,PhD
NationalInstitutesofHealth

GeoffreyLing,MD,PhD
DefenseAdvancedResearchProjects
Agency

EveMarder,PhD
BrandeisUniversity

RichardNormann,PhD
UniversityofUtah

JoshuaSanes,PhD
HarvardUniversity

MarkSchnitzer,PhD
StanfordUniversity

TerrenceSejnowski,PhD
SalkInstituteforBiologicalStudies

DavidTank,PhD
PrincetonUniversity

RogerTsien,PhD
UniversityofCalifornia,SanDiego

KamilUgurbil,PhD
UniversityofMinnesota

JohnWingfield,PhD
NationalScienceFoundation

CarlosPea,PhD
FoodandDrugAdministration

EXECUTIVESECRETARY

LyricJorgenson,PhD
NationalInstitutesofHealth


TABLEOFCONTENTS

EXECUTIVESUMMARY....5
PREAMBLE......................................................................................................................9
SECTIONI.THEBRAININITIATIVE:VISIONANDPHILOSOPHY.........................................11
TheGoaloftheBRAINInitiative.............................................................................12
FoundationalConcepts:NeuralCoding,NeuralCircuitDynamics,
andNeuromodulation.........................................................................................13
WhyNow?.............................................................................................................14
TheBrainandBehavior..........................................................................................15
StrategiesandExperimentalSystems.....................................................................16
TheRoadsNotTaken............................................................................................. 16
StudyingtheHealthyBrainShouldAccelerateUnderstandingofBrain
Disorders............................................................................................................ 17
TheDeliverablesoftheBRAINInitiative................................................................ 18
SECTIONII.SCIENTIFICREVIEWANDHIGHPRIORITYRESEARCHAREAS.......................... 20
1.MappingtheStructureandComponentsofCircuits........................................... 20
2.NeuronalDynamics:RecordingNeuronalActivityAcrossTimeand
Space...............................................................................................................26
3.ManipulatingCircuitActivity..............................................................................34
4.TheImportanceofBehavior...............................................................................35
5.Theory,Modeling,andStatisticsWillBeEssentialtoUnderstanding
theBrain......................................................................................................... 36
6.HumanNeuroscienceandNeurotechnology.......................................................40
7.Education...........................................................................................................48

8.MaximizingtheValueoftheBRAINInitiative:CorePrinciples............................49

9.FurtherReading..........................56

SECTIONIII.IMPLEMENTATION:GOALS,DELIVERABLES,TIMELINES,ANDCOSTS...........59

1.DiscoveringDiversity..........................................................................................60
2.MapsatMultipleScales..................................................................................... 66
3.TheBraininAction.............................................................................................74
4.DemonstratingCausality.................................................................................... 83
5.IdentifyingFundamentalPrinciples.................................................................... 89
6.AdvancingHumanNeuroscience........................................................................ 100
7.FromBRAINInitiativetotheBrain..................................................................... 107
8.SupportingtheCorePrinciplesoftheBRAINInitiative........................................111
9.CostEstimates... 121
10.ConcludingRemarks...............................................................................124
11.References....................................................................................................... 127
APPENDIXAHOWTHEBRAININITIATIVEWILLADVANCECLINICALRESEARCH...........136

APPENDIXBEXPERTCONSULTATIONS............................142
APPENDIXCACRONYMLIST........................................................................................ 145


EXECUTIVESUMMARY

Thehumanbrainisthesourceofourthoughts,emotions,perceptions,actions,andmemories;
itconfersonustheabilitiesthatmakeushuman,whilesimultaneouslymakingeachofus
unique.Overrecentyears,neurosciencehasadvancedtothelevelthatwecanenvisiona
comprehensiveunderstandingofthebraininaction,spanningmolecules,cells,circuits,
systems,andbehavior.Thisvision,inturn,inspiredtheBRAINInitiative.OnApril2,2013,
PresidentObamalaunchedtheBRAINInitiativetoacceleratethedevelopmentandapplication
ofnewtechnologiesthatwillenableresearcherstoproducedynamicpicturesofthebrainthat
showhowindividualbraincellsandcomplexneuralcircuitsinteractatthespeedofthought.
InresponsetothisGrandChallenge,theNationalInstitutesofHealth(NIH)convenedaworking
groupoftheAdvisoryCommitteetotheDirector,NIH,todeveloparigorousplanforachieving
thisscientificvision.Thisreportpresentsthefindingsandrecommendationsoftheworking
group,includingthescientificbackgroundandrationalefortheBRAINInitiativeasawholeand
foreachofsevenmajorgoalsarticulatedinthereport.Inaddition,weincludespecific
deliverables,timelines,andcostestimatesforthesegoalsasrequestedbytheNIHDirector.
ThechargefromthePresidentandfromtheNIHDirectorisboldandambitious.Theworking
groupagreedthatthebestwaytosetthisvisioninmotionistoacceleratetechnology
development,asreflectedinthenameoftheBRAINInitiative:BrainResearchthrough
AdvancingInnovativeNeurotechnologies.Thefocusisnotontechnologyperse,butonthe
developmentanduseoftoolsforacquiringfundamentalinsightabouthowthenervoussystem
functionsinhealthanddisease.TheinitiativeisonlyonepartoftheNIHsinvestmentinbasic,
translational,andclinicalneuroscience,butneurotechnologyshouldadvanceotherareasas
well.Toachievethesegoals,werecommendthattheBRAINInitiativedevelopoveratenyear
periodbeginninginFY2016,withaprimaryfocusontechnologydevelopmentinthefirstfive
years,shiftinginthesecondfiveyearstoaprimaryfocusonintegratingtechnologiestomake
fundamentalnewdiscoveriesaboutthebrain.Thedistinctionbetweenthesephasesisnot
blackandwhite,butratherisamatterofemphasisandopportunity.Discoverybasedscience
willmotivatetechnologydevelopmentinthefirstphase,andfurthertechnologydevelopment
willbeneededasthefocusshiftstodiscoveryinlateryears.
Inconsideringthesegoalsandthecurrentstateofneuroscience,theworkinggroupidentified
theanalysisofcircuitsofinteractingneuronsasbeingparticularlyrichinopportunity,with
potentialforrevolutionaryadvances.Trulyunderstandingacircuitrequiresidentifyingand
characterizingthecomponentcells,definingtheirsynapticconnectionswithoneanother,
observingtheirdynamicpatternsofactivityasthecircuitfunctionsinvivoduringbehavior,and
perturbingthesepatternstotesttheirsignificance.Italsorequiresanunderstandingofthe
algorithmsthatgoverninformationprocessingwithinacircuitandbetweeninteractingcircuits
inthebrainasawhole.Theanalysisofcircuitsisnottheonlyareaofneuroscienceworthyof
attention,butadvancesintechnologyaredrivingaqualitativeshiftinwhatispossible,and
focusedprogressinthisareawillbenefitmanyotherareasofneuroscience.

Withtheseconsiderationsinmind,theworkinggroupconsultedextensivelywiththescientific
communitytoevaluatechallengesandopportunitiesinthefield.Thefollowingareaswere
identifiedashighprioritiesfortheBRAINInitiative.Thesegoalsareintellectuallyandpractically
expandedinSectionsIIandIIIofthisreport.
#1.Discoveringdiversity:Identifyandprovideexperimentalaccesstothedifferentbraincell
typestodeterminetheirrolesinhealthanddisease.Itiswithinreachtocharacterizeallcell
typesinthenervoussystem,andtodeveloptoolstorecord,mark,andmanipulatethese
preciselydefinedneuronsinthelivingbrain.Weenvisionanintegrated,systematiccensusof
neuronalandglialcelltypes,andnewgeneticandnongenetictoolstodelivergenes,proteins,
andchemicalstocellsofinterestinnonhumananimalsandinhumans.
#2.Mapsatmultiplescales:Generatecircuitdiagramsthatvaryinresolutionfromsynapses
tothewholebrain.Itisincreasinglypossibletomapconnectedneuronsinlocalcircuitsand
distributedbrainsystems,enablinganunderstandingoftherelationshipbetweenneuronal
structureandfunction.Weenvisionimprovedtechnologiesfaster,lessexpensive,scalable
foranatomicreconstructionofneuralcircuitsatallscales,fromnoninvasivewholehuman
brainimagingtodensereconstructionofsynapticinputsandoutputsatthesubcellularlevel.
#3.Thebraininaction:Produceadynamicpictureofthefunctioningbrainbydevelopingand
applyingimprovedmethodsforlargescalemonitoringofneuralactivity.Weshouldseizethe
challengeofrecordingdynamicneuronalactivityfromcompleteneuralnetworks,overlong
periods,inallareasofthebrain.Therearepromisingopportunitiesbothforimprovingexisting
technologiesandfordevelopingentirelynewtechnologiesforneuronalrecording,including
methodsbasedonelectrodes,optics,moleculargenetics,andnanoscience,andencompassing
differentfacetsofbrainactivity.
#4.Demonstratingcausality:Linkbrainactivitytobehaviorwithpreciseinterventionaltools
thatchangeneuralcircuitdynamics.Bydirectlyactivatingandinhibitingpopulationsof
neurons,neuroscienceisprogressingfromobservationtocausation,andmuchmoreis
possible.Toenabletheimmensepotentialofcircuitmanipulation,anewgenerationoftools
foroptogenetics,chemogenetics,andbiochemicalandelectromagneticmodulationshouldbe
developedforuseinanimalsandeventuallyinhumanpatients.
#5.Identifyingfundamentalprinciples:Produceconceptualfoundationsforunderstanding
thebiologicalbasisofmentalprocessesthroughdevelopmentofnewtheoreticalanddata
analysistools.Rigoroustheory,modeling,andstatisticsareadvancingourunderstandingof
complex,nonlinearbrainfunctionswherehumanintuitionfails.Newkindsofdataareaccruing
atincreasingrates,mandatingnewmethodsofdataanalysisandinterpretation.Toenable
progressintheoryanddataanalysis,wemustfostercollaborationsbetweenexperimentalists
andscientistsfromstatistics,physics,mathematics,engineering,andcomputerscience.
#6.Advancinghumanneuroscience:Developinnovativetechnologiestounderstandthe
humanbrainandtreatitsdisorders;createandsupportintegratedhumanbrainresearch
networks.Consentinghumanswhoareundergoingdiagnosticbrainmonitoring,orreceiving
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neurotechnologyforclinicalapplications,provideanextraordinaryopportunityforscientific
research.Thissettingenablesresearchonhumanbrainfunction,themechanismsofhuman
braindisorders,theeffectoftherapy,andthevalueofdiagnostics.Meetingthisopportunity
requirescloselyintegratedresearchteamsperformingaccordingtothehighestethical
standardsofclinicalcareandresearch.Newmechanismsareneededtomaximizethe
collectionofthispricelessinformationandensurethatitbenefitspeoplewithbraindisorders.
#7.FromBRAINInitiativetothebrain:Integratenewtechnologicalandconceptual
approachesproducedinGoals#16todiscoverhowdynamicpatternsofneuralactivityare
transformedintocognition,emotion,perception,andactioninhealthanddisease.Themost
importantoutcomeoftheBRAINInitiativewillbeacomprehensive,mechanisticunderstanding
ofmentalfunctionthatemergesfromsynergisticapplicationofthenewtechnologiesand
conceptualstructuresdevelopedundertheBRAINInitiative.
TheoverarchingvisionoftheBRAINInitiativeisbestcapturedbyGoal#7combiningthese
approachesintoasingle,integratedscienceofcells,circuits,brain,andbehavior.Forexample,
immensevalueisaddedifrecordingsareconductedfromidentifiedcelltypeswhose
anatomicalconnectionsareestablishedinthesamestudy.Suchanexperimentiscurrentlyan
exceptionaltourdeforce;withnewtechnology,itcouldbecomeroutine.Inanotherexample,
neuronalpopulationsrecordedduringcomplexbehaviormightbeimmediatelyretestedwith
circuitmanipulationtechniquestodeterminetheircausalroleingeneratingthebehavior.
Theoryandmodelingshouldbewovenintosuccessivestagesofongoingexperiments,enabling
bridgestobebuiltfromsinglecellstoconnectivity,populationdynamics,andbehavior.
Thissyntheticapproachwillenablepenetratingsolutionstolongstandingproblemsinbrain
function,butwealsoemphasizethelikelihoodofentirelynew,unexpecteddiscoveriesthatwill
resultfromthenewtechnologies.Insomesense,BRAINInitiativescientistswhoapplythenew
activitymonitoringtechnologywillbelikeGalileolookingintotheheavenswiththefirstoptical
telescope.Similarly,newperturbationtoolsandquantitativeapproachesarelikelytoyield
extraordinaryinsightsintotherelationshipbetweenbrainactivityandmentalfunctions.We
expecttodiscovernewformsofneuralcodingasexcitingasthediscoveryofplacecells,and
newformsofneuraldynamicsthatunderlieneuralcomputations.
Overthecourseofourdeliberations,specificthemesemergedthatshouldbecomecore
principlesfortheNIHBRAINInitiative.
1. Pursuehumanstudiesandnonhumanmodelsinparallel.Thegoalistounderstandthe
humanbrain,butmanymethodsandideaswillbedevelopedfirstinanimalmodels.
Experimentsshouldtakeadvantageoftheuniquestrengthsofdiversespeciesand
experimentalsystems.
2. Crossboundariesininterdisciplinarycollaborations.Nosingleresearcherordiscovery
willsolvethebrainsmysteries.Themostexcitingapproacheswillbridgefields,linking
experimenttotheory,biologytoengineering,tooldevelopmenttoexperimental
application,humanneurosciencetononhumanmodels,andmore,ininnovativeways.
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3. Integratespatialandtemporalscales.Aunifiedviewofthebrainwillcrossspatialand
temporallevels,recognizingthatthenervoussystemconsistsofinteractingmolecules,
cells,andcircuitsacrosstheentirebody,andimportantfunctionscanoccurin
millisecondsorminutes,ortakealifetime.
4. Establishplatformsforsharingdata.Public,integratedrepositoriesfordatasetsand
dataanalysistools,withanemphasisonreadyaccessibilityandeffectivecentral
maintenance,willhaveimmensevalue.
5. Validateanddisseminatetechnology.Newmethodsshouldbecriticallytestedthrough
iterativeinteractionbetweentoolmakersandexperimentalists.Aftervalidation,
mechanismsmustbedevelopedtomakenewtoolsavailabletoall.
6. Considerethicalimplicationsofneuroscienceresearch.BRAINInitiativeresearchmay
raiseimportantissuesaboutneuralenhancement,dataprivacy,andappropriateuseof
braindatainlaw,educationandbusiness.Theseimportantissuesmustbeconsidered
inaseriousandsustainedmanner.BRAINInitiativeresearchshouldhewtothehighest
ethicalstandardsforresearchwithhumansubjectsandwithnonhumananimalsunder
applicablefederalandlocallaws.
7. AccountabilitytoNIH,thetaxpayer,andthebasic,translational,andclinical
neurosciencecommunities.TheBRAINInitiativeisextremelybroadininterdisciplinary
scopeandwillinvolvemultiplepartnersbothwithinandoutsidetheNIH.Oversight
mechanismsshouldbeestablishedtoensurethatBRAINfundsareinvestedwiselyfor
theultimatebenefitofthepublicandthescientificcommunity.
ToguidetheBRAINInitiativeandensurethatthesegoalsandprinciplesareevaluatedand
refreshedasappropriate,werecommendthatascientificadvisoryboardbeestablished,tobe
composedofscientistswhoareexpertsinthediversefieldsrelevanttotheInitiative
neuroscience,molecularbiology,theclinicalsciences,thephysicalandquantitativesciences,
andethics.Therapidpaceoftechnologicalandconceptualchangeinneurosciencealmost
ensuresthatsomeportionsofthisreportwillbeobsoletewithinseveralyears.Acohesiveand
rigorousscientificadvisoryboardwillbeinvaluableinrespondingtofuturechallenges.
Aspartoftheplanningprocess,theworkinggroupwasaskedtoestimatethecostoftheBRAIN
Initiative.Whilewedidnotconductadetailedcostanalysis,weconsideredthescopeofthe
questionstobeaddressedbytheinitiative,andthecostofprogramsthathavedevelopedin
relatedareasoverrecentyears.Thusourbudgetestimates,whileprovisional,areinformedby
thecostsofrealneuroscienceatthistechnologicallevel.Tovigorouslyadvancethegoalsofthe
BRAINInitiativeasstatedabove,werecommendaninvestmentbytheNIHthatrampsupto
$400million/yearoverthenextfiveyears(FY1620),andcontinuesat$500million/year
subsequently(FY2125).Asustained,decadelongcommitmentatthislevelwillattract
talentedscientistsfrommultiplefieldstotheinterdisciplinarycollaborationsthatareessential
totheBRAINInitiativeanditsambitiousgoals.

PREAMBLE

Westandonthevergeofagreatjourneyintotheunknowntheinteriorterrainofthinking,
feeling,perceiving,learning,deciding,andactingtoachieveourgoalsthatisthespecial
provinceofthehumanbrain.Thesecapacitiesaretheessenceofourmindsandtheaspectsof
beinghumanthatmattermosttous.Remarkably,thesepowerfulyetexquisitelynuanced
capacitiesemergefromelectricalandchemicalinteractionsamongroughly100billionnerve
cellsandglialcellsthatcomposeourbrains.Allhumanbrainssharebasicanatomicalcircuits
andsynapticinteractions,buttheprecisepatternofconnectionsandinteractionsarehighly
variablefrompersontopersonandthereinliesthesourceoftheremarkablevariationwesee
inhumanbehavior,fromthebreathtakingdanceofaballerina,totheelegantcraftsmanshipof
amastercarpenter,totheshrewdjudgmentofanexperttrader.Ourbrainsmakeuswhowe
are,enablingustoperceivebeauty,teachourchildren,rememberlovedones,reactagainst
injustice,learnfromhistory,andimagineadifferentfuture.
Thehumanbrainissimplyastonishingnolessastonishingtothoseofuswhohavespentour
careersstudyingitsmysteriesthantothosenewtothinkingaboutthebrain.PresidentObama,
bycreatingtheBRAINInitiative,hasprovidedanunprecedentedopportunitytosolvethose
mysteries.Thechallengeistomapthecircuitsofthebrain,measurethefluctuatingpatterns
ofelectricalandchemicalactivityflowingwithinthosecircuits,andunderstandhowtheir
interplaycreatesouruniquecognitiveandbehavioralcapabilities.Weshouldpursuethisgoal
simultaneouslyinhumansandinsimplernervoussystemsinwhichwecanlearnimportant
lessonsfarmorequickly.Butourultimategoalistounderstandourownbrains.
LiketheApolloprogram,thischallengingobjectivewillrequirethedevelopmentofanarrayof
newtechnologies,drawingonscientistsandengineersfromamultitudeofdisciplines.These
technologieswillhavetobeintegratedinanunprecedentedmannertoachievetheInitiatives
goals.Weareatauniquemomentinthehistoryofneuroscienceamomentwhen
technologicalinnovationhascreatedpossibilitiesfordiscoveriesthatcould,cumulatively,lead
toarevolutioninourunderstandingofthebrain.Thenewtechnologiesdescribedinthisreport
arealreadylayingafoundationforexceptionalprogress,butmoreinnovationisrequired.
Spectacularopportunitiesfordeeperunderstandingwouldbecreatedbynewmolecular
techniquestoidentifythespecificconnectionsbetweennervecellsthatchangewhenanew
memoryisformedoranewsocialsituationencountered.Similarly,newphysicsand
engineeringmethodsfornoninvasivemeasurementandtuningofactivityinfinescalehuman
braincircuitswouldcreatearevolutionintheunderstandingandtreatmentofdisease.
Whatwillbegainedbysolvingthemysteryofthebrainscircuitsandtheiractivityacrosstime
andspace?Understandingthebrainisarivetingintellectualchallengeinandofitself.Butin
thelongerterm,newtreatmentsfordevastatingbraindiseasesarelikelytoemergefroma
deeperunderstandingofbraincircuits.Forexample,treatmentofParkinsonsdiseasehasbeen
greatlyenhancedbycircuitlevelunderstandingofthebrainsmotorsystems.Ourfrontline
treatmentforParkinsonsisthedopamineprecursordrug,Ldopa,butitsefficacydecreases
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overtimewhileseveresideeffectsincrease.Inresponse,teamsofneurophysiologists,
engineers,andphysiciansfusedanunderstandingofthebrainsmotorcircuitswith
technologicaladvancestocreatedeepbrainstimulation(DBS),whichcanrestoremotorcircuit
functioninmanyParkinsonspatientsforuptoseveralyears.Currentresearchintobrain
circuitsformoodandemotionhasthepotentialtoadvancepsychiatryinsimilarways.
Webelievethistobeamomentinthescienceofthebrainwhereourknowledgebase,ournew
technicalcapabilities,andourdedicatedandcoordinatedeffortscangenerategreatleaps
forwardinjustafewyearsordecades.Likeothergreatleapsinthehistoryofsciencethe
developmentofatomicandnuclearphysics,theunravelingofthegeneticcodethisonewill
changehumansocietyforever.Throughdeepenedknowledgeofhowourbrainsactuallywork,
wewillunderstandourselvesdifferently,treatdiseasemoreincisively,educateourchildren
moreeffectively,practicelawandgovernancewithgreaterinsight,anddevelopmore
understandingofotherswhosebrainshavebeenmoldedindifferentcircumstances.To
achievethisvision,ournationmusttrainandsupportanewgenerationoftransdisciplinary
brainscientistsandprovidetheresourcesneededtounleashtheircreativeenergiesforthe
benefitofall.
Onapersonalnote,themembersofthiscommitteearegratefultoPresidentObamaandthe
NIHfortheopportunitytoembarkonourownjourneyofdiscoveryoverthepastyearin
preparingthisreport.Weareindebtedtonumerouscolleagueswhoparticipatedinourfour
workshopsinthesummerof2013,andinpublicfeedbacksessionsfollowingpublicationofour
preliminaryreportinSeptemberof2013.Andwearegratefultoourmanycolleagueswho
sharedtheirinsightsinoneononeconversations,arguingwithusandeducatingusinthe
process.Wealsovaluetheperspectivesofferedtousbypatientadvocacygroupsand
membersofthelaypublic.Thisjourneyhasalreadyprovedlivelyandenjoyable.Welook
forwardtothenextphaseofdiscoveryintheBRAINInitiative.

Respectfully,themembersoftheBRAINInitiativeWorkingGroup

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SECTIONI

THEBRAININITIATIVE:VISIONANDPHILOSOPHY
OnApril2,2013,theWhiteHouseproposedamajornationalprojecttounlockthemysteriesof
thebraintheBrainResearchthroughAdvancingInnovativeNeurotechnologies(BRAIN)
Initiative.ThePresidentcalledonscientiststogetadynamicpictureofthebraininactionand
betterunderstandhowwethinkandhowwelearnandhowweremember.Inresponsetothe
Presidentscalltoaction,theDirectoroftheNationalInstitutesofHealth(NIH)createdthis
workinggrouptocatalyzeaninterdisciplinaryeffortofunprecedentedscopetodiscoverthe
patternsofneuralactivityandunderlyingcircuitmechanismsthatmediatementaland
behavioralprocesses,includingperception,memory,learning,planning,emotion,andcomplex
thought:
Byexploringthesepatternsofactivity,bothspatiallyandtemporally,and
utilizingsimplersystemstolearnhowcircuitsfunction,wecangeneratea
morecomprehensiveunderstandingofhowthebrainproducescomplex
thoughtsandbehaviors.Thisknowledgewillbeanessentialguidetoprogress
indiagnosing,treating,andpotentiallycuringtheneurologicaldiseasesand
disordersthatdevastatesomanylives.
ChargetotheNIHBRAINWorkingGroup,April2013
ThisambitiousAmericanProject,articulatedeloquentlybyPresidentObamaintheWhite
Houseannouncement,canonlybeachievedthroughinnovative,multidisciplinaryinvestigation
atalllevelsofnervoussystemfunctionbehavioral,electrophysiological,anatomical,cellular,
andmolecular.Inparallel,advancesintheory,computation,andanalyticswillbeessentialto
understandandmanagethelargequantitiesofnewdatathatwillsoonflowfromneuroscience
laboratories.
Overthepastyeartheworkinggroupreviewedthestateofthefieldandidentifiedkeyresearch
opportunities.Itheldworkshopswithinvitedexpertstodiscusstechnologiesinchemistryand
molecularbiology;electrophysiologyandoptics;structuralneurobiology;computation,theory,
anddataanalysis;andhumanneuroscience(afulllistofspeakersandtopicscanbefoundin
AppendixB).Workshopdiscussionsaddressedthevalueofappropriateexperimentalsystems,
animalandhumanmodels,andbehavioralanalysis,andeachworkshopincludedopportunity
forpubliccomments.TheworkinggroupissuedapreliminaryreportinSeptember,2013,
presentinghighpriorityareasforresearch.Aftertheinterimreportwasapprovedbythe
AdvisoryCommitteetotheNIHDirector,theworkinggroupmetwithpublicandprivate
partnersintheBRAINInitiative,andsoughtandreceivedfeedbackfromtheleadershipand
membershipoftheSocietyforNeuroscience(thelargestgroupofneuroscienceprofessionalsin
theworld),theneurosciencemembersoftheNationalAcademyofSciences,andtheleadership
oftheprofessionalsocietiesofclinicianswhospecializeindisordersofthenervoussystem.
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Inthisreportwerecommendspecificscientificgoalsandoverarchingprinciplestoguidethe
BRAINInitiativeoverthecomingdecade,beginninginFY2016.Wedevelopthescientific
backgroundandrationaleforourrecommendationsinSectionIIofthereport,andwe
formulatearangeofdeliverables,timelines,andcostestimatesinSectionIII.SectionIII
envisionstwooverlappingphasesfortheBRAINInitiative,aninitialphaseemphasizing
technologydevelopmentfollowedbyaphaseemphasizingtechnologyintegrationand
discoverydrivenscienceaddressingfundamentalquestionsaboutthebrain.
TheGoaloftheBRAINInitiative
Ourchargeistounderstandthecircuitsandpatternsofneuralactivitythatgiverisetomental
experienceandbehavior.Toachievethisgoalforanycircuitrequiresanintegratedviewofits
componentcelltypes,theirlocalandlongrangesynapticconnections,theirelectricaland
chemicalactivityovertime,andthefunctionalconsequencesofthatactivityatthelevelsof
circuits,thebrain,andbehavior.Combiningtheseelementsisatpresentimmenselydifficult
evenforonecircuit,yetwemustalsoweavetogetherthemanyinterlockingcircuitsinasingle
brain.AsthePresidentsaidinhisWhiteHousepressconference,thisisindeedagrand
challengeforthe21stcentury.
Asforanyfieldandanyera,progresstowardthesescientificgoalsislimitedtoalargeextentby
theexperimentsthataretechnicallypossible.Butwearenowwithinaperiodofrapid
perhapsrevolutionarytechnologicalinnovationthatcouldvastlyaccelerateprogresstoward
anintegratedunderstandingofneuralcircuitsandactivity.Thusourplanningeffortembracesa
substantialtechnologyemphasis,asreflectedinthenameoftheworkinggroup:Brain
ResearchthroughAdvancingInnovativeNeurotechnologies.Ourfocusisnotontechnology
perse,butonthedevelopmentanduseoftoolsforacquiringfundamentalinsightabouthow
thenervoussystemfunctionsinhealthanddisease.Wehaveconsideredhowmature
technologiescanbeappliedtoneuroscienceinnovelways,hownewtechnologiesofobvious
relevancecanberapidlydevelopedandintegratedintoregularneurosciencepractice,andwhat
longerterminvestmentsshouldbemadeinblueskytechnologieswithhigherriskbut
potentiallyhighpayoff.AstheBRAINInitiativeadvances,thesetechnologiesshould
increasinglybeusedtoshedlightonthehealthybrainandontragichumanbraindisorders.
Developingthesenoveltechnologieswillrequireintense,iterativecollaborationbetween
neuroscientistsandcolleaguesinthebiological,physical,engineering,mathematical,and
statisticalandbehavioralsciences.Essentialpartnersshouldcomefromtheprivatesectoras
well:corporateexpertiseinmicroelectronics,optics,wirelesscommunication,andorganization
andminingofbigdatasetscanradicallyacceleratetheBRAINInitiative.Clinicianswillbe
essentialpartnerstotranslatenewtoolsandknowledgeintodiagnosticsandtherapies.The
newtechnicalandconceptualapproachestobecreatedaspartoftheBRAINInitiativewillexert
maximalimpactifaccompaniedbyspecificplansforimplementation,validation,and
disseminationtoalargercommunity.Catalyzingthenecessarycollaborationsanddelivering
reliabletoolsandresourcestoneurosciencelaboratoriesshouldbemajorthemesoftheBRAIN
Initiative.
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FoundationalConcepts:NeuralCoding,NeuralCircuitDynamics,andNeuromodulation
Neuralcodingandneuralcircuitdynamicsareconceptualfoundationsuponwhichtobasea
mechanisticunderstandingofthebrain.Atthemicroscopicscale,thebrainconsistsofvast
networksofneuronsthatarewiredtogetherwithsynapticconnectionstoformneuralcircuits.
Inanactivebrain,eachneuroncanhaveelectricalandchemicalactivitythatisdifferentfrom
thatofitsneighbors;thussomeneuronscanplayspecializedrolesindifferenttasks.Yetthe
activityofeachneuronalsodependsonthatoftheothersinthecircuit,throughthesynaptic
connectionsthatdefinethecircuitsarchitecture.Synapticconnectionscanchangestrengthas
aresultofrecentactivityinthecircuit,meaningthatcircuitarchitectureisconstantlymodified
byexperience.Athinkingbraincanthereforebeviewedasanimmenselycomplexpatternof
activitydistributedacrossmultiple,everchangingcircuits.
Neuralcodingreferstohowinformationabouttheenvironment,theindividualsneeds,
motivationalstates,andpreviousexperiencearerepresentedintheelectricalandchemical
activityoftheneuronsinthecircuit.Inafamiliarexample,theneuralcodeforcolorvision
beginswithjustthreebasicdetectorsintheeyetheconephotoreceptors.Circuitsinour
brainscombinepatternsofconeactivationwithotherinputstodiscriminateoveramillion
differentcolors.Moresophisticated,andpoorlyunderstood,neuralcodesenableusto
recognizeinstantlythevoiceofafriendorthedramaticlightofaRembrandtpainting.
Elucidatingthenatureofcomplexneuralcodesandthelogicthatunderliesthemisonegoalof
theBRAINInitiative.
Asdifferentneuronsbecomesilentoractiveinathinkingbrain,thepatternofactivityshiftsin
spaceandtimeacrossdifferentcircuitsandbrainregions.Theseshiftingpatternsdefinewhat
isknownasneuralcircuitdynamics.Akeytounderstandinghowthebrainworksisto
determinehowtheneuraldynamicsacrossthesevastnetworksprocessinformationrelevantto
behavior.Forexample,whatistheformofneuraldynamicsinacircuitthatmakesadecision?
Whatarethedynamicallychangingpatternsofactivityforspeakingasentenceorimagininga
futureaction?Toprobethemechanicsofthebrainmoredeeply,wemustlearnhowthe
biophysicalpropertiesofneuronsandthearchitectureofcircuitsshapedynamicpatternsof
neuralactivityandhowthesepatternsinteractwithincomingsensoryinformation,memory,
andoutgoingmotorcommands.Inthesamewaythatthebasicelectrophysiologicalproperties
ofsingleneuronsarecommonacrossbrainareasandspecies,itislikelythatmanyfundamental
formsofneuraldynamicswillgeneralizeaswell.OnegoaloftheBRAINInitiativeisthe
identificationandcharacterizationofuniversalformsofneuralcircuitdynamics,likely
representedbydynamicalmotifssuchasattractors,sequencegeneration,oscillation,persistent
activity,synchronybasedcomputation,andothersyettobediscovered.
Accompanyingthisrapidflowofinformationthatdrivescognition,perception,andactionare
slowermodulatoryinfluencesassociatedwitharousal,emotion,motivation,physiological
needs,andcircadianstates.Insomecases,theseslowerinfluencesareassociatedwith
specializedneuromodulatorychemicalslikeserotoninandneuropeptides,oftenproduceddeep
inthebrainoreveninperipheraltissues,thatcanactlocallyorgloballytochangetheflowof
13

informationacrossotherbraincircuits.Ineffect,neuromodulatorymodificationsofsynaptic
efficacycanrewireacircuittoproducedifferentdynamicpatternsofactivityatdifferent
pointsintime.TheBRAINInitiativeshouldstriveforadeeperunderstandingofthesepowerful
butelusiveregulatorsofmoodandbehavior.
WhyNow?
Thisisapropitiousmomentforasustainednationalefforttounlockthesecretsofthebrain.
Thereasonliesinthetechnologicalandconceptualrevolutionthatisunderwayinmodern
neuroscience.Newmolecular,geneticandcellulartoolsaregeneratingexquisiteinsightsinto
theremarkablydiverseneuronalcelltypesthatexistwithinourbrains,thebasicpartslistof
ourneuralcircuits.Novelanatomicaltechniquesareprovidingremarkablenewopportunities
fortracingtheinterconnectionsbetweenbrainregionsandindividualneurons,revealingbasic
braincircuitmapsinunprecedenteddetail.Innovativeelectricalandopticalrecordingtoolsare
allowingustomeasuretheintricatepatternsofelectricalactivitythatexistwithinthosecircuits
acrossabroadarrayofbehaviorsrangingfromdecisionmakingtomemorytosleep.Onlya
shorttimeago,wewererestrictedtostudyingthebrainselectricalactivityonenervecellata
time;nowwecanrecordfromhundredsofnervecellssimultaneously,allowingustoanalyze
thecooperativeactivityofnervecellsastheyoperateinintactcircuits;welooktowardafuture
inwhichwecanmeasureevenricherpatternsofbrainactivity,involvingmillionsofnervecells
atanyinstant.Furthermore,newlyinventedgeneticandchemicallybasedtechniquesare
givingusthepowertomodifyactivityinthosecircuitswithgreatprecision,creating
extraordinaryopportunitiesfordecipheringtheinformationcarryingcodesinpatterned
electricalactivity,andinthelongerterm,creatingafoundationfornoveltherapeutic
treatmentsfordisease.
Withtheseincreasinglypowerfultechniquescomenewdatasetsofmassivesizeand
complexity.Reconstructingneuralcircuitsandtheirdynamicactivityinfinedetailwillrequire
imageanalysisataformidablescaleaswellassimultaneousactivitymeasurementsfrom
thousandsofneurons.Theageofbigdataforthebrainisuponus.Thus,neuroscientistsare
seekingincreasinglyclosecollaborationswithexpertsincomputation,statistics,andtheoryin
ordertomineandunderstandthesecretsembeddedintheirdata.Thesestartlingnew
technologies,manyofwhichdidnotexist10yearsago,forceustoreconceivewhatitmeansto
beanexperimentalneuroscientisttoday.
Thechallengethatnowfacesneuroscienceistomapthecircuitsofthebrain,measurethe
fluctuatingpatternsofelectricalandchemicalactivityflowingwithinthosecircuits,and
understandhowtheirinterplaycreatesouruniquecognitiveandbehavioralcapabilities.To
meetthischallenge,wemustintegratethesediverseexperimentalapproachesandscalethem
uptothelevelofcircuitsandsystems.Previously,wecouldstudythebrainatveryhigh
resolutionbyexaminingindividualgenes,molecules,synapses,andneurons,orwecouldstudy
largebrainareasatlowresolutionwithwholebrainimaging.Continuedprogressatbothof
theselevelsisessential,butouruniquenewopportunityistostudythecriticalintermediate
levelaswellthethousandsandmillionsofneuronsthatmakeupafunctionalcircuit.
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Remarkablenewdiscoveriesarepossibleatthisintermediatelevel,forhereweexpectto
observethecircuits,codes,dynamics,andinformationprocessingstrategiesthatenablea
collectionofnervecellstogenerateacomplex,organizedbehavior.
TheBrainandBehavior
Thepurposeofthebrainistogenerateadaptivebehaviorpredicting,interpreting,and
respondingtoacomplexworld.Asforeshadowedintheprecedingsection,someofthemost
rivetingquestionsinneurosciencerevolvearoundtherelationshipbetweenneuralcircuit
structure,neuraldynamics,andcomplexbehavior.Objectivelymeasureablebehaviorisan
indispensableanchorforthefieldofneuroscienceitdefinesthesetofphenomenathatwe
ultimatelyseektoexplain.Webenefitinthisrespectfromtherichtraditionsofexperimental
psychology,psychophysicsandneuroethology,butnewinnovationisneededintheanalysisof
behavior.DobzhanskyoncesaidthatNothinginbiologymakessenseexceptinthelightof
evolution,anditisnoexaggerationtosaythatnothinginneurosciencemakessenseexceptin
thelightofbehavior.ThusaprimarythemeoftheBRAINInitiativeshouldbetoilluminatehow
thetensofbillionsofneuronsinthecentralnervoussysteminteracttoproducebehavior.
Inadvancedorganismsourconceptofbehaviormustbeextendedtoincludesophisticated
internalcognitiveprocessesinadditiontoexternallyobservableactions.Thispointis
dramatizedbythestoryofJeanDominiqueBauby,aFrenchmagazineeditorwhowasleftina
lockedinconditionbyabrainstemstroke.Baubywasrobbedofallvoluntarymovement
excepttheabilitytoblinkhislefteye.Usingtheonebehaviorlefttohim,hewroteTheDiving
BellandtheButterfly,anastoundingmemoiroftherichinternalmentallifethathecontinued
toexperienceafterhisstroke:
Mydivingbellbecomeslessoppressive,andmymindtakesflightlikea
butterfly.Thereissomuchtodo.Youcanwanderoffintospaceorintime,set
outforTierradelFuegoorforKingMidasscourt.Youcanvisitthewomanyou
love,slidedownbesideherandstrokeherstillsleepingface.Youcanbuild
castlesinSpain,stealtheGoldenFleece,discoverAtlantis,realizeyourchildhood
dreamsandadultambitions.
Mentallifecanflourishwithinthenervoussystem,evenifthebehaviorallinktotheobservable
worldistenuous.ThustheBRAINInitiativeshouldfocusoninternalcognitiveprocessesand
mentalstatesinadditiontoovertbehavior.Accordingly,apreferredexperimentalemphasis
shouldbeonwholeanimals(typicallybehavinganimals)withasecondaryemphasisonreduced
circuitsthatmaintainimportantconnectionsandintegrativeproperties.
Measuringinternalcognitiveprocessesinanimalsischallenging,butrigorousmethodshave
beendevelopedtoassessperception,memory,attention,decisionmaking,rewardprediction,
andmanyotherexamples.Althoughwemustbeconstantlyonguardagainstfacile
anthropomorphism,thecontinuityofbrainstructureandorganizationacrossspeciesprovides
confidencethatsomecognitiveprocessesanalogoustooursarelikelytoexistinthebrainsof

15

animalsotherthanhumans.Improvingthebehavioralanalysisofthesecognitiveprocesses,
bothinexperimentalanimalsandinhumans,shouldbeanemphasisoftheBRAINInitiative.
StrategiesandExperimentalSystems
TheBRAINInitiativewaslaunchedtodiscoverhowthehumanbrainproducescognitionand
behavior,andallofthespecificrecommendationsofthisreportinvolvehumanneuroscience.
However,humanbrainsarecomplicatedanddifficulttoaccessexperimentallybothforethical
andpracticalreasons.Toreachourgoalofunderstandingthehumanbrain,itisthereforevital
thatwealsoinvestigatesimpleranimalbrainsasmodelsystemssomewithbehaviorsas
comparableaspossibletohumans,butsomewithnervoussystemsthataremore
experimentallytractable.Wecannotsatisfyallrequirementswithasingleanimalmodel;a
rangeofexperimentalsystems,fromsimpletocomplex,willbeneededtomaximizeprogress.
Fortunately,manybasicprinciplesofneuralorganizationandfunctionareconservedacross
animalspecies,sothatprogressinunderstandingsimplesystemscanaccelerateunderstanding
ofmorecomplexsystems.
Inbothanimalsandhumans,weshouldenumerateanddescribethebrainscomponentparts
thedifferenttypesofneuronsandgliaandweshouldmaptheirpreciseanatomical
connectionstoobtainanaccuratecircuitdiagram.Weshouldmeasurethedynamicactivityof
thecellsinacircuitunderavarietyofconditionsandacrossarangeofbehaviors,andwe
shouldmanipulatethisactivitytotestcausalhypothesesabouthowcircuitactivityinfluences
behavior.Finally,wewillrequirecomputationallypowerfulwaystoanalyzeandunderstand
themechanismsbywhichdynamicpatternsofactivityinneuralcircuitsgiverisetobehavior.
Theseindividualelementsareclear;thechallengeishowtoaccelerate,facilitateandcombine
themformaximumimpact.
TheRoadsNotTaken
Inanyproject,decisionsmustbemadeaboutwheretofocus.Neuroscienceaddressesbrain
functionfromthelevelofmoleculestothelevelofpsychology,andatmanylevelsinbetween.
ThisplanfortheBRAINInitiativeproposesaconcertedattackonbrainactivityatthelevelof
circuitsandsystems,ratherthansuggestingincrementaladvancesineveryarea.Allareasof
neuroscienceareimportant,however,andtheBRAINInitiativeshouldthereforesupplement,
notreplace,existingeffortsinbasic,translational,andclinicalneuroscience.
Withinneuroscience,newtechnologieshavespurredthefieldforwardatdifferentpointsin
time.Majorconceptualadvancescanbeattributedto50yearsofsingleneuron
electrophysiologyinvivo;30yearsofmolecular,cellular,anddevelopmentalneurobiology;20
yearsofhumanfunctionalbrainimaging;20yearsofhumangeneticsofbraindisorders;and10
yearsofstemcellresearchforregeneration.Toreachitspotential,eachfieldrequiredspecial
supportatitsinception.Similarly,uniqueopportunitiesatthelevelofcircuitsshouldnowbe
seizedbytheBRAINInitiative.

16

Fromitsinception,theBRAINInitiativehasbeenconceivedasascientificendeavortodiscover
generalbrainmechanisms,notasaclinicallydirectedendeavorpointedatspecificdiseasesand
patients.SpecificbraindisordersaretheappropriatesubjectofmuchofNIHneuroscience
research;clinicalstudiesandclinicaltrialsshouldcontinuevigorouslywithinthediseaserelated
NIHinstitutesthatcurrentlyleadthem.Havingsaidthat,theBRAINInitiativesgoaltodefine
circuitlevelbrainprocessesishighlyrelevanttomanybraindisorders,atopicthatisconsidered
inmoredetailinmanyfollowingsections.
Progressinunderstandingthebrainwilladvanceinanincreasinglyintegrativefashionoverthe
comingyears.Synergisticinteractionbetweenmanyareasofneurosciencewillbeessentialto
answerthequestionsofbrainfunctionthatarethefocusoftheBRAINInitiative.Topickone
example,combininghumangeneticswithBRAINsponsoredcircuitanalysishastremendous
potentialtoelucidatediseaseprocessesfrommoleculetobehavior.TheBRAINInitiativeshould
openthefieldtonewdisciplines,notexcludeexistingones.
StudyingtheHealthyBrainShouldAccelerateUnderstandingofBrainDisorders
WhiletheprimarygoaloftheBRAINInitiativeistounderstandhealthybrainfunction,we
expectthisworktoprovideanessentialfoundationforunderstandingneurologicaland
psychiatricdisorders.Theburdenofbraindisordersisenormous.Allofusaretouched,directly
orindirectly,bytheravagesofdegenerativediseaseslikeAlzheimersandParkinsons,thought
disorderslikeschizophrenia,moodandanxietydisorderslikedepressionandposttraumatic
stressdisorder,anddevelopmentaldisorderslikeautismspectrumdisorders.Braindisorders
limitpersonalindependenceandplaceenormousdemandsonfamilyandsociety.The
knowledgegainedthroughtheBRAINInitiativeofferspossibilityhopeforreducingthisburden.
Manybraindisorderslikelyresultinpartfromcircuitdysfunction.Epilepsy,forexample,isbest
understoodasacircuitdiseasewhereinstabilityinneuronalcommunicationleadsto
uncontrolledexcitationandseizures.Wecurrentlystabilizepatientsbytreatingthem
chronicallywithpotentdrugs,butpinpointingabnormalcircuitswithnewtechnologiescould
aidinthepredictionofseizuresandthedevelopmentofmoreprecise,localizedtreatmentsto
stabilizeactivity.Likeepilepsy,mooddisordersandthoughtdisordersareepisodic,withan
unstablewaxingandwaningofsymptomsoverdaysoryears.Theabilityofmanyaffected
individualstofunctionnormallyatsometimes,andtheabsenceofmassivelossofbraincells,
suggeststhattheremaybenoimmovableobstacletorecoveryofstablecognitiveoremotional
processing thecircuitryforinformationflowexists,butitisnotalwaysregulatedcorrectly.
Unfortunately,therehasnotbeenafundamentallynewclassofdrugsforpsychiatricdisorders
sincethe1970s,largelybecauseweunderstandneitherhowthecircuitsworknorhowthe
drugsactonthem.Therearesomeclues,however.Forexample,thedrugswehavefor
depressionmostofwhichaffecttheneurotransmittersdopamine,serotonin,and
norepinephrineappeartoactinpartbymodulatingtheflowofinformationbetween
subcorticalandcorticalbrainareas.Agreaterunderstandingofthesecircuitsandtheir
regulationcouldadvanceourabilitytodiagnoseandtreatthoughtandmooddisorders.

17

Abetterunderstandingofbraincircuitshasthepotentialtoprovidenewpathstothe
treatmentofneurodegenerativedisorders.TheneurodegenerativedisorderParkinsons
diseaseiscausedbythelossofdopaminergicneurons;likemanyneurodegenerativedisorders,
itmanifestsitselfatthelevelofsinglecells.Nonetheless,thosedopaminergicneuronsare
circuitelements.ChangingtheflowofinformationthroughthedamagedcircuitsofParkinsons
patientsusingdeepbrainstimulationcandramaticallyimprovetheirmotorsymptoms,even
aftermostdopaminergicneuronsarelost.Weanticipatethatrefinedknowledgeofmotor
circuitswillmakedeepbrainstimulationmoreeffective,andenableitsuseforothermotor
disordersaswell.ForotherneurodegenerativedisorderslikeAlzheimersdiseaseandmotor
neurondiseases,itmayalsobepossibletodeliveratherapeuticbenefitbymimickingthe
circuiteffectofapermanentlylostpopulationofcells.Butfirstthosecircuiteffectsmustbe
discovered,andinterventionaltoolsfordeliveringtheappropriatecircuitleveleffectmustbe
designedandbuilt.
Wealsoenvisionnewwaystorepairphysicaldamagetothebrain.Stroke,traumaticbrain
injury,andspinalcordinjuryresultinthelossofsightormemory,paralysis,ortheinabilityto
communicate.Bytappingintoexistingbraincircuitswithnewstimulatorsandsensors,itmay
bepossibletoreestablishdamagedbrainpathways,orallowcontrolofprostheticlimbswith
highlevelbrainsignals.Suchimplantabledevicesmaysoundlikesciencefiction,buttheyare
alreadyindevelopmentinafewpatients.Theirsuccessislimitedbyourfragmentary
understandingofthebrainscodesandinstructions;thereisgreatpotentialforhumanbenefit
fromknowingmoreaboutthebrain.
Inthefieldofhumangenetics,longawaitedprogressisbeingmadeinidentifyinggeneticrisk
factorsthatcontributetopsychiatricandneurologicaldiseases.ToolsfromtheBRAINInitiative,
appliedtohumansubjectsandanimalmodels,willallowresearcherstoaskhowthesegenetic
riskfactorscascadeupwardthroughdefinedpopulationsofneurons,circuits,andbrainregions,
toaffectemotional,cognitive,andmotorprocesses.
Anotherareainwhichgreatadvancesareoccurringisstemcellbiology,notablythe
developmentofinducedpluripotentstemcells(iPScells)fromhealthyindividualsandpatients
thatcanbedifferentiatedintomatureneurons.Byprovidinginsightintotheessentialfeatures
ofthebrain,suchasitsconstituentneurons,theirconnections,andtheirpatternsofactivityin
healthanddisease,theBRAINInitiativewillprovideastandardforevaluatingthecompetence
ofiPSderivedneuronstoformfunctionalcircuits,andastimulusforimprovingthemtothe
pointthattheycanbeconsideredastherapeutictools.
TheDeliverablesoftheBRAINInitiative
SevenmajorresearchprioritiesandsevenoverarchingprinciplesoftheBRAINInitiativeare
summarizedintheExecutiveSummaryofthisreport.Foreachresearchpriority,specific
deliverablesareidentifiedinSectionIIIofthereport,rangingfromnewmethodsforaccessing
neuronalandglialcelltypestonewimplantabledevicesfortreatinghumanbraindisorders.

18

TheBRAINInitiativewilldelivertransformativescientifictoolsandmethodsthatshould
accelerateallofbasicneuroscience,translationalneuroscience,anddirectdiseasestudies,as
wellasdisciplinesbeyondneuroscience.Itwilldeliverafoundationofknowledgeaboutthe
functionofthebrain,itscellularcomponents,thewiringofitscircuits,itspatternsofelectrical
activityatlocalandglobalscales,thecausesandeffectsofthoseactivitypatterns,andthe
expressionofbrainactivityinbehavior.Throughtheinteractionofexperimentandtheory,the
BRAINInitiativeshouldelucidatethecomputationallogicaswellasthespecificmechanismsof
brainfunctionatdifferentspatialandtemporalscales,definingtheconnectionsbetween
molecules,neurons,circuits,activity,andbehavior.
Thisnewknowledgeofthehealthybrainshouldformafoundationformoreadvanced
translationalresearchintobraindiseasemechanisms,diagnoses,andtherapies.Itshouldserve
ourcolleaguesinmedicine,biotechnology,engineering,andthepharmaceuticalandmedical
deviceindustries,providingfundamentalknowledgeneededtoamelioratethevasthuman
burdenofbraindisorders.
Inadditiontoacceleratingbiomedicalknowledgeandtreatmentofdisease,theBRAINInitiative
islikelytohavepracticaleconomicbenefitsintheareasofartificialintelligenceandsmart
machines.Ourbrainscanrapidlysolveproblemsinvision,speech,andmotorcoordinationthat
themostpowerfulsupercomputerscannotapproach.Aswelearnmoreabouttheprinciples
employedbythebraintosolvetheseproblems,newcomputingdevicesmaybedevisedbased
onthecognitivearchitecturesfoundinbrains.Informationcompaniesarealreadyinvestingin
braininspiredalgorithmstoenhancespeechrecognition,textsearchandlanguagetranslation;
theeconomicvalueofneurotechnologyindustriescouldsomedayrivalthatofbiotechnology.
Finally,wehopethroughtheBRAINInitiativetocreateacultureofneuroscienceresearchthat
emphasizesworldwidecollaboration,opensharingofresultsandtools,mutualeducation
acrossdisciplines,andaddedvaluethatcomesfromhavingmanymindsaddressthesame
questionsfromdifferentangles.

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SECTIONII

SCIENTIFICREVIEWANDHIGHPRIORITYRESEARCHAREAS
II.1.MappingtheStructureandComponentsofCircuits
Whatclassesofneuronsandgliaareinvolvedinagivenmentalprocessorneuralactivitystate?
Whichcellsandbrainregionscontributetoasingleperceptoraction,andhowarethey
connectedtoeachother?Toanswerthesequestions,wemustdefinethecellularcomponents
ofcircuits,includingtheirmolecularpropertiesandanatomicalconnections.Thisknowledge
willtelluswhatthebrainismadeofatmolecular,cellular,andstructurallevels;itwillalso
provideafoundationforunderstandinghowthesepropertieschangeacrossthenormal
lifespanandinbraindisorders.
1a.CellType:AStartingPointforIntellectualandTechnicalProgress
1ai.ACensusofNeuronalandGlialCellTypes
Thebraincontainsmanyclassesofneuronsandglia,butnotinfinitelymany.Itconsistsof
neuronsthataredistinguishedbytheirneurotransmitters,electrophysiologicalproperties,
morphology,connectivity,patternsofgeneexpression,andprobablyotherfunctional
properties.Thesepropertiesaremajordeterminantsofsystemwideneuralactivitypatterns.
Classificationofneuronsisprerequisitetomanipulatingthemincontrolledways,andto
understandinghowtheychangeinbraindisorders.Informationaboutthetypesofglialcells,
vascularcells,andimmunecellsassociatedwiththenervoussystemmayalsoincreaseour
understandingofbrainfunctioninhealthanddisease.Therefore,avaluableshorttermgoalfor
aBRAINInitiativeistogenerateacensusofcelltypeswithinthebrain.
Thereisnotyetaconsensusonwhataneuronaltypeis,sinceavarietyoffactorsincluding
experience,connectivity,andneuromodulatorscandiversifythemolecular,electrical,and
structuralpropertiesofinitiallysimilarneurons.Insomecases,theremaynotevenbesharp
boundariesseparatingsubtypesfromeachother,andcellphenotypesmaychangeovertime.
Nonetheless,thereisgeneralagreementthattypescanbedefinedprovisionallybyinvariant
andgenerallyintrinsicproperties,andthatthisclassificationcanprovideagoodstartingpoint
foracensus.Thus,thecensusshouldbeginwithwelldescribedlargeclassesofneurons(e.g.
excitatorypyramidalneuronsofthecortex)andthenproceedtofinercategorieswithinthese
classifications.Thiscensuswouldbetakenwiththeknowledgethatitwillinitiallybe
incomplete,andwillimproveoveriterations.Acensusofcelltypesisanimportantshortterm
goalforseveralreasons:
1. Anagreeduponsetofcellsprovidesaframeofreferenceforstudiesinmanylabs,and
possiblyindifferentorganisms,allowingcrosscomparisons.Forexample,totheextent
thatneuronalcelltypesareconservedacrossspecies(itselfanimportantquestion)we

20

canaskwhethertherearedifferencesintheirnumbersandratiosinthecortexof
primatescomparedtorodents.
2. Anagreeduponsetofcellsprovidesafoundationforfurtherexperiments,andshapes
theproblemgoingforward.Forexample,whatgenesareexpressedineachofthe
differentcelltypes?Dothesetsofcellsaddupto100%,suggestingthatallneuronsand
gliaareaccountedfor?AretheregeneticelementssuchasCrelinesorvirusesthat
provideexperimentalaccesstoeachcelltype?
3. Thisproblemcanbesolvedwithreadilyachievableimprovementstoexisting
technology.
4. Thisprojecthasaninitialendpoint,andthelistitselfwillbearesourcethatcanserveto
organizesubsequentBRAINexperimentsanddataanalysisinasystematicway.
Weenvisionaneuronontologybioinformaticframeworkthatmightbeanalogoustothe
geneontologyframeworkinmoleculargenetics(http://www.geneontology.org/).The
frameworkshouldincludethepotentialtocrossreferenceinformationabouthomologouscell
typesfromdifferentanimals,whichcouldbevaluableinthesamewaythatinformationabout
homologousgenesisvaluableforlinkingstudiesacrossspecies.
Theatlasshouldexpandtodescribethedetailedmorphologyandconnectivityofeachneuronal
class,itsactivityunderdifferentconditions,anditsresponsetoperturbations,astheseresults
emerge.Itcouldgrowtoincludeinformationaboutcellsfromhumanpatientsandanimal
modelsofhumandisease,extendingitsreachandprovidinginsightintopathologicalprocesses.
Theultimatecensusofcelltypeswouldincludealloftheneuronsandgliawithmolecular
annotationatsubcellularresolution:notjustmRNAexpressionbutionchannels,synaptic
proteins,intracellularsignalingpathways,andsoon.Thisisbeyondthereachofcurrent
technology,butstatingthegoalwillprovideimpetustotechnologicaldevelopment.TheAllen
InstituteforBrainScienceBrainAtlasforRNAinsituhybridizationisanexampleofthe
annotationofananatomicaldatabasewithmolecularinformation.Similarly,arraytomography
canprovideinformationaboutthelocationofspecificproteinswithincellsbasedonantibody
stainingandopticalimaging.
Acensusanddatabaseofcelltypesmightbeginwiththemouse,wheremanygenetictools
havealreadybeendevelopedandsubstantialdataexistongeneexpressionpatterns.Overthe
longerterm,thecensuscouldbeextendedtodifferentanimalspeciesandtohumans.
1aii.ToolsforExperimentalAccesstoDefinedCellTypes
Theabilitytodefine,monitor,andmanipulateacircuitrequiresexperimentalaccesstothe
individualcellsandgroupsofcellswithinthatcircuit.Developmentofsuchtoolswillbe
facilitatedbymolecularanalysisofcelltypes(section1ai),andshouldinturnfacilitateprogress

21

inmappingneuronalconnectivity(section1b),understandingneuronaldynamics(section2),
andestablishingfunctionthroughcausalneuronalmanipulation(section3).
Thepastdecadehasseenthedevelopmentofremarkablegenetictoolsincludingcalcium
indicators(e.g.GCaMP),optogenetictools(e.g.Channelrhodopsin),synapticmonitors(e.g.
SynaptopHluorin),chemogenetictools(e.g.RASSLs/DREADDs),andavarietyoftagsthatpermit
proteinstobevisualizedinvivo.Bytheirnature,usingthesetoolsrequirestheabilitytodeliver
agenetoaneuronorneuronsofinterest(geneticaccess).ProjectssuchastheHoward
HughesMedicalInstitute(HHMI)Drosophilaproject,theNIHGeneExpressionNervousSystem
Atlas(GENSAT),andtheAllenBrainAtlashavebeen,orarecurrentlyengagedin,developing
geneticaccesstodefinedcelltypesinDrosophilaandthemouse,butwhilethesetoolsare
nearingcompletioninthefly,theyarenotcomprehensiveinanyotherspecies.
Thecurrentmethodsforneuronspecificgenedeliveryinthemousearetypicallybipartite,with
(1)arecombinasegenesuchasCreand(2)aneffector/sensorgenethatisactivatedbythe
recombinase.Thesetwoelementsareindependentlydeliveredastransgenes,through
recombinationintoanendogenouslocusorinsertionintobacterialartificialchromosomes
(BACs),orasstereotacticallyinjectedviruses;theintersectionbetweenthetwoelements
generatesamorerestrictedexpressionpatternthaneitheronealone.Thepotentialvalueof
suchlinesishigh,butthereismuchroomforimprovement,andonlyasmallnumberarein
regularuseinthecurrentliterature.
Inaddition,nongeneticmethodscouldbeusedtodeliveractiveagentstoneuronsofparticular
types,andwouldexpandtherangeofpossibleexperiments.Virusesorliposomesthatcontain
pharmacologicalagents,proteins,ornanoparticlesmightbecoatedwithantibodiesthatdirect
themtocertaincelltypes.Providingreliableaccesstospecificcelltypesinparticularneural
circuitsorbrainareaswillaccelerateallareasofmodernneuroscience.
Afullexplorationofmethodsfortargetinggenes,proteins,andchemicalstospecificcelltypes
ishighlydesirable.Onequestionthatshouldbeconsideredduringtheinitialstagesofthe
BRAINInitiativeiswhethergenomeengineeringbyconventionaltransgenesiscouldbe
supersededbymethodsthatarefaster,cheaper,andmoreeasilygeneralizedacrossspecies.
Mousehusbandryisslowandexpensive,andgeneratingtherightmultitransgenicstrainsisa
financialandtemporaldragontheprogressofneuroscienceresearch.Furthermore,wewish
tostudyotherspeciesaswell.TheBRAINInitiativeshouldsolicitnewideasforcelltypespecific
deliveryoftransgenes,perhapsbasedonvirusesbearingsmallspecificregulatoryregionsfor
intersectionalcelltypedefinitionvia(forexample)multiplerecombinases;orvirusesdriving
efficient,specificintegrationofexogenousgenesintothegenomethroughcuttingedgetools
suchasCRISPRsandTALENs;orantibodytargetedliposomes.Completelynewideasmight
emergetoaddressthisproblem.Themostvaluableideaswillbethosewithpotentialtosolve
thegeneralproblemforanyspecies,inpreferenceoverthosethatwouldworkforonlyone
speciesatatime.Thelongtermvisionisdevelopmentofcomprehensive,generalsuitesof
toolsthattargetexpressiontoabrainareaofinterest,disseminatedforbroad,effectiveusein
neurosciencelabsaroundtheworld.
22

Thenextfrontierwouldbegainingaccesstothehumanbrain,whichismorelikelytoinvolve
transientdeliveryofRNAorachemicalthanpermanentgeneticchange,althoughviralvectors
forhumangenetherapyarecurrentlyunderexplorationinthebrain.Severalpharmaceutical
companiesaredevelopingtaggedantibodiesthatcrossthebloodbrainbarrier(e.g.via
transferrinreceptors),andthesemightbechemicallyorgeneticallyengineeredtoinclude
effectorsorsensorsofneuronalactivity.
Insummary,itiswithinreachtocharacterizeallcelltypesinthenervoussystem,andto
developtoolstorecord,mark,andmanipulatethesepreciselydefinedneuronsinvivo.We
envisionanintegrated,systematiccensusofneuronalandglialcelltypes,andnewgeneticand
nongenetictoolstodelivergenes,proteins,andchemicalstocellsofinterest.Priorityshould
begiventomethodsthatcanbeappliedtomanyanimalspeciesandeventohumans.
1b.TheStructuralMap:TracingAnatomicalCircuitsatDifferentScales

Rapidinformationflowacrossthebrainismediatedbyanatomicalconnectionsbetweencells,
includinglocalconnectionswithinabrainregionandlongrangeconnectionsintoandoutof
thatregion.Definingcircuitfunctionrequiresknowledgeofcircuitstructure.Threelevelsof
anatomyshouldbeconsidered:longrange,intermediaterange,anddetailedconnectivity.
1bi.LongRangeConnectivity
Traditionalneuroanatomyhasfocusedonlargescale,longrangeconnectionsbetween
differentbrainregions(e.g.thethalamocorticaltract).Inhumans,longrangeconnectionsare
beingstudiedwithintheHumanConnectomeProjectbynoninvasiveimagingmethods.In
animals,longrangeconnectionsarebeingpursuedindetailusingserialsectioningcombined
withmoderndyetracingtechniquesandgeneticmarkers,withnewlyemergingwholemount
imagingandstainingmethodssuchasCLARITYandclearingtechniquessuchasScaleandSeeDB
poisedtomakeanimpact.Currently,mosteffortisbeingexpendedonthemousemodel
system,butthesetechniquescanandshouldbeextendedtootherspeciesaswell.Thenew
wholemountmethodsalsoappearpromisingfortracingtractsinhumanpostmortemtissue,
andmayprovideanimportanthighresolutioncomplementtononinvasiveimagingmethods.
Projectomesofthiskindareattainablewithinthenextfewyearswithcurrentandemerging
technology.Thenextstepsareidentifyinggapsandcompletingstudiesofrodent,nonhuman
primate,andhumananatomicaltractsathighquality,integratingtheresultsacrosslabsand
institutions,andmakingtheinformationbroadlyavailabletothecommunity.Inclusionofother
speciesforcomparativepurposesishighlydesirable.Combiningthesedatasetsintoacommon
bioinformaticframework,andregisteringthesedatasetswithotherstreamsofinformation
describingthecellpopulationsandprojectionsofinterest,suchasmolecularphenotypeand
activitypatternsduringbehavior,willincreasetheirdepthandscientificutility.
1bii.IntermediateScaleConnectivity

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Thenextproblemismappingcircuitsatanintermediatescale.Whatlong andshortrange
projectionsmakeupaspecificfunctionalcircuit,whichmayconsistofonlysomeofthecellsin
aparticularbrainregion?Forexample,brainregionssuchasthehypothalamusconsistof
mixedcellpopulations,eachofwhichhasverydifferentinputandoutputconnectionsthatare
notevidentinthelargescaleconnectivity.Mappingtheseconnectionscurrentlyrequires
considerabletimeandeffort.Progressinthisareaisattainableandshouldbevigorously
pursued.
Thereisconsiderablepotentialforimprovingthetoolsforstudyingintermediatelevelcircuitry.
Transsynaptictracingofconnectionsishighlydesirable,butexistingmethods(lectins,dyes,
andrabiesbasedviraltracers)areimperfect.Forexample,rabiestracersarelargelylimitedto
retrogradetracing,eventhoughanterogradetracingisequallyimportantfordefiningcircuits.
Thereisaconcernthatthepresenttracersmayworkononlyasubsetofcelltypes,andthereis
nofullyacceptedanswerastowhetherthesetracersarestrictlytranssynapticormore
generallytransneuronal.
Bettermethodsfortracingcircuitsarecriticaltorapidprogressthroughoutneuroscience,and
wouldprovideimportantstructuralconstraintsforinterpretingvirtuallyallfunctionalstudies.
Bettertranssynaptictracerswouldbeextremelyvaluable,andtheirdevelopmentshouldbe
encouragedbytheBRAINInitiative.Thesemaybebasedonvirusesorondifferentkindsof
transgenictechnologies;combiningthesemethodswithtracttracingorarraytomography
wouldincreasetheirresolution.Otherpotentialtechniquesarebeingexplored,butnonehas
yetmatured:methodsthatusefluorescentproteinstolabelsynapses(e.g.GRASP);or
enzymaticallybaseddetectorsoftranssynapticrecognition(e.g.IDPRIME),whichhavethe
enormousadvantageofamplifyingsignalstoenablerobustdetection.Trulytransformative
technologiescouldbeencouragedfrommolecularbiologyorchemistry.Themostattractive
methodswouldbethoseapplicabletomanyspecies,includinghumans.Methodsthatworkin
postmortembrainswouldbeparticularlyvaluableforhighresolutionmappingofhumanbrain
circuits.IdentifyingintermediatescalecircuitsshouldbeasignificantgoaloftheBRAIN
Initiative.
1biii.DetailedConnectivity:TowardsaFullConnectome
Finally,thereisthequestionofreconstructionofcircuitsatveryhighresolutionthrough
electronmicroscopy,whichiswidelyconsideredtobethegoldstandardforcircuitmapping.To
datesparsereconstructionhasbeenusedtoexaminesmallnumbersofneuronsinavarietyof
systems,butdensereconstructionhasbeenappliedonlytotheverysmallanimalC.elegans,or
tosmallpartsofthenervoussystemsoflargeranimalssuchasDrosophila;ongoingstudiesin
mammalsareextendingthisapproachtotheretina.Thepastfewyearshaveseengreatstrides
insectioningandimagecollectiontechniques,butevenso,electronmicroscopy(EM)is
prohibitivelyslowforlargescalestudies.Thebottleneckisdataanalysis,thepainstakingand
potentiallyerrorproneprocessoftracingfibersandmappingsynapsesfromoneverythin
sectionofabraintothenextacrossthousandsofsuccessivesections.
TheimpactofdenseEMreconstructionwouldbeamplifiedtremendouslyifitwerepossibleto
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increasethroughput100 or1000foldacrossallstepsoftheprocedure,includingsegmentation
andreconstructionaswellassectioninganddataacquisition.Somepromisingimprovements
havebeendemonstrated,includingautomatedcapturingofserialsectionsfortransmissionEM,
andserialblockfacescanningEMthatmaintainsperfect3Dregistrationduringautomated
sectioninganddataacquisition,butmuchremainstobedone.
Possibleareasforincrementalimprovementinclude:
1. Improvedmethodsforthehistologicalpreparationofneuraltissue,especiallylarge
samples.Canweengagechemistsandchemicalengineersintheproblemtobringfresh
approachestothiscenturyoldareaofresearch?
2. Improvedmethodsforautomatedtissuesectioningandimaging,althoughthisareahas
alreadyprogressedgreatly.
Areaswhereprogressismostneededare:
3. Improvedsoftwaremethodsforsegmentingandassemblingthedata.Technological
advancesinmachinelearning,artificialintelligence,andcrowdsourcingapproachesto
reconstructioncouldhaveaprofoundimpactonthefield.
4. Improvedmethodsforsynapseidentification,inparticulartheabilitytoassessthetype
ofsynapse(excitatory,inhibitory,modulatory,electrical)andestimatesynaptic
strength.Celltypespecificmarkersormolecularmarkersofsubsetsofsynapsesthat
arevisibleattheEMlevelcouldbeveryhelpfulinlargescalereconstructions.
EMislaborintensive,butithappensinstages.SectioningforEMisrelativelyquick;scanning
takestentimesaslong;reconstructingisslowerbyordersofmagnitude.Ifhighquality
scannedimagesweremadeavailableontheinternet,individualuserscouldspendtheirown
timereconstructingareasofthebrainofrelevancetothem,usingsoftwaretoolsmade
availablebytheexperts.Underthismodel,thelaboriousreconstructiontaskwouldbe
performedasneededbyaworldwidecommunityofcollaborators.Thescopeandimpactof
EMcouldbebroadenedbeyondtherelativelysmallgroupofexpertlabsbyencouragingsharing
ofprimaryscannedimagesandreconstructiontools.Thereisnoreason,inthemodernera,for
EMmicrographstobetrappedinthelabthatgeneratedthem.Itwouldbeexcitingforthe
BRAINInitiativetogeneratethebasicdataresource(highqualitymicrographs)foravarietyof
brainsandspecies,withentirelyopenaccesstothedata.
Trulyinnovativeapproachestodensereconstructionshouldbeencouraged,withafocusonthe
dataanalysisbottleneckandgreatlyimprovedthroughput.A100 or1000foldimprovement
shouldbeheldupasaseriousgoal.Aswithotherapproachestowiring,registeringthese
denseconnectivitydatasetswithmolecularphenotypesandactivitypatternsduringbehavior
willvastlyincreasethescientificutilityandinterpretabilityofthedata.Futuredecisionsabout
whether,when,andhowtoscaleuptheseanatomicalapproacheswilldependonprogressin
themethodsdescribedabove.
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Developmentofthesenewtechnologiesshouldproceedhandinhandwithapplicationto
importantproblemsinneuroscience.Inthebestcase,densereconstructioncouldbe
performedafterrecordingsofneuronalactivityandbehaviorinthesameanimal.Thelarval
zebrafishisapromisingsystemforafull,densereconstructionofavertebratenervoussystem.
Smallerprojectsinthemammalianretina,hippocampus,orcortexcouldhaveabroadimpact.
Theimportantpointisthatbroadsupportforlargescale,denseconnectomicswillonlyappear
whenitbeginstoyieldanswerstospecificscientificquestionsthatcouldnothaveemergedby
othermeans.
Insummary,itisincreasinglypossibletomapconnectedneuronsinlocalcircuitsand
distributedbrainsystems,enablinganunderstandingoftherelationshipbetweenneuronal
structureandfunction.Weenvisionimprovedtechnologiesfaster,lessexpensive,scalable
foranatomicreconstructionofneuralcircuitsatallscales,suchasmolecularmarkersfor
synapses,transsynaptictracersforidentifyingcircuitinputsandoutputs,andEMfordetailed
reconstruction.Theeffortwouldbegininanimalmodels,butsomemappingtechniquesmay
beappliedtothehumanbrain,providingforthefirsttimecellularlevelinformation
complementarytotheHumanConnectomeProject.

II.2.NeuronalDynamics:RecordingNeuronalActivityAcrossTimeandSpace
Understandingtheelectricalandchemicalactivityofneuronalcircuitsandsystemsiscentralto
theBRAINInitiative.Thechallengeisthatthesecircuitsincorporateneuronalactivityata
varietyofspatialandtemporalscales.Atthespatiallevel,anensembleofneuronsassociated
withagivenbehavioraltaskmaybeconcentratedinonebrainregion,butnotallneuronsin
thatregionmaybepartoftheensemble,andotherimportantneuronswillresideindifferent
regions.Forexample,acircuitforconditionedfearbehaviormightincludesubsetsofneurons
intheprimarysensorycortexandthalamus(threatsensation),thehippocampus(memory
formation),theamygdala(fearlearning),theautonomicnervoussystem(physiologicaloutput),
andtheprefrontalcortex(topdowncontrolofbehavioralresponsetothethreat),amongmany
others.Tosystematicallystudybrainmechanismsunderlyingaparticularbehaviororcognitive
process,itisimportanttosampleneuronalactivitybroadlyacrossbrainstructuresandrecord
frommanyidentifiedcelltypes.Itisalsocriticaltomeasureandanalyzeneuronalactivityat
multipletimescalesthatarerelevanttobehaviorandcognition:fast(e.g.neuronalspikes),
intermediate(e.g.shorttermplasticity,recurrentexcitation)andslow(e.g.globalattentional
andarousalstates;neuromodulation).
Inanidealworld,aneuroscientistmightormightnotwanttoknowtheactivityofeveryneuron
inananimalunderagivenconditionthisisasubjectofdebatebutthereisgeneral
agreementthatweneedtomeasureneuronalactivitywithmuchmorefidelityacrossmuch
largerspatialandtemporalscalesthanwearemanagingatthemoment.Inthevastmajorityof
experiments,weobserveonlyatinyfractionoftheactivityinanyneuronalcircuit,andthen
underaverylimitedrangeofbehavioralconditions.Howcanwebestidentifythespatialand
temporalpatternsofactivitythatunderliespecificcognitiveprocessesandbehaviors?Howwill
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weknowwhenwehaverecordedfromenoughneuronstounderstandacognitiveprocessor
mentalstate?Whatmethodsareneededtorecordallrelevantkindsofactivityinallrelevant
brainregions?
2a.WhatNeuronsShouldWeRecord?IdentifyingDispersedCircuits
Asillustratedabove,itisimportanttoscanthebraintoidentifydistributedcircuits.Ingeneral,
distributedcircuitsmustbedefinedfunctionally,basedonactivityoftheconstituentneurons
duringabehaviororunderspecificexperimentalconditions.Whilestructuralmapslaythe
foundationforourunderstanding,eventhehighestlevelofanatomicalresolutionisnot
sufficienttodefineacircuit,becausesynapsesvaryintheirstrengthandmodulation.An
additionalcomplicationisthatindividualneuronsmayparticipateindifferentfunctionalcircuits
underdifferentexperimentalconditionsorbehavioraltasks.Mappingdispersedand
overlappingcircuitscanbeaidedbylabelingneuronsthatareactiveduringaspecificwindowof
time,whichpermitsidentificationoffunctionallyrelatedcellsthatarespatiallyintermixedwith
othercells.
Existingtoolsforidentifyingfunctionalcircuitsoncellularscalesmustbeimproved,and
developmentofnoveltoolsstronglyencouraged.Therelationshipsbetweencellsincircuitscan
berigorouslyestablishedbyelectrophysiologicalrecordingsinwhichonecellisstimulatedand
theothersactivityisrecorded,sometimesevenwithmanyneurons(e.g.laserscanning
photostimulation),butthisisnoteasilyaccomplishedoverlongdistances.Avarietyofmethods
involvingoptogenetictoolsmayhelpinthiseffort.Forexample,virallydeliveredopsinsand
fluorescentproteinswillspreadthroughoutcellsanddownaxons,allowinganatomically
definedoptogeneticcontrolbylightdeliveryattheaxonterminalregion.Excitingdefinedcells
oraxonterminalswithlightwhilerecordingfromasinglepostsynapticcellcandefinesources
offunctionalinput(channelrhodopsinassistedcircuitmapping).Thismethodinitscurrent
formisnotequallyeffectiveinallsettings,however,andisnoteasilycombinedwithlargescale
recordings.
Oneclassoftoolsforcircuitmappingisbasedontheexpressionofimmediateearlygenes
whoseexpressionisupregulatedbysharpincreasesinneuronalactivity.Initsoriginalform,
eachanimalisonlyexaminedonce,andthecellsaredeadandfixedbythetimetheyare
identified.Initsmodernform,immediateearlygeneexpressioncanbecoupledtoreporters
suchastamoxifenregulatedCrerecombinase,allowingpermanentCremarkingofneuronsthat
werehighlyactiveatthetimethattamoxifenwasdeliveredorremoved.Whileuseful,the
existingpromotersareslowreporterswithunpredictableregionalandcelltypespecificity,and
theirexpressionisonlypartiallycorrelatedwithneuronalactivity.Inshort,thisisatoolto
beginsketchingacircuitforanentirelynovelstimulus,butisnotsufficienttowatchongoing,
moremodestchangesinactivity.
Improvementsinmethodstoidentifyneuronsinactivecircuitsshouldbeencouraged.The
importanceofthesemethodswillbegreatestforcircuitsthataredistributed,orintermixed
withothercircuits,inawaythatfrustratesconventionalanatomicaltracing.Bettertime
resolutionishighlydesirable.Anewmethodusesphosphorylationofaribosomalprotein,S6,
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tolabelactivecellswhileallowingtheirmRNAexpressiontobecharacterized;thismethodis
applicableacrossmammals,notjusttomice.Improvedtranscriptionalreportershavebeen
suggestedthatwouldrequirethecoincidenceoflightactivationandcalciumentrytoinduce
transcription,withlightusedtodefinethepointatwhichactivityismeasured.Theremaybe
entirelynewwaystosolvethisproblemthroughbiochemicalorchemicalreagentsthatmark
activeneurons.Theabilitytomarkseveralcircuitsinseriesinthesameanimalwouldallow
moresophisticatedanalysis,forexampleforwithinanimalcomparisonsoftheeffectof
differentbehavioralstatesonneuronalresponses.
2b.HowManyNeuronsShouldWeRecord?TheTestCaseisCompleteCircuits
Smallmodelsystemsprovideatestbedforaskinghowmuchemergentinformationarises
fromrecordinganentirebrainorbrainstructure,andprovideinitialcluestothedensityof
recordingsneededtocharacterizefunctionalcircuits.Inafirstexamplefromthe1980s,
voltagesensitivedyesrevealedwidespreadactivationofover100abdominalganglionneurons
inthemolluscAplysiaduringgillwithdrawalbehavior.However,otherexperimentsargued
thatexperiencedependentchangesingillwithdrawalanditsregulationcouldbecontrolledby
justafewoftheseneurons.Thesecontrastingobservationsposedimportantquestionsabout
therelativerolesofpopulationactivityandsingleneuronfunctionthatarestillnotanswered.
Toassessthevalueaddedbymonitoringallneuronsinacircuit,completeornearcomplete
recordingsshouldbegatheredfromafewmodelsystemsunderavarietyofconditions.
Itisworthnotinghowfarwestillarefromthegoalofrecordingtheactivityofacomplete
circuit,exceptforafewinvertebrateganglia,eventhoughrecordingmethodshavebeenscaled
upinrecentyears.Forexample,largescaleneurophysiologicalapproacheshaveallowed
recordingsfromthousandsofneuronsinthevertebrateretina,butevensoonlytheretinal
ganglioncellshavebeenrecordedatscale,notthemanynonspikingbipolarandamacrinecells
thatprocessinformationpriortoopticnerveoutput.Amacrinecellsillustrateanadditional
challengetotheconceptofcompleterecordings;somehavesubcellularlycompartmentalized
voltagesignalsthatwouldbeoverlookedifrecordingsweremadeonlyfromthesoma.
Afewtestcasesforlargescale,completeneuronalrecordingswouldbeofgreatinterest,
especiallyifgatheredinclosepartnershipwiththeoryandbehavioralanalysistoprovide
contextandinterpretation.Geneticallyencodedcalciumindicatorsarealreadybeingusedto
imagealargefractionofneuronsinbrainsofthelarvalzebrafishandthenematodewormC.
elegans,althoughnotyetatspeedinbehavinganimals.Completerecordingsfromneurons
withinwelldefinedmammalianbrainareasareappealing,butwillrequirenewapproaches.
2c.HowShouldWeRecord?AdvancingRecordingTechnology
Currently,therearetwoimportantclassesofmethodsforrecordingneuronalactivity.
Classically,electrophysiologywithelectrodeshasbeentheworkhorseofneuroscience.
Microelectrodeandmacroelectroderecordingswillcontinuetobeimportantduetotheirhigh
temporalresolution,theirapplicabilitytostructuresthroughoutthebrain,andtheir
appropriatenessforhumanstudies.Morerecently,opticalmethodsforrecordingactivityhave
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beengreatlyimproved,providingsubstantialopportunityforfurtheradvances.Bothare
importantareasfordevelopment.
2ci.ElectrodeArraysforRecordingVoltageandPassingCurrent
Micro andmacroelectrodesarewidelyusedtoolsforrecordingneuralvoltagesignalsand
stimulatingneuraltissueartificiallyviapassageofelectricalcurrent.Understandingcognitive
andbehavioralprocessesmediatedbydistributedneuralcircuitswillbegreatlyacceleratedby
thedevelopmentofnextgenerationmultielectrodearraysthatcanrecordsinglecellactivity
simultaneouslyfromlargepopulationsofneuronsatmultiplesitesthroughoutthebrain.New
electrodearchitecturesandaccompanyingmethodsforextractingthemeasuredsignalsare
beingpursuedinmanylaboratories.Herewehighlightgeneralproblemswhosesolutionwould
accelerateprogressonmanyfronts,frombasiccircuitresearchinsmallanimalstohuman
clinicalapplication.
Penetratingelectrodearrays:Muchrecentworkhasbeendirectedatdevelopingarraysof
penetratingmicroelectrodesusingintegratedcircuittechnology,withsubstantialefforts
underwaytoincreasethenumberofelectrodeshanksandthenumberofrecordingcontacts
pershank.Nextgenerationelectrodearraysshouldalsohavethecapabilityofsimultaneous
stimulationandrecordingfromindividualelectrodesonthearray,sincethiscapabilitycanbe
criticalforestablishingfunctionalrelationshipsamongrecordedneurons.Advancesshouldbe
soughttoaddressfourprimaryproblemscurrentlyimpedingprogress.Firstisthephysical
designofelectrodearrayswithgreatlyincreasednumbersofshanksandcontacts;different
designswillbeneededforthecomplementarygoalsofmakingsimultaneousrecordingsfrom
verylargenumbersofneuronsatonesite(e.g.acorticalcolumn)versusmoremodestnumbers
ofneuronsatmanydispersedsites.Secondisamajordividebetweenpassiveandactive
electrodedesign.Oneobstacletotruehighdensityrecording(e.g.>1000recordingcontacts)is
physicalmanagementofthelargenumberofwiresthatmustbeattachedtotherecording
contacts.Thisproblemcanbereducedsubstantiallybyincorporatingactivecircuitryintothe
arrayimplantsthatfilters,amplifies,multiplexes,andtelemeterstheprimarysignalscloseto
therecordingsource.Solutionstotheseproblemswillrequiresubstantialengineering
innovationinminiaturizingactiveelectronicsandreducingthepowerneedsofthecircuitry.
Thirdisthecontinueddevelopmentofhybridelectrodearraysthatcombineelectricaland
opticalrecordingandstimulationcapabilities,increasingexperimentalpowerrelativetoeither
methodalone.Finally,particularlyforhumanuse,electrodearraysmustbemademore
compatiblewiththetargettissuesintheirmechanicalcompliance,crosssectionalarea,lifetime
intheimplantedtissues,andimmunetolerance.
Surfaceelectrodesforrecordingaverageneuralactivityfromcorticallociareanestablished
technologywithnotablerecentimprovements:Smallsurfaceelectrodes(20microndiameter)
atveryhighspatialdensities(20micronseparation)havebeencreatedonthin,flexible
parylenesubstrates(4micronsthick)thatconformwelltolocalcurvatureofthecortical
surface.Suchconformalarrayscoupledtosmartelectronicswouldbeparticularlyusefulfor
researchanddevicedevelopment(e.g.prosthetics)inhumans.
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Furtherprogresswillcomefromsupportingadiverseassortmentofpenetratingandsurface
electrodearraydesigns,withemphasisplacedondesignsthat,1)aresmarter,smalleranduse
lesspower,2)integratemultiplecapabilities(e.g.electricalandoptical;recordingand
stimulation),and3)canbeimplementedatmultiplescales,fromsmallanimalstohumans.In
thelongerterm,newmaterialsanddesignsmayprolongtheusefullifetimeofimplanted
arrays.Nextgenerationelectrodearraydesignisanareathatmightbenefitsubstantiallyfrom
interactionwithprivatecompanieswithexpertiseinintegratedcircuitchipdesign,
miniaturization,wirelesstelemetry,andlowpowerapplications.Somecompanieswith
relevantexpertisehaveexpressedinterestinpartneringwiththeBRAINInitiative.Themain
obstacletosuchpartnershipstodatehasbeenthelackoffinancialincentiveduetothesmall
market.
2cii.OpticalSensorsofNeuronalActivity
Theabilitytomonitoractivityinlargenumbersofneuronshasbeenacceleratedoverthepast
twodecadesbyusingopticalmethodsandtoolsfromchemistryandgenetics.Opticalsensors,
whetherchemicalorgenetic,havethepotentialtoreportsubcellulardynamicsindendrites,
spines,oraxons;toprobenonelectricalfacetsofneuraldynamicssuchastheneurochemical
andbiochemicalaspectsofcellsactivities;andtosamplecellsdenselywithinlocal
microcircuits.Thecapacityfordensesamplingholdsparticularpromiseforrevealingcollective
activitymodesinlocalmicrocircuitsthatmightbemissedwithsparserrecordingmethods.
Genetictoolscanalsotargetcellsbygenetictypeorconnectivity,andmaintainlargescale
chronicrecordingsofidentifiedcellsorevenindividualsynapsesoverweeksandmonthsinlive
animals.Suchlargescalechronicrecordingsareespeciallybeneficialforlongtermstudiesof
learningandmemory,circuitplasticity,development,animalmodelsofbraindiseaseand
disorders,andthesustainedeffectsofcandidatetherapeutics.
Althoughtheaccelerationinopticalsensordevelopmentisrelativelyrecent,ithasalreadyhad
agreatimpactonthefield.Presently,mostinvivoopticalrecordingsarestudiesofneuronalor
glialcalciumdynamics.Neuronalcalciumtracksactionpotentialsaswellaspresynapticand
postsynapticcalciumsignalsatsynapses,providingimportantinformationaboutbothinputand
outputsignals.However,itsabilitytoreportsubthresholdorinhibitorysignalsisvariable,and
whileexistingindicatorshaveachievedsinglespikesensitivityinlowfiringrateregimes,they
cannotyetfollowspikesinfastspikingneurons.
Thefutureofthisfieldisnotjustimprovingcalciumsensors,butgeneratingabroadsuiteof
opticalsensors.Voltageindicatorsareripefordevelopment:byfollowingvoltage,onecouldin
principlefollowspikesandsubthresholdsignals,includinginhibition.Severalgenetically
encodedvoltageindicatorshaveappeared,buttheydonotyethavethedesiredcombinationof
signalstrengthandspeed,andcouldbenefitgreatlyfromdisciplined,iterativeimprovements.
Improvedvoltageindicatorsmaywellbegeneticallyencoded,butotherapproachesfrom
chemistryandnanotechnologyshouldalsobeconsidered.Theexperienceofoptimizingthe
calciumindicatorsshouldbedirectlyapplicabletoimprovingvoltageindicators.Indicatorswith
30

ultralowbackgroundemissionsholdparticularimportanceforreliableeventdetectionand
timingestimation.
Amajoradvancethatcouldemergefromopticalapproachesisexpandingthekindsofneuronal
activitythataremeasured.Forexample,synaptictransmissionisarichareaofresearchatthe
singleneuronlevel,andcouldbeaccessibleatthecircuitlevelwithbettertools.Electrical
synapsesandtheirregulationareessentiallyinvisibletomostcurrentrecordingmethods.
Directmeasurementsofreleasedneurotransmittersatsinglecellorsinglesynapseresolution
arehighlydesirable:theprobabilityoftransmitterreleaseatasynapsecanvary100fold,and
synapsesalsohavepropertiessuchasdepressionandfacilitationthatshapesignalinginreal
time.Existingmethodsfordetectingtransmitterssuchasvoltammetryareusefulbuthave
limitedspatialresolution.Directmeasurementofreleasedglutamatehasrecentlybeen
accomplishedwithageneticallyencodedsensor,offeringpotentialimprovementinboth
spatialandtemporalresolution.Toolsthatallowdirectmeasurementsofothertransmitters
suchasGABA,dopamine,serotonin,andneuropeptideswouldprovidetheneededviewof
synapsesinaction.
Inthelongerterm,additionalsignalingpropertiesmaybemonitored.Forexample,
neuromodulatorystatescandramaticallychangepropertiessuchassignalingdynamics,
excitability,andplasticity.Measuringthebiochemicalreadoutsofneuromodulatorystates(e.g.
cAMP)mayprovideviewsoftheslowprocessingthatcircuitsperforminparalleltorapid
computations.Gliaareincreasinglyrecognizedasimportantplayersinneuronalsignalingand
pathology;monitoringglialactivityandmetaboliccouplingmayshedunexpectedlightinto
informationprocessinginthebrain.Monitoringsynapsesatalargescalecoulddefinethe
codesfortransferringinformationacrossneuronalcircuitsandsystems.Agoalofparticular
interestisawaytofindthesynapsesinacircuitthatchangeasaresultofexperienceand
learning.
2ciii.IntegratedOpticalApproaches:NeuroscienceandInstrumentation
OpticalmethodscapturethecentralvisionoftheBRAINInitiative,thatofintegratingmany
approachesintoasingleexperiment.Opticalmethodscanbemultiplexedtocombineactivity
monitoring,manipulation,circuitreconstruction,andcharacterizationofasinglecells
morphologyandmolecularconstituents(oratleastasubsetoftheabove)simultaneously.
Similarly,combiningelectroderecordingwithopticalmethodsprovidesaddedvalue.For
example,includingopticalreporterslikedyesorfluorescentproteinscanhelpidentifythe
recordedcellsidentityandconnectivity.
Allofneurosciencewillbenefitfromastreamlinedintegrationofopticaltechnologiesforlarge
scalerecording,optogeneticmanipulation,andcircuitreconstructionthatallowsmultifaceted
studiesofidentifiedcellsandcircuitsinindividualbrains.Thiswillencompassunified
developmentofcompatibleopticalhardware,geneticorchemicalactivityreporters,and
optogenetictools.Technologyforopticalstudiesofbraindynamicsandcircuitry,celltypes,
andmolecularcontentshouldbeprogressivelydevelopedoverthelongtermtoattain
sufficientthroughputforsophisticatedstudiesofthedifferencesbetweenindividualsubjects,in
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animalsandinhumans.
Toreachtheirpotential,opticalmethodsshouldbeviewedholistically.Wavelengthranges
usedfornextgenerationmulticoloropticalimagingandoptogeneticcontrolshouldideallybe
tunedformutualcompatibility.Likewise,thecapabilitiesandlimitationsofopticalhardware
shouldbetakenintoconsiderationwhendevelopingnewsensormolecules,andviceversa,
sincethecollectiveopticalsystemiswhatultimatelyshouldbeoptimized.Forexample,inthe
domainofopticalsensors,muchworkisdoneatthesurfaceofbrainstructuresbecause
imagingdeeptissuesremainsaproblem.Redornearinfraredopticalindicatorswouldimprove
imagingdepthsinscatteringtissues,butcomplementarystrategiestosolvethisproblemmay
bedevelopedatthehardwaresensorinterface,forexamplevianonlinearopticalexcitation
usinglongwavelengthillumination.
Opticalengineeringandphotonicsarerapidlyprogressingfields;ongoingadvancesinoptical
hardwareandcomputationalopticsarelikelytobehighlypertinenttotheBRAINInitiative.
RecentprogressinminiaturizedopticsandCMOSimagesensorchipsformobilephoneshas
alreadyyieldednewcapabilitiesforfluorescenceimagingofneuralactivityinfreelybehaving
animals.However,mostemergingopticalcomponentswillnothavebeentailoredfor
neuroscienceapplications;systemsengineeringofnewinstrumentationusingthese
componentsshouldpaycarefulheedtotheuniqueneedsofneuroscienceexperimentation.
Greatbenefitcouldcomefromshorttermandsustainedeffortstodevelopnew
instrumentationtoimprovethespeed,tissuevolume,tissuedepth,andnumberofbrain
regionsthatcanbemonitoredinliveanimals.Theseadvancesmightcomeinmanyforms,such
as:newhardwareforhighspeedimaging;parallelizeddetectionsystems;progressinminiature
optics;novellightsources;microscopeswithcapabilitiesforlargescalerecordings;wirelessor
automatedimaginginstrumentation;nextgenerationopticalneedlesforimagingdeeptissues;
flexibleoptoelectronics;holographicorlightfieldtechniquesforpreciseopticalinterrogations
inallthreespatialdimensions;CMOSimagesensorsoflargersize,finerpixelsorbuiltin
capabilitiesforimageprocessingandautomateddetectionofneuralactivity;oropticalsystems
withscalablearchitecturesandautomatedanalyticsforimaginginmultipleanimalsorbrain
areasconcurrently.Manyoftheseinstrumentsmightexhibitbothopticalrecordingand
manipulationcapabilities.
Concurrentwiththeemergenceofintegratedopticalapproaches,itisessentialtodevelop
computationalapproachesfortheanalysisandmanagementoftheenormousdatasetsthe
opticaltechniqueswillyield(seealsosection5).Calciumimagingstudiesinmiceproduce~1
Gbits/secofdata;anatomicaldatasetswillreadilygrowtothe~10Petabytescaleandbeyond.
Sustainedeffortswillbenecessarytodevelopsophisticatedanalytictoolsfortheanalysisof
theseexperiments.Policiesandmethodsfordatasharingwillalsoneedtobedevelopedto
fullyexploitthevalueofthesedatasets(seesectionII.8d).
Atadeeperlevel,theconceptsofopticalimagingshouldbeconsideredacrossothermodalities
suchasmagneticfieldsorultrasound.Thevalueofexistingtechnologiesforhuman
neuroscience,suchasfunctionalMagneticResonanceImaging(fMRI)and
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magnetoencephalography(MEG),isimmense;developinghigherresolutionmethodsfor
humanuseisanaspirationheardacrossthefield.Anoninvasiveorminimallyinvasiveimaging
modalitywithcellularresolutionthatcouldinterrogatelargeportionsofthemammalianbrain
wouldrepresentamajoradvanceforbothanimalandhumanstudies.Anysuchtechnology
thatwassafelyapplicableinhumanswouldrevolutionizeourunderstandingofhumanbrain
function.
2civ.NanotechnologyandUnanticipatedInnovations
Asdevicesmovefromthemicro tonanoscale,propertiesemergethatmayprovidenew
opportunitiestointerrogateneurons.Siliconbasednanodevicesareonesuchexample.
Microwires,threemicronsindiameter,thatprojectoutfromthesurfaceofaconventional
electrodecanachieveintracellularaccesstocellsplatedoverthesewires;nanoposts,lessthan
onemicronindiameter,cancreategigaohmsealswithintracellularaccessforsustainedperiods
oftime.Thesedeviceshaverealpromise;ahighpriorityistomovetheirdevelopmentfromcell
culturestointegratedneuralsystems,inslicesorinvivo.
Intheintermediateorlongterm,revolutionarynewtechnologiesmayemerge,andtheBRAIN
Initiativeshouldencouragetheirexplorationanddevelopment.Nanodiamonds,forexample,
areparticleswhosephotochemicalpropertiesfluorescentlightemissionmightbetailoredto
exhibitsufficientsensitivitytoappliedelectricfieldstoserveasopticalreportersofelectrical
activity.Withrespecttoneuroscienceapplications,however,essentiallyallaspectsofthis
proposedtechnologyareuntested,fromdeploymentoftheparticleswithintheneuronal
plasmamembranetomeasurementofthelightsignals.DNA andRNAbasedtechnologies
havebeensuggestedasindirectreportersofneuronalactivitythatcouldbedecodedby
sequence.
Theseandothertechnologiesshouldbeencouragedandgivenroomtobreathebutheldtoa
standardofprogress:Emphasisshouldbeplacedonsupportingmethodsandresearchteams
thatprovidealogical,clearexperimentalpathwayfromaninvitrodemonstrationtoasetofin
vivoapplicationsinincreasinglycomplexneuronalsystems.Nanoscalerecordingdevicesare
potentiallybeneficialintermsofincreasedrecordingdensity,decreasedtissuedamage,andfor
longtermintracellularrecording.However,theyareallinveryearlystages,andmovingthis
technologyfrominvitrotoinvivoapplicationisasignificantchallengethatwillrequire
sustainedinteractionbetweennanoscientistsandneuroscientists.
Insummary,weshouldseizethechallengeofrecordingdynamicneuronalactivityfrom
completeneuralnetworks,overlongperiods,inallareasofthebrain.Therearepromising
opportunitiesbothforimprovingexistingtechnologiesandfordevelopingentirelynew
technologiesforneuronalrecording,includingmethodsbasedonelectrodes,optics,molecular
genetics,andnanoscience,andencompassingdifferentfacetsofbrainactivity,inanimalsandin
somecasesinhumans.

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II.3.ManipulatingCircuitActivity
Observingnaturalpatternsofneuralactivitygenerateshypothesesabouttheirfunctional
significance,butcausaltestsofsuchhypothesesrequiredirectmanipulationoftheunderlying
neuralactivitypatterns.Inthe1950s,Penfieldselectricalstimulationexperimentssuggested
thatamemoryorthoughtcouldbeelicitedbyactivatingneuronsintheunderlyingnetwork.In
interveningyears,electrical,chemical,andgeneticmethodsforstimulatingorinhibiting
neuronshaveprovidednumerousinsights.Currently,stimulatingelectrodesarebeingplaced
inhumanpatientsforspinalcordstimulationanddeepbrainstimulation(DBS),amongother
therapeutics.Despitethesesuccesses,currenthumanstimulationmethodslackprecisionand
specificity,andcouldbenefitfromtechnologicaladvances.Innonhumanneuroscience,a
majorrecentadvanceincircuitmanipulationhasbeenthedevelopmentofoptogenetictools
basedonlightactivatedchannelsandpumps.Thecombinationofrapidactivation,reliable
effects,andgeneticdeliveryoftheoptogeneticchannelstospecificcelltypesandbrainregions
hasrevolutionizedmodernneuroscience.Optogenetictoolsfordepolarizingand
hyperpolarizingneuronshaveprovedtobeageneralmethodfortestingandgenerating
hypothesesofbrainfunctionacrosssystems,brainregions,and(nonhuman)species.
Theexistingoptogenetictools,generallybasedonChannelrhodopsin(depolarizing)and
HalorhodopsinorArchaerhodopsin(hyperpolarizing),havebeentransformativebutarenot
perfectforalluses.Theyhavebeensubjectedtomultipleroundsofgeneticengineeringfor
optimizationfordifferentpurposes,improvementsdemonstratingtheimportanceofiteration
intooldevelopment.Nonetheless,newadvancescouldmakethemstillmoreuseful.Inthe
presentversions,thelightinducedcurrentsaregenerallysmall,andtheblue/ultravioletlight
thatmostofthesetoolspreferistoxictobiologicaltissues,anddoesnotpenetratedeepinto
tissues.Mostofthetoolshaveoverlappingabsorptionspectrawitheachotherandwiththe
geneticallyencodedsensorsofneuralactivity;theywouldbemoreusefulifthespectrawere
separate.Asmentionedearlier,improvementsinopticalphysicsmayprovidebenefitsfor
existingclassesoftools,forexamplebyallowingstimulationincomplex,rapidlyevolving
patternsthatimitatemeasurednaturalpatternsofcircuitactivity.Thesekindsof
improvementsareincremental,buttheircumulativeimpactcouldbesubstantialbecausethese
toolsaresowidelyused.
Therearebroaderpossibilitiesformanipulatingneuronalactivityinvivo.Chemogenetictools
(suchasRASSLs,DREADDs,andchemicalgeneticswitchesforkinasesandchannels)arealready
ausefulcomplementtooptogeneticsforlongtermmanipulation,andthisisanotherareathat
willbenefitfromcontinuedimprovement.Entirelynewtoolscouldbedevelopedbasedon
magneticstimulation,gases,infraredexcitation,ultrasound,ororganicorphysicalchemistryto
allowaccesstoneuronsdeepwithinthebrain.Techniquesofthissortcouldalsoallow
independentaccesstomultiplecircuits,orindependenttoolsformonitoringandmanipulating
neurons.Noninvasiveandnongeneticapproacheswillbeparticularlyimportantforhuman
neuroscience.

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Thereisalsosubstantialroomforgrowthinmodulatingmoresubtleaspectsofneuronal
function,notjustdepolarizationandhyperpolarization.Amongthetoolsthatcouldhave
enormousimpactaretoolsforsilencingoractivatingparticularsynapses;affecting
neuropeptidereleaseindependentlyofneurotransmitterrelease;oractivatingorinhibiting
secondmessengercascadesinrealtime,includingthosethatmediategrowthfactorand
neuromodulatorysignals.
Insummary,bydirectlyactivatingandinhibitingpopulationsofneurons,neuroscienceis
progressingfromobservationtocausation,andmuchmoreispossible.Toenabletheimmense
potentialofcircuitmanipulation,anewgenerationoftoolsforoptogenetics,chemogenetics,
andbiochemicalandelectromagneticmodulationshouldbedevelopedforuseinanimalsand
eventuallyinhumanpatients.Emphasisshouldbeplacedonachievingmodulationofcircuitsin
patternsthatmimicnaturalactivity.

II.4.TheImportanceofBehavior
Howcanwediscernthemeaningofthecomplex,dynamicactivitypatternsinthebrain?
Neurologistsoftengaininsightintoahumanbraindisorderbyobservingapersonsbehavior,
supplementedbypersonsverbalreports.Forexample,bymeasuringthebehaviorofthe
patientHMonobjectivetests,andbyinteractingwithhimonnumerousoccasions,the
neuropsychologistBrendaMilnerwasabletodemonstratethathisdamagedhippocampus
preventedhimfromformingexplicitmemoriesofevents,butnotimplicitmemoriesorhabits.
Innonhumananimals,however,wemustrelyexclusivelyonbehavioralobservationand
measurementstogaininsightintotheircognitiveprocesses.Tounderstandananimals
perception,cognition,oremotion,wemuststartbyobservingitsactions.
Applyingnextgenerationrecordingandmanipulationtoolstoevaluatebehaviorinsightfullywill
becomeincreasinglyimportanttoneuroscience.Behavioralmetricsaremostusefuliftheyare
objectiveandreliable,buttheyshouldalsopermitthestudyofrichbehaviorsappropriateto
thespecies.Amongexistingbehavioralmethods,formalpsychophysicshasbeenpowerful
becauseofitsuseofdetectiontasksandchoice(discrimination)tasks,whicharestandardized,
quantifiable,andeasilyrelatedtotheoreticalmodelssuchassignaldetectiontheory.An
alternativesetofmethodsbasedonneuroethologyexaminesfreelymovinganimalsin
naturalisticenvironments,wherethebehaviorsforwhichtheanimalhasevolvedcanbe
expressed.Theseexperimentsaretypicallycombinedwithrecordingsfromsmallimplanted
recordingdevices,withflexibletetherstoallowfreemovement.Anewersetofmethods
restrainstheanimalpartiallybyholdingitsheadfixed,butallowsittomoveonatrackingball,
givingittheperceptionofmovement.Theseflyonaballandmouseonaballexperiments
canbecombinedwithvirtualrealityenvironmentsinaclosedloopconfiguration,inwhichthe
animalsbehavioralchoicesresultinapparentchangesinitsenvironment;importantly,they
permitthesimultaneoususeofcomplexopticalorelectrophysiologicalrecordingsystems.

35

Advancedtechniquesformanipulating,tracking,andanalyzinganimalbehaviorwillbecrucial
componentsofrecordingandoptogeneticexperiments.Sincenotwoanimalshaveidentical
brains,matchingneuronalandbehavioraldynamicswillbebestachievedbyconducting
behavioralexperimentsoverlongdurationsinasingleindividual.Giventhecapabilitiesfor
trackingindividualcellsovermanyweeksinthelivingbrain,designsofbehavioralassaysshould
fullyexploittheselongtermcapabilitiestorevealhowthebrainsupportslearningandmemory,
howthebrainisalteredindiseasestates,andhowitrespondstotherapeuticmanipulations.
BuildingthisbehavioralcapabilityshouldbeapriorityfortheBRAINInitiative.Ultimately,
neuronalrecordingsandmanipulationsshouldintelligentlyscanasmuchaspossibleofthe
animalsbehaviorandcognitiverepertoire.
Oneavenueforfurthergrowthisamoredetailedunderstandingofbehavioraldynamics.This,
inturn,requiresaframeworkforcapturinganimalbehaviorsinvideooraudioformat,
segmentingandclassifyingthem,anddeterminingtheirdurationandthetransitionsbetween
them.Inanadvanceovermethodsrequiringexperthumanobservers,anemergingarea
combinesneurosciencewithmachinevisionandmachinelearningtoautomateanalysisofhigh
dimensionalbehavioraldatafromvideoandauditoryrecordings.Subsequentbehavioral
segmentationandclassificationcanbespecifiedbythescientist(supervisedlearning)or
detectedentirelybyacomputer(unsupervisedlearning).Thisautomatedquantificationof
behaviorhasmanyappealingfeaturesthatsupportitsfurtherdevelopment.Itprovidesahigh
levelofobjectivityandconsistency;itislaborsaving,enablinghighthroughputandhigh
contentanalysisofbehavior;andithasthepotentialtouncovernewbehavioralpatternsthat
havebeenoverlookedbyhumanobservers.
Insummary,thecleveruseofvirtualreality,machinelearning,andminiaturizedrecording
deviceshasthepotentialtodramaticallyincreaseourunderstandingofhowneuronalactivity
underliescognitionandbehavior.Thispathcanbeenabledbydevelopingtechnologiesto
quantifyandinterpretanimalbehavior,athightemporalandspatialresolution,reliably,
objectively,overlongperiodsoftime,underabroadsetofconditions,andincombinationwith
concurrentmeasurementandmanipulationofneuronalactivity.

II.5.Theory,Modeling,andStatisticsWillBeEssentialtoUnderstandingtheBrain
Largebraindatasetsareaccumulatingatanunprecedentedratethatwillaccelerateoverthe
nextdecadeastheBRAINInitiativegathersmomentum.Thegoalofbraintheoryistoturnthis
knowledgeintounderstanding,butthisisaformidabletask.Brainsevensmallonesare
dauntinglycomplex:informationflowsinparallelthroughmanydifferentcircuitsatonce;
differentcomponentsofasinglefunctionalcircuitmaybedistributedacrossmanybrain
structuresandbespatiallyintermixedwiththecomponentsofothercircuits;feedbacksignals
fromhigherlevelsconstantlymodulatetheactivitywithinanygivencircuit;and
neuromodulatorychemicalscanrapidlyaltertheeffectivewiringofanycircuit.Incomplex
systemsofthisnature,ourintuitionsabouthowtheactivityofindividualcomponents(e.g.
atoms,genes,neurons)relatetothebehaviorofalargerassembly(e.g.macromolecules,cells,
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brains)oftenfail,sometimesmiserably.Inevitably,wemustturntotheory,simulation,and
sophisticatedquantitativeanalysesinoursearchtounderstandtheunderlyingmechanisms
thatbridgespatialandtemporalscales,linkingcomponentsandtheirinteractionstothe
dynamicbehavioroftheintactsystem.
Theory,modelingandstatisticsplayatleastfourkeyrolesinourefforttounderstandbrain
dynamicsandfunction.First,forcomplex,frequentlycounterintuitivesystemslikethebrain,
mathematicalmodelingandsimulationscanorganizeknowndata,assistindeveloping
hypothesesaboutunderlyingmechanisms,makepredictions,andthusassistindesigningnovel
experimentstotestthehypotheses.Second,confirmatorystatisticalanalysisallowsustomove
intheinversedirectionafterdatacollection,usingformalinferenceapproachestosupportor
disproveastatedtheoryorhypothesis.Third,exploratorydataminingtechniquescanbeused
todetectinterestingregularitiesincomplexdataevenwheninformationcannotyetbe
summarizedwiththeaidofforwardmodelingorwhenpriorhypothesesdonotyetexist.Data
miningtechniquesarepowerful,butgenuineunderstandingofunderlyingmechanismswill
typicallyrequiresubsequentconfirmatoryanalysesoftheusualhypothesistestingvariety.
Finally,formaltheoryseekstoinfergeneralprinciplesofbrainfunctionthatunifylargebodies
ofexperimentalobservations,models,andsimulationoutcomes.Thebraincomputesstably
andreliablydespiteitsconstructionfrombillionsofelementsthatarebothnoisy,and
constantlyadaptingandrecalibrating.Elucidationofthegeneralprinciplesunderlyingthis
remarkableabilitywillhaveaprofoundimpactonneuroscience,aswellasonengineeringand
computerscience.
5a.CombiningTheory,Modeling,Statistics,andExperiments
Theoryandmodelinghaveilluminatednumerousareasofneuroscienceinthepast:the
mechanismsofactionpotentialgeneration(HodgkinHuxley),synapticplasticity(Hebb),visual
motioncomputation(HassensteinReichardt),theefficiencyofsensorycodes(Barlow),therole
ofinferenceandpriorsinperception(Helmholtz),theroleofdopaminergicsystemsin
computingpredictionerrorsforreinforcementlearning(Schulz,Sutton,Dayan),anddecision
makingunderuncertainty(GreenandSwets,Luce).Truepartnershipsbetweentheoristsand
experimentalistswillyieldlargedividendsforalmosteveryconceptualandexperimental
problemtobetackledundertheBRAINInitiative.
Modelingandtheorydevelopedthroughclosecollaborationsoftheoristsandexperimentalists
aremostlikelytoyieldpenetratinginsightanddrivecreativeexperimentalwork.Data
gatheredbyanexperimentalistuninformedbytheory,evenexcellentqualitydata,maynotbe
thedatathatwillgeneratethemostdefinitiveconclusionsorgreatestconceptualclarity.
Similarly,theoristswhoparticipateactivelyintheacquisitionofdataaremorelikelytoacquire
abiologicalsenseofthesystem,itsreliability,anditslimitations,increasingthelikelihoodthat
theirtheoriesreflectbiologicalrealityandmakepredictionsthatarefeasibleforexperimental
verification.
Ideally,theoristsandstatisticiansshouldbeinvolvedinexperimentaldesignanddata
acquisition,notjustrecruitedatthestepofdatainterpretation.Thecloseworking
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relationshipsweenvisioncouldbesupportedbygrantopportunitiesthatrequirethe
participationofastatisticianortheoristincollaborationwithanexperimentalist;ahighly
successfulmodelforthishasbeenthejointNIHNationalScienceFoundation(NSF)
CollaborativeResearchinComputationalNeuroscience(CRCNS)program.
Wenexthighlightafewofthemanyareasthatappearpromisingforthecollaborativeeffortsof
theoristsandexperimentalistsunderthegoalsoftheBRAINInitiative.
5ai.NewStatisticalandQuantitativeApproachestoNewKindsofData
Thenextgenerationofneuralactivityrecordingswillbedifferentfrompreviousones.Allsigns
pointtoamajorincreaseinthequantityofneuronalrecordings,butthequalityofneuronal
recordingswillalsochangeduringtheBRAINInitiative.Electrophysiologicaltechniquesare
beingcomplementedincreasinglybyopticalrecordingmethods,whichwilldictatedifferent
analyticapproaches.Theabilitytoidentifyspecificcelltypes,andmapthisinformationonto
activitymaps,willprovideanadditionaldimensiontotheserichdatasets.Theabilitytorecord
multipleformsofactivitysimultaneouslyspiking,subthresholdactivity,synchrony,
neuromodulatorystateswillincreaseaswell.Wewillneednewtoolstoanalyzethese
complexdatasets,aswellasnewtoolsandalgorithmsfordataacquisitionandinterpretation:
e.g.,1)differenttypesofmeasurementwillneedtobefusedtoextractmeaningfulinformation,
2)thesheeramountofdatawilldemandhighlyefficientalgorithms,3)insomecases,analyses
willneedtobedoneinrealtime,eitherbecausedatavolumesaretoolargeforstorage,or
becausetheexperimentisdesignedtoadapttotheresponses,orforapplicationssuchas
neuralprosthetics.
Asnewkindsofdatabecomeavailablethroughadvancesinmolecularsensorsandoptical
recording,equaleffortmustbeexpendedtoextractmaximuminsightfromthesenoveland
oftencomplexdatasets.Dataanalyticandtheoreticalproblemsarelikelytoemergethatwe
cannotanticipateatthepresenttime.Resourcesshouldbeavailableforexpertsfromessential
disciplinessuchasstatistics,optimization,signalprocessing,andmachinelearningtodevelop
newapproachestoidentifyingandanalyzingtherelevantsignals.
5aii.DimensionalityandDynamicsinLargeScalePopulationRecordings
InlargescalepopulationrecordingslikethoseenvisionedundertheBRAINInitiative,theissue
ofdimensionalityiscritical.Dimensionalityreductiontechniquesdetectcorrelatedactivity
amongsubsetsofthesampledneuronalpopulation,identifyingensemblesofneuronsthat
mightbefunctionallyrelatedtoeachotherininterestingways.Incurrentrecordingsoftens
tohundredsofneurons,thedimensionalityofthedataistypicallymuchlowerthanthenumber
ofrecordedneurons,encouragingthenotionthatdifferentbehavioralvariablesorneural
circuitryconstraintsmightbereflectedintheactivityofneuronsindifferentensembles.Low
dimensionalityisalsointerestingbecauseitimpliesthatonecancapturethemajorsourcesof
variationinasystembyrecordingfromarelativelysmallproportionofitsneurons.Plainly,the
issueofdatadimensionalityhassubstantialimplicationsforwhatourexperimentalgoalsshould
beinlargescalepopulationrecordings.Inalowdimensionalsystem,itwouldbefarmore
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importanttosampleneuronalactivitystrategicallythantorecordfromeveryneuroninthe
system.
Thereisreasonforcaution,however.Thenumberofapparentdimensionsinthedatamaybe
artificiallylowifthebehavioraltaskistoosimpleorifneuronalactivityisnotmeasuredfor
sufficientlylongperiodsoftime.Thusitisessentialnotonlytorecordmoreneurons,butto
alsoincreasebehavioralandstimuluscomplexityinordertoobtainricher,higherdimensional
datasets.Asecondproblemisthatmanyofthesemethods,suchasindependentcomponent
analysis,prinicipalcomponentanalysis,supportvectormachines,andgraphicalmodels,are
designedforproblemsinwhichthestructureinthedataisstatic.Moresophisticatedstatistical
methodsexisttoanalyzetimeseries,andshouldbefurtherdevelopedtoanalyzethehighly
nonlineardynamicstructureofmostneurosciencedata.
Thedynamicsofneuralactivityinsinglecells,smallcircuits,andlargepopulationsarecomplex,
andincludenonstationarycalibration,adaptation,andlearningmechanismsthatoccur
simultaneouslyandondifferenttimescales.Thesearecurrentlynotwellunderstood,andwill
requiredevelopmentofnewtheoreticalandanalysistoolsbasedoncontroltheory,information
theory,andnonlineardynamicalsystems.
Resolvingthetheoreticalissuesassociatedwithdimensionalityanddynamics,anddeveloping
newtechniquesandcomplexbehavioralparadigmsthatcanreleasethepotentialpowerof
largeneuraldatasets,areimportantcontributionsthattheoryandmodelingcanmaketothe
BRAINInitiative.
5aiii.LinkingActivityAcrossSpatialandTemporalScales
Oneofthemostremarkablepropertiesofnervoussystemsisthatthetemporallyenduring
behaviorofanorganismemergesfromthecollectiveactionofmoleculesandcellsoperatingon
timescalesmanyordersofmagnitudeshorter.Atthecellularlevel,informationisencodedin
thepatternsofactionpotentialsgeneratedbyindividualneurons,eachenduringforroughlya
millisecond.Yetaworkingmemorymaylasttensofseconds,andasinglepurposefulbehavior
canextendforminutesorhours.
Theintegrationofinformationacrosstemporalscalesisaproblemthatwillinvolvebiochemical
signalingpathwaysthatoutlastanelectricalinput,circuitpropertiessuchasattractors,in
whichalargepopulationofinteractingnervecellsachievesanenduringactivitystate,and
experiencedependentchangesinthestrengthofsynapticconnectionsbetweenneurons.
Meaningfulmodelsofbrainactivitywillneedtoincorporateeventsatallofthesetemporal
scales.
Nolessimpressiveistheextensionofcoordinatedneuralactivityoverlargespatialscaleswithin
thebrain.Apurposefulbehaviorassimpleasaneyemovementcaninvolvemillionsofneurons
distributedacrossmorethanadozenareasbrainareas.Howiswidespreadactivityinthe
cortex,basalganglia,thalamus,midbrain,andbrainstemorchestratedtoachieveasingle
behavioralgoal?
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Theory,modeling,andbiophysicallyrealisticsimulationswillplayacriticalroleindeepeningour
understandingoftheseandmanysimilarphenomena.Theorycanhelpusdevelophypotheses
anddesigntherightexperimentstoaskhowpurposefulsystemslevelbehavioremergesat
extendedspatialandtemporalscales.
5aiv.FlexibleBehaviorandDecisionMaking
Muchofourknowledgeofbrainfunctioncomesfromexperimentalmeasurementsfromoneor
afewneuronsinasinglebrainarea.Asweattempttounderstandtheremarkablycomplex
behavioralandcognitiveabilitiesexhibitedbyhumans,wewillneedtoconsiderthe
interactionswithinandbetweenlargerneuralsystemsandbrainareas.Complexactionsare
drivenbysimultaneousinputsfrommultiplesensorymodalities,aswellasinternalstatesand
memoriesthatrepresentgoals,constraints,andpreferences.Theseactionsarereadilyadapted
todifferentenvironmentsandcontexts,andtheycanbelearnedandrefinedwithexperience.
Inadditiontohumans,manyanimalsalsodemonstratebehaviorsthatcanbeflexiblyreshaped
oradaptedaccordingtocontextortaskrequirements.Forexample,neuronsinthefrontal
lobesofnonhumanprimatesarecentrallyinvolvedindecisions,andhavebeenshownto
respondtobothtaskrelevantandtaskirrelevantsensorystimuli,alongwithsignalsrelatedto
behavioralchoices.Therepresentationoftheseattributeswithinneuronalensemblescan
changemarkedlyduringtheexecutionofanygiventask.Wedonotyethaveasystematic
theoryofhowinformationisencodedinthechemicalandelectricalactivityofneurons,howit
isfusedtodeterminebehavioronshorttimescales,andhowitisusedtoadapt,refine,and
learnbehaviorsonlongertimescales.Finally,humansandperhapssomeanimalshavethe
capacityforsymboliccomputationusinglanguageandinotherdomainsaswell;abrainbased
theoryofthesehigherfunctionsisnotablylacking.
Coordinatedworkintheory,modelingandexperimentwillberequiredtounderstandthe
mechanismsofcontextdependentinformationflowinthebrain,whichliesattheheartof
flexiblebehaviorssuchasdecisionmaking.
Insummary,rigoroustheory,modeling,andstatisticsareadvancingourunderstandingof
complex,nonlinearbrainfunctionswherehumanintuitionfails.Newkindsofdataareaccruing
atincreasingrates,mandatingnewmethodsofdataanalysisandinterpretation.Toenable
progressintheoryanddataanalysis,wemustfostercollaborationsbetweenexperimentalists
andscientistsfromstatistics,physics,mathematics,engineering,andcomputerscience.

II.6.HumanNeuroscienceandNeurotechnology
AprimarygoaloftheBRAINInitiativeistounderstandhumanbrainfunctioninawaythatwill
translatenewdiscoveriesandtechnologicaladvancesintoeffectivediagnosis,prevention,and
treatmentofhumanbraindisorders.Thestudyofhumanbrainfunctionfacesmajorchallenges
becausemanyexperimentalapproachesapplicabletolaboratoryanimalscannotbedeployedin
humans.Nevertheless,directstudyofthehumanbrainiscriticalbecauseofourunique
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cognitiveabilitiesaswelltheprofoundpersonalandsocietalconsequencesofhumanbrain
disorders.
Improvementstoexistingtechnologieslikemagneticresonanceimaging(MRI)andpositron
emissiontomography(PET)haverevolutionizedourabilitytononinvasivelystudythestructure,
wiring,function,andchemistryofthehumanbrain.Otherimportantopportunitiesare
emergingfromtheincreasingnumberofhumanswhoareundergoingdiagnosticbrain
monitoringwithrecordingorstimulatingelectrodes,orarereceivingneurotechnological
devicesfortherapeuticapplicationsorinvestigationalstudies(e.g.DBS).Someofthemost
promisingnewopportunitiesinvolvecombiningtheseandothertechniquestocrossbarriersof
spatialandtemporalscalethathaveimpededprogressinthepast.Forexample,theinabilityto
measureactivityandchemistryatthecellularlevelwithnoninvasivetoolscreatessignificant
uncertaintyaboutthefunctionalmeaningofsomeoftherecordedsignals.Wecanpotentially
addressthisproblembycombiningnoninvasivebrainimagingwithhigherresolutiondata
obtainedfromdiagnosticmonitoringofhumansorfromimplanteddevicesinhumans.Insight
isalsoemergingbycombinedmeasurementofnoninvasiveandcellularlevelsignalsinanimal
models.Breakingthesebarriersofscale(Section6aii)wouldyieldsubstantialbenefitsfor
diagnosisandtreatmentofdiseaseaswellasforbasicdiscoveryaboutthehumanbrain.These
andothercreativeapproachesforunderstandinghumanbrainfunctionshouldreceivevigorous
supportundertheBRAINInitiative.
6a.HumanBrainImaging
Thelasttwentyyearshaveseenexplosivegrowthinthedevelopmentanduseofnoninvasive
brainmappingmethods,predominantlyMRI,complementedbyMEGand
electroencephalography(EEG),toinvestigatethehumanbrainundernormalandpathological
conditions,andacrossthehumanlifespan.Inthefuture,weanticipatesignificantprogressin
usingthesemethodstomeasurethewiringdiagramandfunctionalactivityofthehumanbrain
atmultiplescalesneuronalensembles,circuits,andlargerscalenetworks(circuitsof
circuits).Inturn,thesecapabilitieswillallowustovisualizeandunderstandcircuitlevel
disruptionsrelatedtohumanbraindiseases.Brainimagingtechniquesarealsovaluablefor
evaluatingtheeffectsofpharmacologicaltreatmentsandnoninvasivebrainstimulation
methods,orforvalidatingotherfunctionalmeasurementmethodslikenearinfrared
spectroscopy.
6ai.MRIApproaches
MRItechniquescontributeextensivelytohumanneuroscienceinthreebroadways:fMRI
enablescorrelationoffunctionalbrainactivitywithcognitionandbehavior;diffusionweighted
MRI(DWMRI)providesestimatesofthetrajectoriesoflongdistancepathwaysinthewhite
matter;restingstatefMRI(rfMRI)enablesustodeducefunctionalconnectivitybetween
dispersedbrainregions.Alloftheseinvestigationswillbeacceleratedgreatlyifthespatialand
temporalsamplinglimitationsofthemagneticresonance(MR)measurementscanbereduced.
ThevastmajorityofcurrentMRstudiesaimforwholebraincoverageandachievespatial
resolutionof2mm(isotropic)orcoarser.An8mlvoxelfromsuchanimagecontainsa
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veritableworldofsmallercircuitcomponentsmorethan600,000neuronsandglialcells,
manycolumnarensembles,intermixedcorticallayers,or(inthewhitematter)several
fasciculatedfiberbundlesthatmaycrosseachother,fanoutorturnwithinthatvolume.
TheproblemofrelatingMRsignalstotheunderlyingcircuitrycanbeamelioratedsomewhatby
improvedphysicalmeasurements.Forexample,inpreciselytargetedexperimentsusinghigh
fieldstrengthmagnets,hemodynamicallybasedMRmeasurementshavereachedspatialscales
below1mmtothelevelofcorticalcolumnsandindividualcorticallaminae.Evenatthisscale,
however,MRmeasurementsreflectacomplexcombination,atthevascularlevel,of
electrochemicalactivityofmanythousandsofneuronsandglia.Thusitiscriticallyimportantto
developandexperimentallyvalidatetheoriesofhowMRsignalsarebasedintheunderlying
cellularlevelactivity,asweconsiderinthenextsection.
6aii.BridgingSpatialScales
TolinktheintegrativefunctionalsignalsmeasuredbyMRItocellularresolutionactivity,two
separateissueswarrantintensiveinvestigation.First,wemustfirmlyestablishhowthe
electricalandchemicalactivityindifferentpopulationsofexcitatoryandinhibitoryneurons,
glialcells,axons,andpresynapticterminalscontributetothelocalvascularresponsethe
classicneurogliovascularcouplingproblem.Thisknowledgeisimmediatelyrelevantnotonly
forinterpretationoffMRIsignals,butalsoforinvestigationofneurologicalandpsychiatric
diseasesinwhichadisruptioninneuroglialcommunicationand/ordeteriorationof
neurovascularcouplingcontributestomotorandcognitivedecline.
Thesecondissue,whichhasreceivedmuchlessattention,concernswhatinformationcodedin
theneuralactivityofpopulationsofneuronswithintheimagedvoxeliscapturedinthe
hemodynamicresponse.Byanalogytobridgingscalesinphysics,thebasicintellectualquestion
ishowtheelectricalandchemicalactivityofneurons,glia,andsynapsesinimagedvoxelsare
integratedoraveragedtogenerateahemodynamicsignal.Thesequestionscanbebest
answeredbydirectcomparisonofcellularresolutionpopulationactivityofneuronswith
hemodynamicresponsemeasurements,ideallyinanimalsengagedinsophisticatedbehavior
likelytoinvokethefullcomputationalpowerofneuralcircuits.Additionalapproachesinclude
theuseofoptogenetics,pharmacology,andmutantanimalstoperturbneuronalsignalsand
directlyobservetheeffectsattheleveloffMRI.Theseapproachesoffertheopportunityto
bridgeanatomicalandphysiologicalscales,goingfromcellularresolutionneuronalandglial
activitytomacroscopiccircuits,networksandultimatelybehavior.
DWMRIestimatestheorientationofaxonalfiberbundles,capitalizingonthefactthatwater
diffusesmostrapidlyalongthelengthofaxons.Byprobingatmanydifferentorientations,DW
MRIcanestimatenotonlythedominantfiberorientationineachvoxel,butalsotheorientation
ofcrossingfiberbundles,whichareverycommoninthewhitematterthicket.Tractography
algorithmscombineinformationacrossasuccessionofvoxelstoestimatetheoveralltrajectory
oflongdistancepathways.SomeoftheproblemsfacedbyDWMRIinchartinganatomical
connectivityinthehumanbrain,suchascrossingfibers,fiberfanning,andsoforth,maybe
alleviatedbyhigherspatialresolutionandmoresensitiveimagingtechniques.Thebenefitsof
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improvedresolutionhavealreadybeendemonstratedbyresultsfromtheHumanConnectome
Project,buttheseachievementsstillfallshortofwhatisneeded.Ourabilitytoinferstructural
connectivitypatternsusingDWMRIwillbefurtherimprovedbyusinganatomicallyinformed
priorsthatarebasedonaccuratestatisticalmodelsofthedistributionoftrajectoriestakenby
axonsandfiberbundlesinwhitematter.Suchinformationcanbeobtainedfromcuttingedge
microscopymethods(e.g.,opticalcoherencetomography,polarizedlightimaging,CLARITY)and
usedtoimprovethefidelityofDWMRIbasedtractographymethods,thusbridgingmicroscopic
andmacroscopicscalesattheanatomicallevel.Itiscriticalthatateachstageoftheprocessof
improvement,theoverallvalidityofDWMRIbasedtractographyisdemonstratedbydirect
comparisonwithanatomicaltracttracinginanimalmodels,includingnonhumanprimates.
Thus,specificopportunitiesforMRItechnologyundertheBRAINInitiativeinclude
submillimeterspatialresolutiondescriptionsofneuronalactivity,functionalandstructural
connectivity,andnetworkanalysisinthehumanbrainthroughadvancesininstrumentation,
dataacquisitionandanalysistechniques,andtheoreticalmodelinglinkingactivitywith
behavior.
6aiii.RestingStatefMRIandBrainNetworkDynamics
rfMRIenablesinferencestobemadeaboutfunctionallyconnectednetworksthatmaybe
widelydispersedwithinthebrain.Itreliesontheobservationthatfunctionallyrelatedareas
thatarecoactivatedduringperformanceofataskalsoexhibitcorrelatedspontaneous
fluctuationswhensubjectsaresimply"resting"intheMRscanner.Manylargescalecorrelated
temporalpatterns,referredtoasrestingstatenetworks(RSNs)havebeenidentifiedinthis
manner.RSNspersistduringsleepandunderanesthesia,andareconsistentacrosssubjectsand
tosomeextentacrossspecies.Importantly,RSNsdisplaysomedegreeofcorrespondencewith
anatomicalconnections,butthecorrespondenceisfarfromperfect.RSNsappeartoreflect
functionalcoordinationoperatingacrossmultiplesynapseswithinacircuit,providing
informationaboutcorrelatedactivitythatisdifficulttoinferfromanatomicalmapsalone.
Recentdevelopmentsinsignificantlyacceleratingwholebrainfunctionalimages(e.g.2mm
isotropicresolution,wholebrainimagesacquiredinlessthanasecond)haveenabledmajor
improvementsinspatialandtemporalsamplingofrestingstatefluctuations,leadingtomajor
gainsinstatisticalpowertodetectRSNs,increasesinthenumberandgranularityofnetwork
nodes,andanenhancedabilitytoanalyzeneuraldynamics(e.g.detectionofregions
dynamicallyparticipatingindifferentnetworks).Theserecentadvancesemphasizethe
importanceofgainsenabledbyimprovingspatialandtemporalresolutionoftheMRIdata,and
theneedtopushthetechnologyfurther.
ChangesinRSNshavebeenimplicatedaspossiblebiomarkersforfunctionalclassificationin
severalcognitivedisorders,andhaveenormouspotentialforfurtherdevelopmentinthisarea.
WhethersuchrfMRIderivednetworksand/ornetworkdynamicscaninformusaboutindividual
differencesinpsychiatricdisordersorguideindividualizedtherapiesisyettobedetermined,
butitisoneofthesignificantpotentialpayoffsofapplyingimprovedMRImethodsandanalysis
techniquestobedevelopedundertheBRAINInitiative.
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6b.EEGandMEG
EEGandMEGprovideauniquecapabilityfornoninvasiveanalysisofhumanbrainactivitywith
hightemporalresolution.NumerousstudieshavedemonstratedthemeritsofEEG/MEGfor
detectingneuralcorrelatesofabroadrangeofhumancognitiveprocessesaswellasbrain
disorderssuchasepilepsy.ThesimplicityandmobilityofEEGmonitoringsystemshas
facilitatedthestudyofhumanbrainsignalsinnaturalisticsettings.
EEG/MEGislimitedinitsspatialresolution.LocalizingEEGsignalstospecificbrainstructures
(sourceimaging)hasbenefittedsignificantlyfromtheapriorianatomicconstraintsmeasured
withstructuralMRI.Thissynergisticinteractionhighlightsthevalueofcombiningdataacross
imagingmeasurementmodalities.Recentadvancesinsourceimaginghavesignificantly
improvedlocalizationofeventrelatedbrainactivityinhealthyhumansubjectsandofinterictal
spikesinepilepsypatients.Asignificantchallengeforthefutureistodevelopadvancedsource
imagingtechniquesthatcanmapspontaneousbrainactivity,includingRSNsinhealthysubjects,
aswellasabnormalnetworkconnectivityassociatedwithneurologicalorpsychiatricdisorders.
AnimportantopportunityliesinintegratinghightemporalresolutionEEG(andMEG)source
imagingwithhighspatialresolutionfMRI.Significantprogresshasbeenmadetoleveragethe
complementarynatureofEEGandfMRI,whichcanbeperformedsimultaneouslyinanMRI
scanner.ChallengesexisttobetterunderstandthecorrelationbetweenBOLDsignalsand
electrophysiologicaleventsvianeurovascularcoupling,technologiesforhighfidelityrecordings
ofbrainactivityusingEEGfMRI,andtechniquestoenhanceperformanceofEEGsource
imagingfromsimultaneouslyacquiredfMRIdata.ItisnoteworthythatMEG/EEGmethodsfail
torecordspikingactivity(theoutputsignalsofmostneurons);thisscaleismissinginnon
invasiverecordings.Newmethodsforrecordingneuronspikingexternallywouldhaveavery
largeimpact.
6c.PETandNeurochemistry
Assessmentofdynamicneurochemicalandothermoleculareventshasbeenrelatively
neglectedinrecentyears,inlargemeasurebecausethetechniquesaredifficultcomparedto
fMRI.WhileMRspectroscopyoffersaviewofsomeimportantintrinsicmolecules,ithasnot
yetshownchemicalspecificityforneurotransmitter/receptorinteractions.OpticalandMR
basedimagingmethodsoffersignificantpotentialformolecularimaginginanimalmodelsusing
exogenousprobes,butthetranslationofthesemethodologiestohumansisnot
straightforward.Intheshort tomidterm,nucleartechniques,includingsinglephoton
emissioncomputedtomography(SPECT)andprincipallyPET,providethebestmeansto
translatestudiesofneurotransmitters,receptors,andneuromodulatorstohumans.
Twoprincipalchallengeslimittheroleofthesetechniquestoday.Thefirstistoexploitthe
potentialforbetteruseofexistingPETtracersthattargetdozensofimportant
neurotransmittersystemsandtheirreceptorsubtypes.Withinthelibrariesofcompounds
testedfortherapeuticpotencybythepharmaceuticalindustryliehundredsofcompounds
awaitingevaluationoftheirpotentialasimagingagents.Public/privatepartnershipsunderthe
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BRAINInitiativecouldunlockthispotentialtreasuretroveofcompounds,notastherapeutic
agents(forwhichtheywereoriginallyevaluated),butascompoundsfordiscoveryofreceptor
function.Second,whiletheprincipleofusingPETtoevaluatechangesinreceptoroccupancy
secondarytopharmacologicalorcognitivestimulationhasbeendemonstrated,themeansfor
dynamicassessmentofneurochemicalspecificbrainactivation,analogoustofMRIlocalization
ofactivation,isnotyetinhand.
Significantprogressispossible,however,inbothshortandlongerterms.Truedynamic
assessmentofreceptoroccupancyandmetabolism,atspatialresolutionapproachingtodays
fMRIstudiesandtemporalresolutionofminutes,isafeasiblemidtermgoalwithkeyreceptor
subtypesofthedopaminergic,serotonergicandglutamatergicneurotransmittersystems.In
thelongerterm,therangeofmoleculartargetsandreceptorsubtypesamenableforstudy
shouldsteadilygrow,tappingintothebreadthofneurochemicalexpertiseavailablethrough
partnershipswithpharmaceuticalcompanies.
Insummary,thereisaneedtoimprovespatialresolutionand/ortemporalsamplingofhuman
brainimagingtechniques,anddevelopabetterunderstandingofcellularmechanisms
underlyingcommonlymeasuredhumanbrainsignals(fMRI,DWMRI,EEG,MEG,PET)for
example,bylinkingfMRIsignalstocellularresolutionpopulationactivityofneuronsandglia
containedwithintheimagedvoxel,orbylinkingDWMRIconnectivityinformationtoaxonal
anatomy.Understandingtheselinkswillpermitmoreeffectiveuseofclinicaltoolsfor
manipulatingcircuitactivity,suchasdeepbrainstimulationandtranscranialmagnetic
stimulation(TMS).
6d.DevicesforMonitoringandStimulatingtheHumanBrain
Anewgenerationofmedicaldevicesforinterfacingwiththelivinghumanbrainhasbeen
fueledbythemergerofengineeringadvanceswithneurosciencediscovery.Devices,some
alreadyinhand,arebeingusedtomonitorbrainfunction,todiagnoseandtreatmoodand
movementdisorders,andtorestoresensoryandmotorfunctionslostfollowinginjuryor
disease.Thousandsofhumansarereceivingtheseneurotechnologiesinclinicallyapprovedor
investigationalapplications.Withtheirinformedconsent,theseindividualsprovidean
extraordinaryopportunityforrigorousresearchonnormalbrainfunction,aswellasonthe
effectsofbraininjuryordisease.Whencoupledwithnoninvasiveimagingthereisareal
opportunitytobridgescalesfromlimitedcellulartowholebrainfunctionalimagingmethods.
Thepopulationofhumansreceivingrecordingorstimulatingdevicesislargeandgrowing.
Mostnotably,DBSelectrodesimplantedinaspecificbasalgangliacircuithavehelpedtorelieve
morethanahundredthousandpeopleoftherigidity,tremor,andslowmovementsof
Parkinsonsdisease.DBSisalsowidelyandsuccessfullyemployedinmotordisorderssuchas
dystoniaandtremor,andthereisreasontothinkthatitspotentialuseismuchbroader:
promisingresultshaveappearedforDBSuseinintractabledepression,anditisbeingexplored
asatreatmentforobsessivecompulsivedisorderandevenmemorydecline,whichcouldhave
majorpublichealthimplications.Anotherfrontierisclosedloopimplantedsystemsinwhich
dataanalysisisperformedinrealtimebyacomputerandusedtogeneratefuturepatternsof
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brainstimulation.Forexample,asensormightdetectanepilepticseizureintheearlystagesof
itsdevelopmentandreduceorblockitbystimulatingthebrainintoquiescence.
Inthesensingdomain,braincomputerinterfaces,stillearlystageinvestigationaldevices,can
enablepeoplewithparalysistousetheirownbrainsignalstocontrolassistiveprostheticslike
computersorroboticarmswellenoughtoperformsomeeverydayactivitiesofliving.Inthese
individuals,chronicallyimplantedmultielectrodesensorsprovideunprecedentedhigh
resolutionrecordingoveryears.Developmentsinsensingandstimulationtechnologypromise
aseriesofnewdevicesthatwillincreasethequalityoflifeandindependenceofindividuals
limitedbyawiderangeofbraininjuriesordisorders.Eachpersonwithadevice,whoiswilling
toparticipate,becomesapossibleresearchparticipantwithpotentialtoyieldvaluabledata
aboutbrainfunction.
Theavailabilityofthislargecohortofpeoplewithimplantedtechnologyopensthepossibility
notonlytoadvanceclinicalcare,buttocarryoutdetailedstudiesthatwerebarelyconceivable
adecadeago.Duringintraoperativemappinginepilepsy,researchersfoundneuronsinthe
medialtemporallobeofahumanpatientthatrespondedtopicturesofindividualactorsor
politiciansandalsotothespelledoutnameofthesameperson.Theseneuronsprovidea
fascinatingexampleoftheencodingofcategoriesorabstractconceptsinthebrain.Direct
brainrecordingsduringanesthesiahaverevealedcharacteristictransformationsinbrainactivity
asconsciousnessislost.Chronicmultielectrodearrayrecordingsfrombraincomputer
interfacesinpeoplewithlongstandingparalysishaveshownhowthemotorcortexretains
representationsofthearmevenyearsafterastroke,raisingnewquestionsaboutplasticityin
thehumanbrain.Astheseapplicationscontinuetoexpand,therewillbeanunprecedented
opportunitytostudyhumancircuits,bothbyrecordingtheiractivityandbymodulatingtheir
activity.
6e.TeamsforBasicandClinicalHumanResearch
Takingadvantageofthescientificopportunitiesofferedbyneurotechnologydevelopmentsand
volunteerhumanpatientsisanexceptionallycomplexendeavor.Everyopportunityshouldbe
maximizedwhilemaintainingthehigheststandardsforresearchparticipantsafetyand
protection.Meetingresearchgoalsandhumanresearchstandardsrequirescloselyintegrated
researchteamsincludingclinicians,engineers,andscientistswhoworktogethertoorganize
andcarryoutresearchofthehighestintegrityandrigor.Clinicianswhousenew
neurotechnologiesinhumanresearchshouldinteractcloselywiththeengineers,scientistsand
companiesdevelopingthem,toensuretherapidcreation,validation,anddisseminationof
effectivetools.Theregulatoryoversightofhumanresearch,aswellasthecloseclinical
relationshipandpotentiallylongtermcommitmenttoparticipants,canplaceaspecialtimeand
financialburdenoninvestigators.Inaddition,storingandprocessingdataincompliancewith
federalprivacyprotectionlawsarechallenging.Becauserelatedclinicalresearchactivitiescan
occuracrossmanyuniversitiesandmedicalcenters,mechanismstostandardizeandshare
preciousdatafromhumansubjectsareessential.Further,becauseresearchisoftenaimedat
creatingnewmedicaldevicesfortreatmentofhumandiseaseorinjury,theobjectivesofthe
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researchteammustoftenbealignedwithregulatorypathsandindustrystandardsneededto
translateearlystagetestingintoacommerciallyviabletechnology.Thesevarieddemandsmust
bemetwhilealsoadheringtothehigheststandardsofscientificqualityanddesignof
preclinicalstudies.
Thesestandardscanandarebeingmetbydedicatedteamsofcollaborativeresearchers,but
considerationshouldbegiventoreducingunnecessarybureaucratichurdlesintheacademic
setting.Thisdifficultbutextremelyvaluableareaofresearchshouldbemadeasefficientas
possibletomaximizetheeffortsofboththeresearchersandthepatients.Initiatingsuchsteps
couldaccelerateinnovativeresearch,ultimatelydrivingdowncostsandprovidingbetterclinical
devicesandtherapeuticoutcomes.Becausethiskindofresearchissovaluableyetsocomplex,
wemustdevelopnovelincentivesandstraightforwardmechanismstotranslatebasicscience
advancesintohumanpilottesting,whilemaintainingtheethicalstandardsandregulatory
proceduresinplaceforhumanresearch.
Insummary,humanswhoareundergoingdiagnosticbrainmonitoringorreceiving
neurotechnologyforclinicalapplicationsprovideanextraordinaryopportunityforscientific
research.Thissettingenablesresearchonhumanbrainfunction,themechanismsofhuman
braindisorders,theeffectoftherapy,andthevalueofdiagnostics.Meetingthisopportunity
requirescloselyintegratedresearchteamsincludingclinicians,engineers,andscientists,all
performingaccordingtothehighestethicalstandardsofclinicalcareandresearch.New
mechanismsareneededtomaximizethecollectionofthispricelessinformationandensure
thatitbenefitspeoplewithbraindisorders.
6f.HumanNeuralTechnologyDevelopment
Forhumanresearch,TheBRAINInitiativeshouldultimatelysupporttwobroadtypesof
technologydevelopment:(1)researchtoolsthatallowustobetterinvestigatebrainstructure
andfunction,and(2)clinicaltoolsthatenableustobetterdiagnose,prevent,treat,andcure
braindiseases,includingtechnologiesthatcanrestorelostfunctions.Devicesforusein
humansneedsubstantialimprovementoverexistingtechnology:theyneedtobemorereliable,
stable,andlonglasting,whichwillrequirebettermaterials,biocompatibility,andfeatures
optimizedforhumanuse.Weneedelectrodearrayswithhigherspatialresolutionfor
recordingandstimulationbothwithinandacrossbrainareas.Inthemedium tolongterm,
newmonitoringcapabilities(acoustic,optical,chemical,etc.)shouldbeincorporatedintoall
implanteddevices;whendevicesareimplantedintohumansubjects,theyshoulddeliverthe
maximalscientificbenefitconsistentwithhealthandsafetyoftheparticipant.Asdetailedin
section2ci,implantabledevicesmustgetsmarter,smaller,andmoreenergyefficient;they
requirewirelesscommunicationincompactpackagingabletolastforyearsinthebody.
Engineersandscientistsmustrisetothechallengeofdevelopingthisnextgenerationof
neurotechnologicaldevices.
Bothpenetratingandsurfacesensorsneedtobesubstantiallyimprovedandtestedfortheirfull
capabilities.PrecisioninplacingsensorswithinidentifiedcircuitswillrequireMRIcompatibility,
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whichwillalsoprovideanopportunitytoadvancebasicknowledgethatlinksMRIidentified
circuitswithclinicaloutcomesandcellandcircuitscalefunction.
Potentiallytransformativetechnologiesshouldalsobeentertained.Forexample,theuseof
optogeneticstoolsinhumansisconceivableinthemid tolongterm.Initialsafetystudiesof
adenovirusassociatedvirusvectorsinhumanbrainsareencouraging,suggestingthatviral
deliveryoftherapeuticgenescanbeexploredinthenearfuture,withcarefuland
comprehensivetestingofviraldeliverysystemstoevaluatelongtermsafetyandefficacy.
Aspreviouslymentioned,noninvasivetoolsforfineresolutionstimulationofthehumanbrain
wouldbetransformative,potentiallyreducingoreliminatingtheneedforinvasiveelectrode
implants.Presentnoninvasivestimulationtechniquesarebeingexploredfortherapeutic
effects,includingTMS,anddirectcurrentandslowalternatingcurrentstimulation.These
techniquesareabletoactivate~cmscaleareasofbrainforpotentialneurologicaland
psychiatricapplications.PrefrontallobeTMSisalreadyapprovedbytheFoodandDrug
Administration(FDA)totreatdepression.However,thescale,duration,mechanismofaction,
andthepotencyoftheireffectsneedtobebetterelucidated.AlongtermgoaloftheBRAIN
Initiativeshouldbetofindwaystoobtainhighspatialandtemporalresolutionsignalrecording
andstimulationfromoutsidethehead,perhapsthroughtheuseofminimallyexploredenergy
deliverytechniquessuchasfocusedultrasoundormagneticstimulation.

II.7.Education
Newtools,whethertheycomeintheformofequipment,molecularclones,ordataanalysis
algorithms,shouldbedisseminatedtoawidescientificuserbase,alongwiththeknowledge
requiredtowieldthem.
7a.EducationandTraininginEmergingandInterdisciplinaryMethods
Newtrainingmechanismswillberequiredtosuccessfullydeploythetools,technologies,and
methodsdevelopedundertheBRAINInitiativetotheneurosciencecommunity.Funding
trainingcentersandpersonnelforteachingnewtechniqueswouldrequirerelativelymodest
fundsandspace,butwouldbeagreatbenefitfortheentireneurosciencecommunity.
Optogeneticshasbeensuccessfulinpartbecauseoforganizedminicoursetrainingoffaculty
andstudentsfromaroundtheworldintherequiredsurgeriesandtechniques,bothin
universitysettingsandincoursemodulesatColdSpringHarborandWoodsHole.Minicourses
innewtechnologiesrepresentawaytobringanentirecommunityofusersuptoahighlevelof
understandingandproductivityinashortperiodoftime.Theyleveltheplayingfield
betweenscientistsatlargeinstitutionsandthoseatsmallerinstitutionswhomaynothavethe
sameresources.Theseteachingmechanismshavetheaddedbenefitofcommunicating
experimentalstandardsandpitfalls,whichoftentripupearlyusersofnewtechnologies,but
currentlysufferfromalackofstandardizedspaceandfundingsupportinthetraditional
academicsetting.
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TraininginquantitativeneuroscienceshouldbeanareaofspecialfocusfortheBRAINInitiative.
Thisincludesteachingtheoryandstatisticstobiologists,andexposingphysicists,engineers,and
statisticianstoneuroscience.Mechanismsincludefellowshipsaswellasshortcoursesand
workshopsinneuroinformatics,statistics,andcomputationalneuroscience.
7b.BuildingStrengthinQuantitativeNeuroscience
Attractingnewinvestigatorstoneurosciencefromthequantitativedisciplines(physics,
statistics,computersciences,mathematics,andengineering),andtraininggraduatestudents
andpostdoctoralstudentsinquantitativeneuroscience,shouldbehighprioritygoalsforthe
BRAINInitiative.WhileforwardlookingprogramsliketheSloanSwartzCentersinTheoretical
Neurosciencehaveattractedtraineesfromthequantitativedisciplinesandpromotedtheir
careers,thiscriticalhumanassetremainstoosmallandtootenuouslyestablishedwithin
neuroscience.Toomanyneurosciencedepartmentsremainskepticalofhiringfacultywhose
researchdoesnotfocusprimarilyonexperimentallabwork,andtoomanystatistics,physics,
mathematicsandengineeringdepartmentsarehesitanttohirefacultywhofocusintensivelyon
thenervoussystem.
Thefieldwouldbenefitgreatlyfromincentivesforfacultyrecruitmentatthiscriticalinterface.
Amajorbenefitofattractingnewfacultyfromthequantitativedisciplinestoneuroscience
wouldbetheirteachingofquantitativeconceptsandskillstheory,modeling,statistics,signal
processing,andengineeringinitsmanyformswithemphasisonrealworldapplicationsto
neurosciencedatasets,includingthoseintroducedtothepublicdomainunderBRAIN
sponsoredresearchprojects.Moststudentscurrentlyenterneurosciencegraduateprograms
withlittletonotraininginstatistics,computerscience,ormathematicalmodeling,andmany
receivelittleformalquantitativetrainingduringtheirgraduateeducation.Thismustchange.
Allareasofneuroscience,notjustthoseofparticularemphasisundertheBRAINInitiative,will
becomeincreasinglydependentonquantitativeperspectivesandanalysesinthefuture;
trainingofstudentsinquantitativereasoning,principles,andtechniquesmustincrease
accordingly.
Insummary,progresswouldbedramaticallyacceleratedbytherapiddisseminationofskills
acrossthecommunity.Toenablethebroadestpossibleimpactofnewlydevelopedmethods,
andtheirrigorousapplication,supportshouldbeprovidedfortrainingforexample,summer
coursesandcoursemodulesincomputationalneuroscience,statistics,imaging,
electrophysiology,andoptogeneticsandforeducatingnonneuroscientistsinneuroscience.

II.8.MaximizingtheValueoftheBRAINInitiative:CorePrinciples
Theemphasisinthisreportisonposingquestions,notdictatingsolutions.However,certain
principlesandapproachescanmaximizetheintellectualvalueandlongtermimpactofall
aspectsoftheBRAINInitiative,asenumeratedbelow.

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8a.PursueHumanStudiesandNonHumanModelsInParallel
Ourultimategoalistounderstandthehumanbrain,andasstatedabove,humanneuroscience
shouldbeakeyelementoftheBRAINInitiative.However,bothethicalprinciplesandscientific
feasibilitywillrequiremanymethodsandideastobedevelopedinnonhumananimalmodels,
andonlylaterappliedtohumans.Withafewexceptions,wedonotemphasizeparticular
species,butinsteadencourageadiversityofapproaches.Thehistoryofneuroscienceteaches
usthatmanydifferentmodelsshouldbeenlistedfortheuniqueadvantagesthattheyprovide,
andalsothatcomparativeapproachesareverypowerfulindiscoveringbiologicalprinciples.
WeexpecttheBRAINInitiativetoincludenonhumanprimatessuchasrhesusmacaques,
becausetheyareevolutionarilytheclosestanimalmodelforhumans,andthiswillbereflected
intheirbehavioralandcognitiveabilities,genetics,anatomy,andphysiology.Weexpectthe
mousetobetheinitialmammalianmodelfortheuseofgenetictools,supplementedbytherat,
longappreciatedforitsbehaviorandneurophysiology,wheregenetictoolsarealsoemerging.
Thetransparentzebrafishlarvashouldfacilitateopticalrecordingmethodsinthecontextofa
simplifiedvertebrateneuroanatomy.Invertebrateanimalswithsmallernervoussystemsoffer
rapidexperimentalturnaround,rapidtestingandvalidationofnewtools,andtheeaseof
genetics(forwormsandflies)orofelectrophysiology(formolluscs,crabs,andleeches)
targetedtodefinedneurons;mostneuroscientistshavebeensurprisedtoseehowmany
featuresofthebrainandbehavioraresharedbyvertebratesandinvertebrates.
Finally,thelistofspeciesaboveisnotcomplete.Itisimportanttorealizehowmuchhasbeen
gainedfromstudyingawidervarietyofanimalspecies,recognizingtheirspecialabilitiesand
theperspectivetheyprovideonthebrain.Forexample,theonlyanimalsforwhichateacher
instructsvocallearning,otherthanhumans,aresongbirds.Therichnessofthebehavioral
repertoireinsongbirdshasledtoremarkableinsightsintolearning,motorcontrol,andthe
importanceofsocialcontextinbehavior.Importantinsightsintothebrainhavecomefrom
studiesofmanyothercreatures(barnowls,electricfish,chickens,bats,andmore).Themost
significanttechnologiesdevelopedbytheBRAINInitiativeshouldfacilitateexperimentsinthese
andotherspecializedanimals,broadeningthereachandscopeofquestionsthatcanbeasked
aboutthebrain.
Thefundamentalprincipleisthatexperimentalsystemsshouldbechosenbasedontheirpower
toaddressthespecificquestionathand.AlthoughtheemphasisoftheBRAINInitiativeison
thewholebrain,sometechnologieswillrequirecarefulanalysisinculturesystemsorslices
beforetheycanbeusedinintactanimalsorhumans.TheBRAINInitiativeshouldnotbe
dogmaticwhenfacedwithacompellingscientificargumentforadifferentapproach.
8b.CrossBoundariesinInterdisciplinaryCollaborations
Surveyingthelandscapeofneurotechnologiesrevealssomethataremature,somethatare
emergingandinneedofiterated,disciplinedimprovement,andsomethatrequirere
imagination.ItiscriticalthattheBRAINInitiativeboldlysupportstheverybestideasaddressing
eachneed.Thisreportdescribesthecurrentstateofthefield,buttransformativenewideas
willemergeinthefuturethatarenotontodayshorizon.TheBRAINInitiativemustfindaway
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torecognizesuchnewideasandletthemflourish.Someinnovativeideaswillcertainlyfail,but
thisisnotthetimetoplayitsafe.Ifthemajorityofproposalssucceedinapredictablemanner,
wearenotbeingadventurousenough.
Atthisstage,itissenselesstochooseasinglefundingmechanismorsetofinvestigatorsforthe
BRAINInitiative;theremustbeexploration.Applicationsshouldbesolicitedwidely,withopen
competitionforresources.Someideaswillbeinitiatedbyindividualinvestigatorswhoseea
newwayforward.Otherideaswillrequirelargerteamsofscientists,particularlyinhuman
neurosciencewithitsuniqueethicalandscientificchallenges.
Athemethatemergedclearlyfromtheworkinggroupsworkshopsanddiscussionsisthe
benefittobegainedbynewscientificpartnershipsthatcrosstraditionalareasofexpertise.
Thispointwasmadeinmanyspecificcontexts:
Thephysicistsandengineerswhodevelopopticalhardwareshouldpartnerwiththe
biologistsandchemistswhodevelopnewmolecularsensors.
Thetoolbuilderswhodesignnewmoleculesforsensingorregulatingneuronsshould
partnerwithneuroscientistswhowillrigorouslyexaminetheirvalidityinneuronsand
brains.
Thetheoristswhodevelopmodelsforunderstandingneuronaldynamicsshouldpartner
withexperimentalists,frominitialexperimentaldesigntoexecutiontointerpretation.
Thecliniciansandneuroscientistswhodevelopsophisticatedimagingmethodsin
humansshouldpartnerwithscientistsworkinginanimalmodelswhocanrelateimaging
signalstotheunderlyingcellularmechanismswithgreatprecision.
Supportingcollaborationsacrossdisciplines,withoutstandingscientistswhoareintellectual
equals,couldlightnewfiresintechnologydevelopment.Suchgroupsneednotbeatone
institutiontobeeffectivethequantitativeandphysicalscientistsmightbeatengineering
schools,theirneuroscientistpartnersmightbeatmedicalschools.Smallcollaboratinggroups
oftwoorthreeinvestigatorscouldopennewdoorsinwaysthatnosingleinvestigatoror
conventionaldepartmentwouldimagine;theBRAINInitiativeshouldparticularlystimulatethis
kindofpartnership.
8c.IntegrateSpatialandTemporalScales,andAccelerateAllofNeuroscience
Asmandatedbythechargetoourworkinggroup,thisreportfocusesonnewresearch
opportunitiesatacriticallevelofneuroscienceinvestigationthatofcircuitsandsystems.As
describedindetailinthisreport,however,circuitsandsystemscannotbeunderstoodincisively
withoutreferencetotheirunderlyingcomponentsmolecules,cells,andsynapses.Neither
cancircuitsandsystemsbeunderstoodwithoutreferencetothewholebrain,thebehaviorof
theorganism,andhowbraincircuitsareshapedbytheuniqueexperiencesoftheindividual.
Thebrainmustbeunderstoodasamosaicunityencompassingalloftheselevels.
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TheparticularfocusoftheBRAINInitiativerepresentsonlyoneimportantaspectof
neuroscience,butonethatcanbenefitmanyotherareas.ThefundsdevotedtotheBRAIN
InitiativeareaverysmallfractionoftheNIHstotalinvestmentinneuroscienceand
neurologicaldisorders.Tohavemaximalimpact,thenewknowledgeandtechnologycreated
underBRAINmustfocus,butitsproductsmustaccelerateallothersubdisciplinesof
neurosciencesothattheyalsoadvanceandflourish.
Appropriately,asubstantialfractionoftheNIHsinvestmentinneuroscienceisallocatedto
specifichumanbraindisorders.Thescientificplanlaidoutinthisreporthasbeencomposed
withaspecificeyetowardtheBRAINInitiativeseventualimpactforhumansintranslational
neuroscienceresearch,inmedicalpracticetoalleviatesuffering(sometechnologies,suchas
brainimagingandstimulation,arealreadyinwidespreaduseinmedicine),andinotherareas
suchaseducation.Inthenearerterm,methodsfromtheBRAINInitiativecanbeappliedin
animalmodelsofhumanbraindisorders,seekinginsightaboutfundamentaldisease
mechanismsandaskingaboutthesourcesofvariationinneurologicalfunctionacross
individuals.
Therearemanypointsofintersectionbetweenotherareasofbasicneuroscienceandthe
BRAINInitiativeaswell.Adelineationofneuronalcelltypesandtheirpatternsofgene
expressionshouldbearesourceforcellularandmolecularneuroscience.Thecensusofcell
types,andstudiesoftheirconnectivity,shouldprovidenewtoolstostudycentralquestionsin
developmentalneuroscience.Technologiesforrealtimemeasurementsofneuronalactivity,
neuromodulators,andsynapticconnectionsareideallysuitedforuseincellularandslice
neurophysiology;indeed,manywillbeusedtherebeforetheycanbeappliedinwholeanimals.
8d.EstablishPlatformsforSharingData
Thetraditionalwaytoexchangescientificinformationisthroughpublicationsandbooks,but
wehaveenteredanewageofinformationthatisnotlimitedbythenarrowbandwidthof
journals.Highspeedcomputingandmassivestoragecapabilitieshaveenabledcollectionof
muchlargerdatasetsthanwaspreviouslypossible,andtheInternethasenableddatasharing
onafarwiderscale.However,manydatasetsthatarecurrentlyavailablearediverse,
fragmented,andhighlydynamic,whichistosayunstable.Currentlymostoftherawdatathat
gointopublishedpapersarenotavailableoutsidethelaboratorywheretheywerecollected.
Inevitably,thisleadstoduplicationofeffort,inefficiency,andlostknowledge.
Wellcurated,publicdataplatformswithcommondatastandards,seamlessuseraccessibility,
andcentralmaintenancewouldmakeitpossibletopreserve,compare,andreanalyzevaluable
datasetsthathavebeencollectedatgreatexpense.Thiswouldbeofgreatbenefitto
neuroscience,justastheavailabilityofpublicgenomicandproteinstructuredatabaseshave
transformedgeneticsandbiochemistry.Analysistoolsanduserinterfacesshouldbedeveloped
thatcanberunremotely,suchastheBasicLocalAlignmentSearchTool(BLAST)programfor
sequencealignmentingenomicdatabases.Creatingandmaintainingsuchdataplatforms
wouldentailamajoreffortofthecommunitytodecidewhatdataandmetadatatoinclude,
controlsontheuseofdata,andsupportforusers.Valuablelessonsandbestpracticescanbe
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learnedfromexistingpublicdatasets,whichincludetheAllenBrainAtlas,theMouse
ConnectomeProject,theOpenConnectomeProject,theCRCNSdatasharingproject,ModelDB,
andtheHumanConnectomeProject,aswellasdatasetsgeneratedbythephysics,astronomy,
climatescience,andtechnologycommunities.Afirstunifyingattempt,theNeuroscience
InformationFramework(NIF)sponsoredbyNIH,providesaportaltotrackandcoordinate
multiplesites,butthemyriadgenetic,anatomical,physiological,behavioralandcomputational
datasetsaredifficulttomanagebecauseoftheirheterogeneousnature.TheNIHBigDatato
Knowledge(BD2K)Initiativeoffersopportunitiestoneuroscientiststodevelopnewstandards
andapproaches.
Methodsandsoftwareaswellasdatashouldbeshared.Someneuralsimulatorssuchas
Genesis,NEURONandMCellarewellestablished,opensourceandwelldocumented,butthe
softwareformanymodelsandsimulationsinpublishedpapersareundocumentedor
unavailable.Thedescriptionofamodelinapublishedpaperisofteninsufficienttoreproduce
thesimulations;itisessentialthatsoftwarebemadeavailablesothatallmodelsinpublished
papersarereproducible.Asdatasetsbecomelargerandasnewtypesofdatabecome
available,thereisincreasingneedforpublic,validatedmethodsforanalyzingandpresenting
thesedata.Asanexample,microelectroderecordingsoftenpickupspikesfromseveral
neuronsthatneedtobeseparatedintosingleunitsaprocedureknownasspikesorting.A
plethoraofcustomspikesortingprogramshavebeencreatedbymanyindividuallaboratories.
Buttherearenowidelyacceptedstandardsforrigorousspikesorting,anditcanthereforebe
difficulttocomparedatapreciselyacrosslaboratories.Thecommunitywouldbenefitfrom
commonstandardsforspikesortingandforothercommondataanalysisprocedures.
Newdataplatformswouldalsoencouragechangesinthecultureofneurosciencetopromote
increasingsharingofprimarydataandtools.Weheardfrommanyresearchersaboutthevalue
ofsharingdata,andtheirdesireforstable,easilyinterconvertibledataformatsthatcould
acceleratethefield.DataanddataanalysistoolsthatemergeintheBRAINInitiativeshouldbe
freelysharedtotheextentpossible,nolaterthanthedateoftheirfirstpublicationandinsome
casespriortothatdate.Someareasofneuroscience,suchashumanbrainimaging(theHuman
Connectomeproject;theInternationalNeuroimagingDataSharingInitiative),arealready
sharingdataonalargescaledespitetheenormousdatasetsinvolved.Havingsaidthat,
extendingthismodeltoallfieldsisadifficultproblem,andcannotbesolvedatonestep.Based
onthehistoryofdatasharinginmanyfieldsofbiology,thesolutionwillcomefromthe
engagementofsophisticated,motivatedmembersofthescientificcommunityfromthebottom
up,notfromadirectivefromabove.
Tomeetthesegoals,BRAINInitiativewillrequireinfrastructureforintegratingandsharing
relevantdatasetsanddataanalysismethods.Thereismuchthatcouldbedoneinpartnership
withcomputerscientistsanddatabaseexpertstosetstandardsfordataformatsandbest
practicesformaintaininganddisseminatingheterogeneousdata.Theinfrastructurefor
maintainingcommondatabaseswillrequirededicatedresources,whichmaybeprovidedbythe
NIHBD2KInitiativeortheNIHBlueprintforNeuroscienceResearchtosupporttheBRAIN
Initiative.
53

8e.ValidateandDisseminateTechnology
AprimarygoaloftheBRAINInitiativewillbetoidentifyandsupportnewtechnologieswith
potentialtosubstantiallyacceleratehighqualitybrainresearch.Technologydevelopment
beginswithinnovation,butitisacontinuingprocess.Thefirstgeneticallyencodedfluorescent
calciumindicator,cameleon,waspublishedin1997;thecurrentversions,suchasGCaMP6,
werepublishedin2012afterafocusedandsustainedeffortover~5yearsatatotalcostof~$10
million.Thebasisofthemethodhasnotchanged,butthebreadthofitsutilityandapplications
hasincreasedimmensely.
Thisexampleandothersshowthattechnologiesbecomevaluableaftertheyhavegonethrough
theprocessesofvalidationinbiologicalsystems(withcomparisontothecurrentbest
practices),iteration(serialimprovementsinproperties),application(toavarietyoftest
systems),anddissemination(includingeducationandtraining).Theentireneuroscience
communitywouldbenefitfromsupportforacceleratedtechnologydevelopmentbetweenthe
initialproofofprincipleandthematuresystem;incisivenewresearchcouldbeacceleratedby
decades.
Followingtechnologydevelopment,theBRAINInitiativeshouldbuildaninfrastructurefor
sharingrelevanttoolsofallkinds,whetherbiological,chemical,orphysical.Molecularbiology
toolsandvirusesareeasilydisseminated,althoughthereissomeassociatedcostthatmustbe
supported.Othertoolsindiscussionfromchemistry,nanoscience,andphysicsarenotsoeasily
sentinthemail.IftheBRAINInitiativedevelopsnextgenerationelectrodes,nanotechnologies,
orchemicalprobes,itshouldensurethattheycanbesynthesized,fabricated,orreadily
purchasedbyresearchers,asappropriate.IftheBRAINInitiativefundsdevelopmentofanext
generationmicroscope,itshouldensurethatprivateorpubliclysupportedmechanismsmakeit
availabletoavarietyofusers,notjusttheinventors.Apathwaytodisseminationshouldbe
expectedforBRAINderivedtools,whetherthatiscommercialization,corefacilities,or
somethingelse.ComputationalandstatisticaltoolsdevelopedundertheBRAINInitiative
shouldalsobesupportedandbroadlyavailable.Extremelycomplextechnologieslikenext
generationhighfieldMRIinstrumentsmightneedtobecentralized,likethecentralizedXray
beamlinesusedbystructuralbiologists.Corefacilitiescouldbeestablishedwithstateofthe
arttechnology,perhapsatafewuniversitiesorresearchinstitutes,butallowinguseby
researchersfromacrossthecountry.Suchcorefacilitiescouldbeattractiveenoughtothehost
institutionsthattheywouldcoinvestinequipmentandsupportpersonnel.
Insummary,acoreprincipleoftheBRAINInitiativeisthatnewtechnologiesandreagents
shouldbemadeavailableacrossthecommunityattheearliestpossibletime.Thiswillrequirea
thoughtfuldevelopmentofdisseminationpoliciesbythescientificcommunity,aswellas
specializedsupportmechanisms,privatepublicpartnerships,andtrainingprograms.
8f.ConsiderEthicalImplicationsofNeuroscienceResearch
TheworkinggroupispleasedthatthePresidenthaschargedhisBioethicsCommissionwith
exploringtheethicalissuesassociatedwiththeconductofneuroscienceresearch,andalsothe
54

ethicalissuessurroundingtheapplicationofneuroscienceresearchfindingsinmedicineand
othersettings.ManyethicalandpolicyissuesraisedbytheBRAINInitiativearenotuniqueto
neuroscienceresearch,andthuswecanlearnfromongoingexperiencesinotherfields.For
example,theNIHBRAINWorkingGrouphasendorseddatasharing,sinceadvancesinscience
areoftencatalyzedbycollaborationsandopenaccesstodata.However,ourexperienceswith
geneticdatahaveshownthatprivacyconcernsmustbemanagedcarefullytoprotecthuman
researchparticipants.Otherissuessuchasdefiningwhatconstitutesenhancementandhow
weobtainconsentfrompotentiallyvulnerablepopulationshavebeendebatedwidelyacross
biomedicalresearch,andwillcontinueundertheBRAINInitiative.
Althoughbrainresearchentailsethicalissuesthatarecommontootherareasofbiomedical
science,itentailsspecialethicalconsiderationsaswell.Becausethebraingivesriseto
consciousness,ourinnermostthoughtsandourmostbasichumanneeds,mechanisticstudies
ofthebrainhavealreadyresultedinnewsocialandethicalquestions.Canresearchonbrain
developmentbeusedtoenhancecognitivedevelopmentinourschools?Underwhat
circumstancesshouldmechanisticunderstandingofaddictionandotherneuropsychiatric
disordersbeusedtojudgeaccountabilityinourlegalsystem?Cancivillitigationinvolving
damagesforpainandsufferingbeinformedbyobjectivemeasurementsofcentralpainstates
inthebrain?Canstudiesofdecisionmakingbelegitimatelyusedtotailoradvertising
campaignsanddeterminewhichproductsaremoreattractivetospecificconsumerbases?
Brainresearchmustproceedwithsensitivityandwisdom.Theworkinggrouplooksforwardto
thedeliberationsoftheBioethicsCommission,andtointeractingwiththegrouptoestablisha
scientificallyrigorousplanfortheBRAINInitiativethatisgroundedinsoundethicalpolicies.
Asisclearfromthescientificissuesreviewedinthisreport,developingadeepunderstandingof
thebrainisonlypossiblethroughresearchonanimalsandinformed,volunteerhumansubjects.
Withoutquestion,researchundertheBRAINInitiativeshouldadheretothehighestethical
standardsforresearchwithhumansubjectsandwithnonhumananimals,withintheregulatory
frameworkoftheUnitedStatesandhostresearchinstitutions.
8g.MaintainAccountabilitytoNIH,theTaxpayer,andtheBasic,Translational,andClinical
NeuroscienceCommunities
TheBRAINInitiativehasthepotentialtoadvancehumanknowledge,tocreateafoundationof
knowledgeandmethodsappropriateforprevention,diagnosis,monitoring,andtreatmentof
humanbraindisorders,andtostimulatenewtechnologiesthatblossominindustry.Afocused,
sustainedinvestmentintheBRAINInitiativehasthepowertochangeourfuture.Nonetheless,
theNIHanditsleadershipmustchooseamongmanyopportunitiesinthelargercontextof
scientificandpublichealthneeds.Likeotherinvestmentsmadebygovernmentagencies,the
BRAINInitiativeshouldbeevaluatedregularlybyscientists,patients,andthegeneralpublicto
askwhethertheongoingresearchplanrepresentsthemosteffectiveuseofNIHfunds.
EvaluationofresearchundertheBRAINInitiativeposesspecialchallengesduetothe
interdisciplinarynatureoftheresearchandtheneedtoaligneffortswiththeexistingNIH
neuroscienceresearchportfolio,suchastheBlueprintforNeuroscienceResearch,a
55

collaborativeneuroscienceeffortthatspans15ofthe27NIHInstitutesandCenters.To
exerciseappropriateoversight,theevaluationmechanismshouldbesimilarlybroadand
interdisciplinary.

II.9.FurtherReading
TheresourceslistedbelowintroducesomeoftheneurotechnologiesandBRAINInitiative
relatedresourcesthataredescribedinthereport.Mostpapersarereviews,althoughafew
recentmethodspapersareincluded.Thisisnotacomprehensivecitationlist.

TheBRAINInitiative
Obama,BHwww.whitehouse.gov/thepressoffice/2013/04/02/remarkspresidentbrain
initiativeandamericaninnovation.
NIHBRAINInitiative,http://www.nih.gov/science/brain/index.htm
InselTR,LandisSC,CollinsFS(2013)Researchpriorities.TheNIHBRAINinitiative.Science
340(6133):687688.

MappingtheStructureandComponentsofCircuits
CellType
BernardA,SorensenSA,LeinES(2009)Shiftingtheparadigm:newapproachesfor
characterizingandclassifyingneurons.CurrOpinNeurobiol19(5):530536.
LeinESetal(2007)Genomewideatlasofgeneexpressionintheadultmousebrain.Nat
445(7124):168176.

ExperimentalAccesstoCellTypes
GajT,GersbachCA,BarbasCF3rd.(2013)ZFN,TALEN,andCRISPR/Casbasedmethodsfor
genomeengineering.TrendsBiotechnol.201331(7):397405.
JenettAetal(2012)AGAL4driverlineresourceforDrosophilaneurobiology.CellRep2:991
1001.
HuangZJ,ZengH(2013).Geneticapproachestoneuralcircuitsinthemouse.AnnRevNeurosci
36:183215.

StructuralMaps
DenkW,BriggmanKL,HelmstaedterM(2012)Structuralneurobiology:missinglinktoa
mechanisticunderstandingofneuralcomputation.NatRevNeurosci13(5):3518.
GingerM,HaberlM,Conzelmann,KK,Schwarz,MK,FrickA(2013)Revealingthesecretsof
neuronalcircuitswithrecombinantrabiesvirustechnology.FrontiersinNeuralCircuits
7(2):115.
KleinfeldDetal(2011)Largescaleautomatedhistologyinthepursuitofconnectomes.J
Neurosci31(45):1612516138.
OstenP,MargrieTW(2013)Mappingbraincircuitrywithalightmicroscope.NatMethods
10:515523.
HumanConnectomeProject,http://www.humanconnectome.org/
56

MouseConnectomeProject,http://www.mouseconnectome.org/
ClarityResources,http://clarityresourcecenter.org

NeuronalDynamics:RecordingNeuronalActivityAcrossTimeandSpace
RecordingfromCompleteCircuits
AhrensMB,OrgerMB,RobsonDN,LiJM,KellerPJ(2013)Wholebrainfunctionalimagingat
cellularresolutionusinglightsheetmicroscopy.NatMethods10(5):413420.
AlivisatosAP,ChunM,ChurchGM,GreenspanRJ,RoukesML,YusteR(2012)Thebrainactivity
mapprojectandthechallengeoffunctionalconnectomics.Neuron74:970974.

AdvancingRecordingTechnology(Electrophysiology)
BuzkiG(2004)Largescalerecordingofneuronalensembles.NatNeurosci7(5):446451.
SzutsTAetal(2011)Awirelessmultichannelneuralamplifierforfreelymovinganimals.Nat
Neurosci14(2):263270.

AdvancingRecordingTechnology(Opticalsensors)
LoogerLL,GriesbeckO(2012)Geneticallyencodedneuralactivityindicators.CurrOpin
Neurobiol22(1):1823.
PeterkaDS,TakahashiH,YusteR(2011)Imagingvoltageinneurons.Neuron69:921.

IntegratedOpticalApproaches:NeuroscienceandInstrumentation
WiltBA,BurnsLD,WeiHoET,GhoshKK,MukamelEA,SchnitzerMJ(2009)Advancesinlight
microscopyforneuroscience.AnnuRevNeurosci.32:435506.

NanotechnologyandUnanticipatedInnovations
AlivisatosAPetal(2013)Nanotoolsforneuroscienceandbrainactivitymapping.ACSNano
7(3):18501866.
SpiraME,HaiA(2013)Multiarraytechnologiesforneuroscienceandcardiology.Nat
Nanotechnol.20138(2):8394

ManipulatingCircuitActivity
FennoL,YizharO,DeisserothK(2011)Thedevelopmentandapplicationofoptogenetics.Annu
RevNeurosci34:389412.
FarrellMS,RothBL(2013)Pharmacosynthetics:Reimaginingthepharmacogeneticapproach.
BrainRes1511:620.
PackerAM,RoskaB,HausserM(2013)Targetingneuronsandphotonsforoptogenetics.Nat
Neurosci16(7):805815.

TheImportanceofBehavior
DombeckDA,ReiserMB(2012)Realneuroscienceinvirtualworlds.CurrOpinNeurobiol
22(1):310.
KabraM,RobieAA,RiveraAlbaM,BransonS,BransonK(2013)JAABA:interactivemachine
learningforautomaticannotationofanimalbehavior.NatMethods10(1):6467.

57

Theory,Modeling,andStatistics
GanguliS,SompolinskyH(2012)Compressedsensing,sparsity,anddimensionalityinneuronal
informationprocessinganddataanalysis.AnnuRevNeurosci35:485508.
MarderE,TaylorAL(2011)Multiplemodelstocapturethevariabilityinbiologicalneuronsand
networks.NatNeurosci14:133138.
ShenoyKV,SahaniM,ChurchlandMM(2013)Corticalcontrolofarmmovements:adynamical
systemsperspective.AnnuRevNeurosci36:337359.
WangXJ(2013)Theprefrontalcortexasaquintessentialcognitivetypeneuralcircuit:
workingmemoryanddecisionmaking.In:Principlesoffrontallobefunction,Secondedition
(StussDT,KnightRT,eds),pp.226248.NewYork:OxfordUP.
KassRE,VenturaV,BrownEN(2009)Statisticalissuesintheanalysisofneuronaldata.J
Neurophys94(1):825.

HumanNeuroscienceandNeurotechnology
DonoghueJP(2008)Bridgingthebraintotheworld:aperspectiveonneuralinterfacesystems.
Neuron60(3):511521.
FoxMD,HalkoMA,EldaiefMC,PascualLeoneA(2012)Measuringandmanipulatingbrain
connectivitywithrestingstatefunctionalconnectivitymagneticresonanceimaging(fcMRI)
andtranscranialmagneticstimulating(TMS).Neuroimage62:22322243.
HoltzheimerPE,MaybergHS(2011).Deepbrainstimulationforpsychiatricdisorders.AnnuRev
Neurosci34:289307.
LozanoAM,LipsmanN(2013)Probingandregulatingdysfunctionalcircuitsusingdeepbrain
stimulation.Neuron77(3):406424.
McNabJAetal(2013)TheHumanConnectomeProjectandbeyond:Initialapplicationsof300
mT/mgradients.Neuroimage80:234245.
SmithSMetal(2013)RestingstatefMRIintheHumanConnectomeProject.Neuroimage
80:144168.
SotiropoulosSNetal(2013)AdvancesindiffusionMRIacquisitionandprocessingintheHuman
ConnectomeProject.Neuroimage80:125143.

Principles
DataPlatforms,DataSharing,andBigData
AkilH,MartoneME,VanEssenDC(2011)Challengesandopportunitiesinminingneuroscience
data.Science331(6018):708712.
BermanF,CerfV(2013)Sciencepriorities.Whowillpayforpublicaccesstoresearchdata?
Science341(6146):616617.
NgLetal(2009)Ananatomicgeneexpressionatlasoftheadultmousebrain.NatNeurosci
12(3):356362.

EthicalConsiderations
PresidentialCommissionfortheStudyofBioethicalIssuesBRAINInitiative,
http://bioethics.gov/node/2629

58

SECTIONIII

IMPLEMENTATION:GOALS,DELIVERABLES,TIMETABLES,ANDCOSTS
Initsfinalreport,theworkinggroupwaschargedwithdevelopingshort,medium,andlong
termgoalsfortheNIHBRAINInitiative,asetoftimelines,milestones,andcostestimates,and
proposalsforscientificmechanisms.Thisprojectwasthepredominantfocusofworkinggroup
activitiesfromSeptember2013toMay2014,andisthesubjectofthisSection.
ThereleaseoftheinterimreportinSeptember2013wasfollowedbyaperiodofextended
discussionbetweentheworkinggroupandthebroaderscientificcommunity.Anopentown
hallwasheldattheSocietyforNeuroscienceMeeting.Thepast,present,andfutureleadership
oftheSocietyforNeurosciencewereconsulted(seeAppendixB).Inaddition,thepresidentsof
clinicalsocietiesinneurology,psychiatry,neurosurgery,anesthesiology,neuroradiologyand
neuropsychologywereconsultedinpersonaldiscussionsandconferencecalls,seekingtheir
adviceforthebestapproachestotheunsolvedproblemsintheirfields.Theworkinggroup
heldameetingwiththeleadershipofthefoundingBRAINInitiativepartnersfromNSF,the
DefenseAdvancedResearchProjectsAgency(DARPA),HHMIJaneliaFarmResearchCampus,
theAllenInstituteforBrainScience,andtheFDA.Opensolicitationofadvicecontinued
throughtheNIHBRAINInitiativewebsite.
TheworkinggroupbelievesthatthevisionoftheBRAINInitiativeexpressedbyPresident
ObamaandNIHDirectorFrancisCollinswillrequireasustainedten totwelveyearresearch
program,describedbelow.Thegoalsandprinciplesoftheinterimreportareembracedbythe
finalreport,butinthissectionthesegoalsareregroupedtomoreeffectivelyprojectthem
forwardoverthislongertimeframe.Forthesakeofthisdocument,atenyearprogramis
describedbeginninginFY16,toallowadequateplanningbeyondFY14(alreadyunderway)and
FY15(whichbeginsinJuly2014).
ThefirstfiveyearsoftheBRAINInitiative(FY1620)areenvisionedprimarilytosupport
technologydevelopmentandvalidation,withthecreationofnewmethodsfollowedbytheir
maturationandintegrationintheserviceofimportantscientificquestions.Technology
developmentwillcontinuethroughouttheBRAINInitiative,perhapspeakingaroundyear5
(FY20).Explorationofscientificquestionscanandwilloccurwhilenewtechnologiesarebeing
validated,butthemostseriousscientificadvanceswilltakeplaceaftertechnologieshave
proveneffective,whentheycanbepursuedinavigorousfashion.Thusbeginningmoreslowly,
butpeakinginyears610(FY2125),collaborativegroupsfundedbytheBRAINInitiativewill
increasinglyusethesetechnologiestoanswerfundamentalquestionsaboutthebrain.
BelowweconsidersevenmajorscientificgoalsoftheBRAINInitiative(SectionsIII.17)aswell
asinfrastructuretosupportitscoreprinciples(SectionIII.8).InSectionIII.9weestimatethe
overallcostoftheBRAINInitiative.Withineachofthesevenmajorgoalsdescribedbelow,
short andlongtermmilestonesaresuggestedformeasuringtheoverallprogressofa
particularBRAINproject.Theproposedmilestonesareveryambitious,andwedonot
59

anticipatethatallmilestoneswillbeachievedwithinthespecifiedtimeperiods.Indeed,future
scientificdiscoveriesandtechnologicaldevelopmentsarelikelytorevealhigherpriority
opportunitiesforrapidprogress,orshowthatsomeofthecurrentmilestonesareless
importantforreasonsthatcannotbeforeseenatpresent.ThefutureleadershipoftheBRAIN
Initiativemustjudgetheprogressandcontinuedrelevanceofanyparticularprojectbasedon
overallscientificmomentumandachievementinthecontextofarapidlychangingfield.We
concludewithexamplesoffundamentalquestionsthatshouldbeaddressedbytheBRAIN
Initiative(SectionIII.10).
RelationshiptoPrivateEffortsandInternationalProjects
TheannouncementoftheBRAINInitiativebyPresidentObamaproposedpartnershipsbetween
privateandpublicorganizationscommittedtobrainresearch.Communicationbetweenthe
NIH,NSF,DARPA,andtheFDA,communicationbetweenprivateandpublicpartnersintheUS,
andinternationalcommunicationarehighlydesirableatallstagesoftheBRAINInitiative.The
brainistoocomplextobesolvedbyindividualorganizations.
Duringtheplanningprocess,theworkinggroupconsultedallpartnersintheoriginalWhite
Houseannouncementandconsideredtheirresearchagendascarefully.Forexample,effortsto
characterizecelltypesandconnectivityinspecificorganismsandbrainregionsareongoingat
theAllenInstituteforBrainScience13andHHMIsJaneliaFarmResearchCampus4,5.Inasmuch
astheresultsoftheseprivateeffortsaremadeavailabletothebroadercommunity,theBRAIN
Initiativewillbenefitfromthem.However,theHHMIandAllenInstituteprojectsarefocused
onspecificanimalmodelsandbrainstructures,andwillnotsolveallproblemsofcelltypeand
connectivityevenifdataareshared;thebroadscopeoftheBRAINInitiativerequiresadditional
commitmenttotheseareas,especiallyinthehumanbrain.
Atapracticallevel,theprivateeffortshavegeneratedbrainrelatedtechnology,reagents,
organizationalmodels,publiclyaccessibledatabasesandsearchalgorithms.NIHprojectscan
leveragetheseeffortsorpartnerwiththesegroupstoincreasetheircosteffectiveness.
In2013,theEuropeanUnionannouncedtheHumanBrainProject,a1billionprojectwithan
emphasisoninformationcomputingtechnologyinfrastructureforneuroscience
(https://www.humanbrainproject.eu/).Theworkinggrouphasbeenincontactwith
participantsintheHumanBrainProject,andmeetingsbetweenrepresentativesoftheUnited
StatesBRAINInitiativeandtheHumanBrainProjecttodiscusssharedinterestssuchasdata
platformsareplanned.WeexpectusefulinteractionsbetweentheBRAINInitiativeandthe
HumanBrainProjecttodevelopasopportunitiesarise.

III.1.DISCOVERINGDIVERSITY
1a.ScientificGoal:Identifyandprovideexperimentalaccesstothedifferentbraincelltypes
todeterminetheirrolesinhealthanddisease
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1b.OverallObjective
Themammalianbraincontains~108(mouse) 1011(human)neurons.Theseneuronsarenot
homogeneous,butconsistofdiversesubpopulationswithgenetically,anatomically,
physiologically,andconnectionallydistinctproperties.Definingthesecelltypesandtheir
functionsindifferentbrainregions,andprovidingmethodsforexperimentalaccesstothemin
avarietyofanimalsandinhumansisessentialtogeneratingacomprehensiveunderstandingof
neuralcircuitfunction.
1c.Deliverables
1. Acensusofneuronalandglialcelltypesinkeybrainregionsusingmultipleanalysis
modalities(thepartslist),andanintellectualframeworkforcelltypeclassification.
Themodalitiesofinterestinclude(butarenotlimitedto)transcriptional/protein
profiling,electrophysiologicalrecording,cellularanatomy,andconnectivity.This
informationisfundamentalbecauseitwillprovideknowledgethatisessentialtoadeep
understandingofneuralcodingandcomputation.
2. Experimentalaccesstodefinedneuronalandglialsubpopulations,andtoolsforcell
typespecificconnectivitymapping,recording,andmodulation.Byaccess,wemean
waystotargetreporters,indicators,andeffectorstoadesiredneuronalorglial
subpopulation.Intheshort tointermediateterm,thiswilllikelyinvolvegenetic
methods.Thisenablingtechnologywillallowanalysisofmesoscaleconnectivity,
functional(causal)manipulations,andelectrophysiologicaloropticalrecordingof
activitytobelinkedtoeachotheratthelevelofadefinedcelltype.Inhumans,
experimentalaccesswillprovidearoutetonoveltargetedtherapiesforneurological
andpsychiatricdisorders.
Amongthescientificquestionstobeaddressedbythisgoal:
Howmanycelltypesexistinthebrain,toafirstapproximation?
Isthereabasicorganizationallogictocelltypediversitythroughoutthebrain?
Dowelldefinedcelltypesshapeneuralcircuitfunctiontoagreaterextentinsomebrain
regionsthaninothers?
Whatlevelofgranularityofcelltypedefinitionisrequiredforunderstandingthefunction
ofagivenneuralcircuit?
Canwetargetspecifichumancelltypestodevelopnewtherapiesforneurologicaland
psychiatricdisorders?
1d.RationaleandPrinciples
SeealsoSectionII.1Aofthisreport.
61

Thereisuniversalagreementthatimportantphenotypicdistinctionsexistamongdifferent
classesofneurons68.Glia,whichoutnumberneuronsandplaymultiplerolesinbrainfunction
9
,arealsoheterogeneous10,11.Aconsensusdefinitionandtaxonomyofbraincelltypeshasnot
yetbeenachieved.Nevertheless,objectiveclassifierscanbebuiltbasedonaprincipled
approachcombiningelectrophysiological,geneexpression,andanatomicalandconnectional
data8,12.Itislikelythatthebestworkingdefinitionsofnaturalcelltypeswillemergefrom
empiricalclassificationsbasedonfunctionallyrelevantphenotypicdimensions7.Working
definitionswillbeupdatedcontinuouslyasmoredataarecollectedanddeeperunderstanding
emerges.
Animportantcontributiontotheconceptualdefinitionofcelltypewillcomefromiterative
interactionswiththeoryandmodeling(SectionIII.5).Forexample,theoreticalconsiderations
mayspecifythelevelofgranularityofcelltypeidentificationthatisnecessarytounderstand
thecomputationsinaparticularbrainregion,providinganinitialguideforexperimental
analysis.Inturnthelevelofcellularheterogeneityobservedinagivenbrainregioncan
constrainmodelsandgeneratenewpredictionsconcerningcircuitfunctionordisease
intervention.
ChallengesfortheBRAINInitiative:
Increasingthethroughput,scale,anddimensionalityofcellularphenotyping.Theability
tosystematicallycharacterizedifferentcelltypesacrossthebrain,usingmultiple
phenotypiccriteria,islimitedbythethroughput,multiplexingcapacity,and
compatibilityofexistingexperimentalmethods.Newmethods,suchasmultiplexedin
situhybridization13,arraytomographyforantibodystaining14,singlecellmultiplexed
PCR,andsinglecellRNAsequencing15,arebeingdevelopedtoaddresssomeofthese
limitations,andimprovementsinthesemethodswilloccuroverthenextseveralyears.
Thereis,nonetheless,aneedto1)expandtherepertoireofreagentsforcelltype
characterization,particularlyintheantibodydomain(emphasizingcrossspecies
reactivitytohumans);2)increasethethroughputandmultiplexingcapabilityofcellular
phenotypingmethods;3)improvethecompatibilityofmethodstoquantitatively
characterizecelltypediversityalongmultiplephenotypicdimensions,atthesinglecell
level.
Measuringdynamicsofphenotypicmarkerexpression.Anotherchallengeisour
currentlyinabilitytomeasurethestabilityofmolecularpropertiesacrosstimescalesor
conditions:standardmethodsforanalyzinggeneorproteinexpressioninvivocan
typicallyonlybeperformedatasingletimepoint.Somemarkersorphenotypic
propertiesmaybestablyexpressedinagivencellpopulationacrossdifferentconditions
(canonicalmarkers),whileothersmaybedynamicallyexpressed16;itiscurrently
difficulttodistinguishbetweenthetwo.Dynamicalmethodsusinggeneticallyencoded
fluorescentreportersexist,butarelimitedtooneorafewgenesatatime17.Therefore,
thereisaneedtodevelopnewtechnologytomeasurethetemporaldynamics,or
conditionalproperties,ofmanyphenotypicmarkersatasinglecelllevelinvivo.
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 Adequatespecificityofexperimentalaccess.Thecurrentapproachtoexperimental
accessistotargetthedesiredcellpopulationbasedontheexpressionofonegene,or
theintersectingexpressionoftwoormoregenes,typicallyusingrecombinasessuchas
CreorFlp1821.Anatomicalselectivity,inmammals,isprovidedbystereotacticinjection
ofviruses,oftencombininggeneexpressionspecificitywithprojectionstoorfroman
anatomicaltarget22.Anotherapproachistobeginwithamolecularlydefinedcell
population,andthenusetranscriptionalprofiling2325,activityoranatomicalcriteriato
askhowmanysubtypesofcellsitrepresents1,8,26.Wedonotyetknowthenumberand
complexityofphenotypicdimensionsthatwillberequiredtodistinguishdifferentcell
typesastheyemergefromthecensus.Themoredimensionsrequired,thegreaterthe
complexityofcombinatorialmethodsneededforspecificexperimentalaccess.Thiswill
requiretransformativenewtechnologiestofacilitateintersectionalapproachesin
whichmultipleconditionsaremetsimultaneously.Oneexamplewouldbeamethodto
trapcelltypesbasedontheiractivityunderparticularconditions;suchmethods
alreadyexist27,28,butitwouldbeidealtorestricttheirtimeresolutiontomillisecondsor
secondsratherthanhours,andtocombinesuchactivitytrappingwithanatomicaland
geneexpressionselectivity.
Achallengeforhumanapplicationsisthatgermlinemodificationofthegenomeis
unacceptableforethicalandpracticalreasons.Existingmethodsforaccessingneurons
basedontheiranatomicallocationsandprojections29invariablyrecruitavarietyofcell
types.Therefore,transformativenewtechnologieswillberequiredtosolvethis
problemforhumanuse.Anexamplewouldbethedevelopmentofvirallybased
methodsforgenomeeditinginpostmitoticneuronsinthecontextoftherapeutictrials
30
.Anotherexamplewouldbedeliveryofgenesorpharmaceuticalagentstocellsbased
oncombinationsofsurfacemarkerproteins,perhapsbesttargetedbyasuiteof
antibodies,eitherasdirectconjugatesorasameansofpseudotypingenveloped
recombinantviralvectors31.
1e.Implementation
Werecommendthattheinitialstagesofthisprojectbefocusedonobtaininganinventorywith
molecular,anatomical,andelectrophysiologicaldescriptionsofallofthecelltypesinseveral
selectedbrainregionsoforganismssuchasC.elegans,Drosophila,zebrafish,mouse,andnon
humanprimate,aswellasthedevelopmentoftoolsforgeneticaccesstoallofthesecells.
Theseorganismsandbrainregionswouldbeprioritizedbasedontheirinteresttolarge
communitiesofneuroscienceresearchersandtheirrelevancetohumandisease.Thisstrategy
wouldidentifychallengesandopportunitiesforiterativetacticalimprovementsintechnology
andprocess.Amongmultiplepossiblestartingpoints,wesuggestthefollowinglistof
importantareasinthemouseasanexample.Thissetisintendedtocomplementongoing
effortsinprivatelyfundedprojects15.
Examplebrainregionsforinitialanalysisinthemouse:

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 Retina.Theretinaistheregioninwhichthemostprogresshasbeenmadeinthe
characterizationofdifferentcelltypes,andinthegenerationofreagentstoprovide
accesstothosecelltypes.Itthereforehasthegreatestchanceofbeingcompleted
withina35yearperiod,andcouldserveasaflagshipprojectfortheBRAINInitiative.It
isrelevanttothefieldsofvision,generalsensoryandsignalprocessing,andtoclinical
issuesincludingneurodegenerativediseasesandvisiondisorders.
Spinalcord.Thisspinalcordisanotherareainwhichagreatdealofprogresshasbeen
madeintheidentificationofdifferentcelltypes.Itisimportantforunderstandingthe
controloflocomotionandthefunctionofcentralpatterngenerators,andtohuman
neurologicaldisorderssuchasparalysis,traumaticspinalinjury,chronicpain,andmotor
neurondegenerativediseasessuchasamyotrophiclateralsclerosis(ALS).
Hippocampus.Thisareaisanintensefocusofbasicneuroscienceresearchintolearning,
memory,andspatialnavigation,andisimportanttohumanmemorydisorderssuchas
Alzheimersdisease.
Striatum.Thisareaisafocusofneuroscienceresearchinmovementcontrol,reward,
motivation,anddecisionmaking.Itishighlyrelevanttoaddictionandtomovement
disorderssuchasParkinsonsdiseaseandHuntingtonsdisease.
Amygdala/Hypothalamus.Theseinterconnectedregionsareafocusofbasic
neuroscienceresearchintofear,anxiety,feeding,andsocialbehaviors.Theyareof
centralconcernforpsychiatricdisorderssuchasposttraumaticstressdisorder(PTSD)
andanxietydisorders,andforobesityandeatingdisorders.
Prefrontalcortex.Thecerebralcortexishighlydevelopedinhumanscomparedtoother
animals,andtheprefrontalcortexinparticularisassociatedwithhumandecision
making,cognition,andemotionalbehaviors.Itsfunctionsaredisruptedin
schizophreniaanddementia.
Atlaterstages,astechnologyevolvestoincreasethethroughputofdescriptiveanalysis,the
censusofcelltypesshouldbeexpandedtoadditionalbrainregionsandspecies,including
humans.
1f.Mechanisms
Themajorgoalsofthisprojectmaybeachievedusingavarietyoforganizationaloroperational
modelsrangingfromindependentlaboratories,todistributedcollaborativeconsortia,to
regionallaboratoriesorinstitutes.Inanymodel,itisessentialthatdatabecollectedina
standardizedmanner,sothattheresultsobtainedfromthedifferentbrainregionsaredirectly
comparableandcanbeeffectivelyintegratedintoacommondatabase32.Thisischallenging
becauseofthenumberofdifferentexperimentalmodalitiesrequiredandthelackof
standardizationinmanyofthem(especiallyelectrophysiology).Thisis,therefore,a
considerablymorecomplexundertakingthantheHumanGenomeProject,wheredifferent
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laboratoriesallusedthesame,standardizedDNAsequencingtechnology.Thebestchanceof
addressingthisconcernistoemphasizeearlysharingofstandardized,highqualitydataacross
differentlaboratories.
1g.TimelinesandMilestones
Thefollowingspecificadvancescanbeanticipatedfromthisproject:
Fundamentalknowledge censusofcelltypes,logicofcelltypediversificationin
differentbrainregions.
Openaccessdatabaseofintegratedinformationwithcomputationalsearchtools.
Reagentsforcelltypeaccess,includingbothnewapproachesandimprovedandscaled
upversionsofexistingmethods(e.g.viralvectors,Crelines).
Standardizedmethodsforcelltypecharacterization(transcriptionalprofiling,
proteomics,electrophysiology,anatomy,connectionalmapping,etc.).
Newmethodstoapproachthecelltypesprobleminnontraditionalorganisms,
includinghumansandotherprimates,andtoreducecostofexperimentsinnonhuman
animals.
Shorttermgoals(15years)
Arriveatconsensusforphenotypiccriteriausedtodefinecelltypes.
Completeacelltypecensusintworegions(perhapsretina,spinalcord),andgeneratea
preliminarycelltypecensusinatleastfourotherregionsofinterest.
Increasethroughputandscaleofdescriptivecelltypecensusby10foldover5years.
Initiatecelltypecensusforotherorganisms,includingnonhumanprimatesand
humans.
Produceantibodyreagentsforcelltypeidentification,emphasizingcrossspecies
reactivity(rodents,nonhumanprimates,humans)andimmunohistochemical
applications.Cocktailsofmonoclonals,andimmunereagentsdirectedtocellsurface
antigens,areofparticularinterest.
Expandthesetofreagentsforgeneticaccesstocelltypesininitialbrainregionsof
interest,usingexistingCre,Flp,Drerecombinasetechnologyandemerginggenome
editingtechnologytofacilitateintersectionalstrategies.
Createorcontributetoapubliclyaccessibledatabaseofcelltypes;developassociated
softwareforsearching/computingonthedatabase.
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 Developnewtechnologiesforgermlinemodificationindependentapproachestocell
typeaccessacrossspecies,includingnonhumanprimatesandhumans.
Developnewtechnologiesforimprovedmultiplexing,compatibility,anddynamicsof
cellularphenotyping.
Longtermgoals(610years)
Generatefirstdraftcelltypecensusforallmajorbrainregionsinmouse.
Providespecificgeneticaccesstoatleast200differentcelltypesinthemousebrain,
andcomprehensiveaccesswithinspecificregionsofinterest.
Produceacelltypecensusforselectedbrainregionsinnonhumanprimatesand
humans.
Achievecelltypespecifictargetingofopticalimagingandoptogeneticperturbationsin
multiplemammalianspecies,includingnonhumanprimates.
Achieveproofofprinciplecelltypespecifictargetingoftherapeuticmanipulationsin
humans.

III.2.MAPSATMULTIPLESCALES
2a.ScientificGoal:Generatecircuitdiagramsthatvaryinresolutionfromsynapsestothe
wholebrain
2b.OverallObjective
Anatomicalconnectivityisessentialforunderstandingandpredictingthefunctionalsignalsthat
underliecognitionandbehavior.Inaddition,anatomicalcircuitmapswillprovidenewinsight
intohowhealthybraincircuitsdevelopinearlylifeandhowcircuitdevelopmentandfunction
goawryinpsychiatricandneurologicaldisorders.
2c.Deliverables
1. Improvementsintheresolutionandaccuracyofimagingmethodstoenablecomplete
andaccuratemappingofneuralcircuitstructureinhumanandanimalbrains.
2. Integrationofstructuraldataacrossscales(fromwholebraintoultrastructural)and
withothermodalities(physiology,molecularbiology,biochemistry).
3. Discoveryofanatomicaldifferencesbetweenhealthyanddiseasedbrains.
Amongthescientificquestionstobeaddressedbythisgoal:
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 Aretherecircuitsuniquetothehumanbrainthatcouldhelpaccountforitsamazing
capabilities,suchaslanguage?
Canmacroconnectomicconnectivitypatternsserveasbiomarkersforbraindisorders?
Howwidelycantheybeusedfordifferentialdiagnosisofbraindisorders,monitoring
diseaseprogression,andpredictingormonitoringresponsestotherapy?
Dosomebraindisordersresultfromanatomical"connectopathies"withstereotyped
defectsinneuralcircuitry?
Whatchangesincircuitsaccompany,andperhapscause,agerelatedcognitivedecline?
Canwepredictcircuitfunctionfromwiringdiagramsofconnectivity?
Howdifferentareconnectivitypatternsingeneticallyidenticalorganismsinaspecies,
rangingfromisogenicfliesandwormstoidenticaltwinhumans?
Canindividualvariationsinconnectivityberelatedtoorevenpredictindividual
differencesinbrainfunction?
2d.RationaleandPrinciples
SeealsoSectionsII.1Band6ofthisreport.
TheBRAINInitiativeaimstodeveloptechnologiesthatwillallowustodiscoverhowpatternsof
activityinneuralcircuitsaccountformentalprocessesandbehavior.Formuchofthepast
century,fewmethodswereavailabletomapcircuitfunction,sostructuralmapsservedas
proxiesforfunctionalmaps.ThebeautifulcircuitdiagramsofRamonyCajalepitomizeboththe
powerofthisapproachanditslimitations.Overthepastdecade,newmethodshaveemerged
tomapcircuitactivitydirectlyandonalargescale.Nonetheless,anatomicalconnectivity
remainsessentialforidentifyingtheactualmechanismatworkinthenervoussystemand
makingusefulpredictionsaboutthedevelopmentandfunctionofneuralcircuitsinhealthand
disease.
Structural(anatomical)connectivitycanbemappedatseverallevels,whichhavebeentermed
macro,meso,andmicroscale.
Themacroconnectomeisthemapofconnectivitypatternsacrosstheentirebrainat
thelevelofcentimeterstomillimeters.Thistermisgenerallyappliedtoanalysesofthe
humanbrain,becausefewofthefinerscalemethodsusedinexperimentalanimalsare
currentlyapplicabletohumans.Macroconnectomiceffortsarebestsuitedfor
determiningwhichbrainregionsareinterconnected.
Themesoconnectomeisintermediateinspatialresolution.Itreferstothemappingof
connectionstoandfrombrainareasatmillimetertomicronscale.Suchmapsare
sometimescalledprojectomes.Newmethodsallowextensionoftheseapproachesto
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mappingprojectionsofspecificcelltypesandenhancingmapswithmeasuresof
synapticconnectivity.Mesoconnectomiceffortsareunderwayforexperimental
animals32,33,buttheirapplicationtohumansisjustbeginning.
Themicroconnectomeisamapatmicrontonanometerresolution,whichaspiresto
documentthelocationofeveryneuronand/orsynapseinarestrictedbrainregion.It
currentlyreliesonultrastructuralmethodsthatinprinciplecanbeappliedtoanytissue
orspeciesbuthave,infact,sofarbeenappliedinahighthroughputfashiononlyto
invertebratesandrodents.
2di.MacroConnectomicMethods
CurrenthumanconnectomiceffortsrelyonnoninvasiveMRIbasedmethods3436.DWMRI
exploitstheanisotropyofwaterdiffusionalongmyelinatedaxonstomapwhitemattertracts37.
rfMRImeasurescorrelationsinspontaneousactivityacrossareasinrestingsubjects.Itprovides
anindirectmeasureofanatomicalconnectivitybasedontheassumptionthatcorrelationsare
greatestamongstconnectedregions38.
Thesemethods,whicharetheonlyonescurrentlyapplicabletolivinghumans,haveprovided
valuableinformationandaretransformingbothbasicandclinicalhumanneuroscience.They
are,however,limitedinseveralrespects.First,theirspatialresolutionisrelativelycoarse:the
smallestvoxelthatcanbediscriminated(>1mm3)containstensofthousandsofneurons.
Second,limitedsensitivityleadstoahighincidenceoffalsenegativesandpositives.Third,
whilediffusionandrestingstatemeasureshavebeenshowntoreliablyidentifyseveralknown
connections,theyhavenotbeenadequatelyandcomprehensivelyvalidated.Notably,current
tractographymethodsarebiasedtowardsomebrainregions,suchasthecapsofgyri,andaway
fromothers.Inaddition,thedirectionalityofconnectionscannotbeinferredfromthese
methods.Toovercometheselimitations,higherresolutionimagingmethods,improvedmeans
forcapturingrelevantsignals,andcriticaltestsofcurrentmethodsareneeded.
2dii.MesoConnectomicMethods
Thebestdevelopedmesoconnectomicmethodsinvolveinjectionofatracerintoasmall,well
mappedbrainarea,followedbyenumerationoftheareasandcelltypesthatsendprojections
to(retrogradetracers)orreceiveprojectionsfrom(anterogradetracers)thelabeledregion.
Tracersincludefluorescentdyesandviralvectors39.Suchmapsarecalledprojectomes.
Projectomescanbeenhancedinseveralways.(a)Viralvectorscanbetargetedtospecificcell
types,usingCreLoxtechnology,fractionatingasingleprojectomeintomapsthatrevealdistinct
connectivityofthemanycelltypesthatresidewithinaregion40.(b)Multicolormethodscanbe
usedtoresolvesubsetsofaxonswithinatract4143.(c)Transsynapticmethods,generallyusing
viralvectors,enablespreadofatracerfromaneurontootherneuronsthatitsynapsesupon
(anterograde)orthatsynapseonit(retrograde),revealingcharacteristicpatterns,ormotifs,of
synapticconnectivity44.(d)MethodssuchasGRASPidentifysynapsesmadebetweenlabeled

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pre andpostsynapticcells,revealingnotonlytheidentityoftheconnectedcellsbutalsothe
locationofthesynapsesthatconnectthem45,46.
MesoscalemethodsarevaluabletoBRAINInitiativeeffortsforseveralreasons.First,they
provideinformationneededtointerpretactivitybasedmaps,assumingthattheanatomicaland
physiologicaldatasetscanberegistered.Second,whenusedinconjunctionwithnovel
methodsforclearingandvisualizingtissue4750largeblocksoftissuecanbeimaged,speeding
analysis.Third,someofthesemethodscanbeusedtomaphumantissueobtainedatautopsy
andfrombrainbanks49.Fourth,thesemethodscanbescaleduptopermitanalysisofmultiple
samples,allowingassessmentofvariabilityamongindividualsandcomparisonofnormaland
pathologicaltissue.Fifth,mesoconnectomiceffortscanbeaugmentedtoprovideinformation
aboutchemicalcircuitry,asexemplifiedbyneuromodulatorysignalingmechanisms,which
canbedetectedmolecularlywithantibodiesorgeneticmarkers.
Ontheotherhand,substantialchallengesremain.First,thefractionofallauthentic
connectionsthatarereliablydetectedremainsuncertain.Second,currentprojectomic
methodsarewellsuitedtomaplongrangeconnectivitybutpoorlysuitedtomapconnectivity
withinsmallregions,becausemanycellsaregenerallytargetedatonceandthedensityof
interconnectionishigh.Third,methodsbasedonviralvectorsandtranssynaptictracersrequire
increasedsensitivity,resolution,andgeneralityanddecreasedtoxicity.Fourth,humanbrain
bankresourcesareinadequatetomeetnewmesoconnectomicopportunities,intermsof
tissueavailability,qualityandcuration.
2diii.MicroConnectomicMethods
Todate,microconnectomeshavebeenobtainedexclusivelybyEM,becauseonlythismethod
hastheresolvingpowerneededtomapindividualsynapsesandthefinestcaliberneuriteswith
certainty.Theoriginalconnectome,thatofC.elegans,wasobtainedbyserialsection
transmissionelectronmicroscopy(TEM)51.Thisapproachremainsthegoldstandardbutis
technicallyarduous.Muchattentionhasbeenfocusedrecentlyondevisingmethodsthatare
moreamenabletoautomationofsectionpreparation,suchasserialblockface(SBF)and
focusedionbeam(FIB)scanningEMandautomatedtapeultramicrotomy(ATUM).
ConventionalandSBFmicroscopyhavebeenusedtogeneratelargeconnectomicdatasetsover
thepastfewyears5257.Itshouldbenotedthatspecimenpreparationandfixationarestilldark
artsthatcouldbearmodernizationandimprovement.Technologydevelopmentinthisarea
shouldcontinue,butatthiswritingitremainsunclearwhichofthecurrentlyavailablemethods
willbebestsuitedforlargescaleefforts.
Amajorandseriouschallengetothisfield,whichcouldbeaddressedbytheBRAINInitiative,is
thatadvancesinmethodsforsectioningandimaginghavenotbeenmatchedbyadvancesin
methodsforimagesegmentationandreconstructionand,forconventionalmethods,section
alignment.Ittakesordersofmagnitudemoretimetogeneratereconstructionsthantoobtain
theoriginaldata.Thus,thebottlenecknowisdataanalysisratherthandataacquisition58,59.
Evenforblockfacemethodsinwhichnospecimenalignmentisneeded,noexisting
computationalsegmentationalgorithmsaresufficientlyaccuratetoreplacehumanannotators.
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Oneroughestimateisthatcompletereconstructionofasingle1mmcubeofcortex(~0.2%of
thewholebrain)wouldtake10,000personyears59andcost>$100million.Ongoing
improvementsincomputationalmethodsandcrowdsourcingapproachesarechippingawayat
theproblem,butlargescaleinvestmentinmicroconnectomicsshouldbetiedtosubstantial
progressinthisarea.
Becausemicroconnectomicmapsaresoexpensiveinmoneyandtime,andbecausetheycan
onlybeobtainedforverysmallbrainsorforlocalcircuits(microcircuits)withinlargebrains,
thereisnoconsensusconcerningtheirprioritywithintheBRAINInitiative.Thereisnodoubt
thatreferenceconnectomeswouldbeofgreatvalue59.Ontheotherhand,itremainsunclear
howvariablemicroconnectomeswillbeamongindividualswithinaspecies,orevenovertime
inasingleindividual60,61.Thisvariabilitywouldnotbeaninsurmountableproblemifitwere
feasibletoroutinelymapmicroconnectivityonthesameindividualsthathavebeenanalyzed
physiologically,ortocomparenormalandpathologicaltissuesinsubstantialnumbersof
individuals.Thisisnotyetfeasible,however.Thusitisespeciallyimportanttofocusnowon
developingtechnologiesthatwilldrivedownthecostofconnectomics.
Itisalsoworthconsideringalternativemethodsforgeneratingmicroconnectomes.Amajor
advanceoverthepastdecadehasbeentheinventionofasuiteofsuperresolutionlight
microscopicmethodsSTORM,PALM,STED,etc.witharesolutionfargreaterthanthatof
diffractionlimitedlightmicroscopy62,63.Superresolutionmethodsallowuseofmultiplecolors,
superpositionofmolecular(immunohistochemical)labelsonneuritesandsynapses,andeven
liveimaging.Currentresolutionofthesemethodsisintherangeof1030nanometers,whichis
nearlysufficientformicroconnectomicmappinginatleastsometissues.Substantial
improvementinsuperresolutionmethodscouldprovideanattractivealternativeto
ultrastructuralapproaches.
2e.Implementation
Methodsforstructuralmappingatalllevelsremaininadequate.Wethereforefocusinthefirst
fiveyearsondevelopingnewtechniquesandimprovingpromisingones.Asmethodsimprove,
weanticipatethattheywillbeincreasinglyusefulforhighthroughputcomparisonofcircuitsin
normalandpathologicaltissue,bothinexperimentalanimalsandinhumans.
2ei.TheMacroConnectome
Shorttermgoals(15years)
Anurgentneedistodeterminetherelationshipofcurrentlyusedproxiesofconnectivity
inhumans(DWMRIandrfMRI)todirectmeasuresofsynapticconnectivityas
determinedstructurallyorfunctionally.Werecommendinvestmentinimaginative
studiesaimedatthatgoal.Forexample,recentworksuggeststhatfocusedultrasound
couldbeusedforfocalstimulationofsmall(~1mm3)brainregions6466.Couplingsuch
stimulationwithmeasurementofBOLDbasedfunctionalimagingsignals(fMRI)could
beusedtogenerateamapofconnectivitythatcouldbecomparedwiththoseinferred
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fromMRI.OtherapproachestobepursuedinparallelincludedirectvalidationofMRI
measuresinhumanornonhumanprimatesusingprojectomicmethods,withthegoal
ofdecreasingtheregionalbiasesofDWMRIanatomicalimagingmethodsand
increasingtheirsensitivity;studiesinnonhumanprimatessuggestthatclassicaltracing
methodsandDWMRItractographyonlycorrelatewellforthestrongest20%of
connections.Combinationsofimaginginvivofollowedbyprojectomicanalysisexvivo
innonhumanprimatesmightrevealnewMRIsignaturesthatcouldbeappliedto
humans.
AsecondimpedimenttoprogressisthelimitedresolutionofMRImethods,whichwill
facilitatestudiesofbothconnectivity(thissection)andactivity(nextsection)ofhuman
brains.Resolutionlimitsarecurrently~8mm3(e.g.2x2x2mm3)forrfMRIand~2mm3
(e.g.1.25x1.25x1.25mm)forDWMRIusingadvanced3Teslaimagingplatforms.We
supporteffortstoimproveresolutionsignificantlytoreachvoxelvolumesof~0.3to0.4
mm3.
Longtermgoals(610years)
Resolutionof~0.4mm3forrfMRIandDWMRIwillenablenumerousnewstudies,but
weshouldnotbesatisfiedwiththisgoal.Vigorouspursuitofnewapproacheshold
promiseforimprovementinresolutionto0.1mm3orbetterin610years.Thiswould
providetheabilitytovisualizeconnectivityinthehumanbrainattheleveloflayersand
smallensemblessuchascorticalcolumns.
MRImethodsarealreadybeingusedtodetectindividualdifferencesamonghuman
brainsthatcorrelatewithindividualdifferencesinbrainfunctionandgenotype.As
resolutionandaccuracyimprove,newopportunitieswillariseforgeneratingbiomarkers
forearlydiagnosisandprovidingmechanisticanalysisofbraindisorders.Wesupport
pilotprojectstotestthepotentialofthesemethods.
2eii.TheMesoConnectome
Shorttermgoals(15years)
Thegreatestneedinthisareaistoimprovethespecificityandreliabilityofmethodsfor
projectomeandcelltypetocelltypetracing.Forexample,transsynaptictracingmethodsare
inadequatelyvalidated;itisnotclearwhetheriterativeimprovementswillsufficeorwhether
newapproachesareonthehorizon.Forviralvectors,decreasingtoxicityandexploring
methodsforselectivetargetingtospecificcelltypesingeneticallyinaccessiblespecies,
especiallyhumans,isessential.Opticalandcomputationalmethodsforefficient,high
resolutioncollectionofmultidimensionaldatasetsfromlargevolumes,andregistrationofthese
datasetswithcellularresolutionactivityinformation,willneedtobedevelopedandimproved.
Emphasisshouldbeplacedonmethodsthatcanbeappliedtononhumanprimatesinvivo,and
tohumanautopsyorbiopsymaterial.

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Longtermgoals(610years)
BasedonanticipatedmethodologicaladvancesinthefirstfewyearsoftheBRAINInitiative,we
proposevigorouseffortstomapprojectomeswithcelllevelresolutionandcelltypespecificity
inhealthyandpathologicaltissue.Mappingcouldbeginwithprojectomesofkeybrainregions
innormalanimals,andinanimalmodelsofhumanbraindisorders(e.g.autismorParkinsons
disease).Asmethodsimprove,itwillbepossibleto(a)registerconnectivitywithactivity
mappedinthesamebrains,(b)scaleupmappingtocomparestructureandfunctioninwhole
brainsofnormalanimalsanddiseasemodels,and(c)mapprojectomesinkeyareasofnormal
humanbrainsobtainedatautopsy,aswellasbrainsofpeoplewithbraindisorders.
2eiii.TheMicroConnnectome
Shorttermgoals(15years)
TestsofcompetingEMapproachese.g.,FIB,ATUM,SBF,TEMCAarealreadyunderway,as
areeffortstogeneratesampleconnectomes e.g.ofC.eleganslarvae,flyopticlobe,and
mouseretina.AmajorcontributionoftheBRAINInitiativeshouldbetospurimprovementsin
segmentationandreconstructionmethodsbecausethesearethebottlenecksinmicro
connectomicresearch.Machinelearning,crowdsourcingandotherpromisingapproaches
couldbepursuedinparallel.Importantly,segmentationmethodsdevelopedinthiseffortwill
beapplicabletolightaswellaselectronmicroscopicdatasets.
Wealsorecommendexploringthepossibilitythatsuperresolutionlightmicroscopicmethods
couldbeimprovedtothepointofprovidingmicroconnectomic(nanometerlevel)mappingof
atleastsomecircuits.
Althoughsegmentationalgorithmswillcontinuetomature,weanticipatethatwithinafew
yearsmethodswillbesufficientlydevelopedtosupportcollectionofafewlargedatasetsthat
willnotonlybeimmediatelyusefulbutalsoprovideawaytoexplorehowmicroconnectomes
canbeusedinconjunctionwithothertypesofdata.Weproposethischallenge:Monitorthe
behaviorofanindividualzebrafishoveraprotractedperiod(atleastseveralhours)while
simultaneouslyrecordingactivityfromasmanyneuronsaspossible.Then,preparethebrainof
thatsamezebrafish,submitittovolumeEMorultrahighresolutionlightmicroscopywith
multiplemolecularlabels,andreconstructmanyandperhapsallconnectionsinitsbrain.
Longtermgoals(610years)
Assegmentationmethodsimprovefurther,itwillbepossibletocompletesparse
reconstructionsofkeyareasinbrainsofnormalanimalsandinselectedanimalmodelsof
humanbraindisorders.Likewise,weanticipatethatinitialsegmentationofkeyareaswithin
normalandpathologicalhumanbrainwillbefeasiblewithin10years.
Anaspirationalgoal,dependentondecreasedcostandincreasedspeed,willbetoreconstruct
keyareasfrommultipleindividuals,therebymappingindividualvariationsinconnectivity,first
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inexperimentalanimalsandlaterinhumans.Thisaccomplishmentwouldbetransformational,
becauseindividualvariationsinneuralconnectionsandactivitypatternsunderliethe
remarkablebehavioralandcognitivedifferencesamongindividuals.
2f.Mechanisms
Duringthefirstfewyears,theemphasiswillbeonimprovingcurrenttechnologyandexploring
thebroadestpossiblespaceinsearchofnewtechnologies.Thisworkisbestsupportedby
investigatorinitiatedmechanisms.Inlateryears,weanticipatethatcontinuedtechnology
developmentwillbeaccompaniedbyconsensusonbestpracticesformorefocusedefforts
forexample,formappingprojectomesinhealthyandpathologicaltissue.Thisworkmay
requirealargerinvestment,andconsortiainvolvingseveralsitesworkingincoordinationmay
bedesirable.Verylargescalecentersmayeventuallyberequiredforlargescaleconnectomic
efforts,butthatwilldependonthescientificproblemstobeaddressedandtheavailable
technology.
2g.TimelinesandMilestones
Shorttermgoals(15years)
ValidateMRIbasedmethodsformacroconnectomicmappingofconnectivityin
humans.
ImproveMRIresolutionto~0.30.4mm3(alsoseeSectionIII.3).
Developahighqualitytoolboxofmethodsforefficientlymappingandannotating
projectomesinexperimentalanimals,includingnonhumanprimates,aswellasin
humantissueblocks.
ReducethetimeneededtosegmentvolumeEMdatasetsbyonehundredtoone
thousandfold.
Reconstructmicroconnectomesofindividualanimalsthathavebeenstudied
physiologicallyandbehaviorallye.g.densereconstructionofazebrafishbrain
followingactivityimagingofthebehavinganimal.
Developnewtechniquesforusingelectronand/orsuperresolutionlightmicroscopyto
integratemolecularsignaturesofcellsandsynapseswiththeirnanoscaleconnectivity
LongtermGoals(610years)
ImproveMRIresolutiontobetterthan0.1mm3(seealsoSectionIII.3).
Obtainhighresolution,macroscaleconnectomesof100sto1000sofnormaland
disorderedhumanbrains,withaccuracysufficienttoprovideindividualmapsunder
differentconditions,instandardizedformatsthatallowbroadaccessandcomparisons
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ofthesereferencedatawithnewdata.Identifyconnectionalstructuresunderlying
psychiatricandneurologicaldisorders.
Obtainprojectomesinnormalanimalsanddiseasemodels.
Obtainprojectomesinhealthyandpathologicalhumanbrain.
Producemicroscalereconstructionofkeyareasfrommultipleindividualsinananimal
model,followingbehavioralandphysiologicalanalysis,therebyrelatingindividual
variationsinconnectivitytofunctionaldifferences.

III.3.THEBRAININACTION
3a.ScientificGoal:Produceadynamicpictureofthefunctioningbrainbydevelopingand
applyingimprovedmethodsforlargescalemonitoringofneuralactivity
3b.OverallObjective
LargescalemonitoringofneuralactivityisattheheartoftheBRAINInitiative,providingthe
meanstomapandcharacterizethechangesinelectricalandchemicalsignalingunderlying
mentalprocesses.Itwillalsoserveasafoundationintranslationalapplicationsinvolvingbrain
monitoringandstimulation,includingtherestorationoflostoraberrantneuralfunction.As
such,itisacoretechnologyfortheBRAINInitiativeandconsiderableeffortshouldbemadeto
developbothnewandimprovedlargescalerecordingmethods.Technologydevelopment
shouldproceedwithspecificbiologicalapplicationsinmindthatwould,ifsuccessful,provide
newinformationontheneuralcircuitbasisofbrainfunction,orprovidenewcapabilitiesin
therapeutics.Thus,theemphasisisontechnologyapplicabletothestudyoftheawakebrain
duringquantifiablebehavior,providingabasisfortheinterpretationofneuralsignals.
3c.Deliverables
1. Newandimprovedelectrodesforlargescalerecording.Objectivesincludeincreased
numberanddensityofrecordedneurons,accesstomorebrainareas,increased
reliability,andminimalinvasivenessandtissuereaction.Longertermobjectivesinclude
practicaldevicesincorporatingnanowiresorothernanofabricatedstructuresforinvivo
highdensityextracellularorintracellularrecording.
2. Newandimprovedopticalsensorsofneuralactivity,bothelectricalandchemical.
Objectivesincludebetterfluorescentindicators,spectroscopicmolecularsignatures,or
nanoparticleprobes,preferablywithcelltypespecifictargeting,formembranevoltage,
neurotransmitterandneuromodulatorconcentrations,synapticactivity,and
biochemicalprocesses.

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3. Newandimprovedinstrumentsforopticalmonitoringofneuralactivity.Objectives
includenewandimprovedimagingmethodsformonitoringpopulationsofneuronsat
highdensitywithinlocalbraincircuitsinanybrainarea,and,ultimately,acrossmany
brainregionssimultaneously,duringquantitativelymeasuredbehavior.Compatibility
withperturbationtechnology(SectionIII.4)willbehighlydesirable.
4. Developmentofimprovedtechnologyformonitoringhumanbrainactivity,including
extendingtheresolutionofcurrenttechnologyfMRImeasurementsto0.1mm3
(0.46mmvoxels)andnewmethodsformakinghumanfMRImeasurements.Suchnew
methodscouldinvolvecurrentfMRIapproachesimplementedwithnew
instrumentationandspatialencodingtechniquestoperformstudiesinnaturalsettings.
Alongtermgoalisanewtechnologywithcellularspatiotemporalresolutionthatcould
interrogatelargeportionsofthehumanbrain.
Scientificquestionsaddressedbythisgoal:
Howissensoryinformationtransformedintohigherorderperception?
Howisshorttermworkingmemoryencoded,maintained,andreadout?
Whatarethecircuitmechanismsunderlyingdecisionmaking?
Whatfundamentallogicandmechanismsmediatemotorcontrol?
Howdomultiplebrainareascommunicateandworktogetherasbehaviorandtask
demandschange?
Howcanwereliablydetectmultiplebrainstatesthatoccurduringwakefulnessand
sleep?Whataretheuniquefunctionsofthesestates?
Howdoneuromodulatorysignalsremodelcircuitdynamicsandbrainstates?
Howareinternalcognitivemodelsoftheworldencoded,updatedandaccessedtomake
predictionsandguidefutureactions?
3d.RationaleandPrinciples
SeealsoSectionsII.2andII.6ofthisreport.
Adiversesetofnewandimprovedmethodsformonitoringneuralactivityinthefunctioning
brainwillbethefirstdeliverableanticipatedfromthisprojectduringthefirst5years.Asthe
projectdevelopsandmatures,weanticipatethatthesemethodswillbeincreasinglyusedto
produceaseconddeliverableandaprimarygoaloftheBRAINInitiative:theconstructionofa
dynamicpictureofbrainfunctionthatintegratesneuronalandcircuitactivityovermultiple
temporalandspatialscales.Accordingly,progressinlateryearswillincreasinglyapplylarge
scalerecordingmethodstobiologicalquestions,ofteninexperimentsinwhichrecordingis
75

integratedwithothermethodssuchascelltypeidentification(SectionIII.1),anatomicalcircuit
mapping(SectionIII.2),perturbation(SectionIII.4),behavior,andtheoreticalanalysis(Section
III.5).
Newrecordingtechnologiesshouldprovidetheabilitytomapatunprecedentedresolutionand
scaletheelectricalandchemicalactivityofpopulationsofneuronsintheawakebrainduring
cognition,emotion,andbehavior.Thisnewdatawillprovidethebasisforaconceptual
understandingofneuralcoding:howinformationrelevanttothebrainstate,sensorystimuli,or
othervariablesareencodedinthisactivity.Followingthechangesinneuralactivityovertime
theneuraldynamicswillprovidekeyinformationforestablishingthecomputationalfunction
ofaneuralcircuit,andhypothesesabouthowthebrainworkswillbesubjecttodirect
experimentalobservation.Forexample,aredecisionsrepresentedbydivergingsequencesof
neuralactivitythatbecomeprogressivelylesssimilarovertime(i.e.abifurcationinneural
dynamics)?Istheshorttermmemorytraceofafacerepresentedbyapatternofactivityona
lowdimensionalattractormanifoldwithintheconnectedbrainareasthatprocessface
information(thecontinuousattractorhypothesis)?
3e.MetricsforProgressinRecordingTechnology
Adiversesetofmethodsandinstrumentationisusedfordetectinglargescaleneuralactivity.
Nevertheless,thetechnologiesforlargescaleneuralrecordingcanbeevaluatedusingmetrics
thatallowcomparisonsbetweentechnologiesandprovidequantitativemeanstodefinegoals
andmilestones.Formanyofthesemetricsweexpecttransformationalimprovements(e.g.10
100ormore),whichprovidesthemotivationandthebasisforsettingmilestonesforlarge
scaleneuralrecordingwithintheBRAINInitiative.
Thereareoftenimportantengineeringtradeoffsbetweenthedifferentmetrics,andwedonot
expectthatindividualtechnologieswillbeabletosimultaneouslyachieveoptimum
performanceonallmetrics.Rather,weexpectarangeoftechnologieswillarisethatpossess
complementarystrengthsandaddressdifferentexperimentalchallengesandgapsinour
presentknowledgeofbrainfunction.Forexample,althoughthenumberofneuronsthatcan
beconcurrentlyrecordedisanimportantmetric,onemustadditionallyunderstandtheextent
towhichacandidatetechnologyoffersthecapabilitytorecordfromspecifiedcelltypes,andto
sampledenselyandinavolumetricfashionwithinbasicmicroarchitecturalunitssuchas
individualcorticalcolumns(seeSectionIII.7).
TheMetrics:
Numberofneuronsrecorded.Forextracellularrecordingwiththepresent
generationofmicroelectrodes(tetrodes67,68/siliconprobes6971),orforcurrent
calciumimagingmethods7274athighspeed,thenumberofneuronsrecorded
simultaneouslytypicallyrangesfromtenstohundreds.Thereisatradeoffinoptical
imagingbetweenthenumberofneuronsrecordedandtemporalresolution:atlow
temporalresolution,upto100,000neuronshavebeenrecordedinthetransparent
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larvalzebrafish75.Increasingthenumberofneuronsrecordedataparticular
temporalresolutioncanbeusedasametricforprogress.

Volumetricrecording.Recordingmethodsdifferwithrespecttothegeometrical
arrangementoftheindividuallyrecordedneurons.Forexample,anindividual
tetroderecordsfromaclusterofcloselyspacedneuronsnearthetip,whilethe
clustersrecordedbyeachtetrodearetypicallyatleastseveralhundredmicrons
apart.Singlesiliconprobescantypicallysamplemanypointsalongtheprobes
shaft,buthavelimitedsamplingorthogonaltotheprobesaxis76.Inoptical
imaging,imagedneuronstypicallyhavecellsomatageometricallylocatedwithina
limitedtwodimensionalimageplane.Inallcases,itwouldbedesirabletodevelop
methodsinwhichanyneuronwithinthetissuecouldbeaccessedbyagiven
recordingtechnology,enablinglargescalerecordingsofneuralactivityacrossa3D
volumeoftissue.Examplesofapproachesfor3Drecordingincludemulticontact
siliconelectrodearrays77andmultiplane3Dvolumetricopticalcalciumimaging78.

Densityofrecordings.Manyregionsofthebrainhaveconserved,repeatingmotifs
intheirmicrocircuitrythatseemtorepresentbasicmicroarchitecturaland
functionalunits.Tounderstandthefunctionandcollectiveactivitypatternsofthese
units,suchascorticalcolumnsorcerebellarmicrozones,weneedrecording
techniquesthatofferdense,ideallycomplete,samplingcapabilities,acrossthe
volumesoftissuetypicaloftheindividualunits(fromfractionstomultiplecubic
millimeters).

Temporalresolution.Actionpotentialscanhaveadurationoflessthan1
millisecond;synapticeventslast10500milliseconds;slowmodulationcurrentsand
potentialsdevelopoversecondstominutes.Recordingmethodsdifferintheir
abilitytofollowthesedifferenttemporalscales.Fastertimeresolutionforaction
potentialmeasurementisacommongoalofrecordingmethods,butitisnotan
exclusivegoalorbenchmark,sincethereismuchtobelearnedatthesynapticand
neuromodulationtimescales.

Successfulandroutineaccesstoanyneuralstructure.Atechnologythatisvery
informativemayneverthelesshavealowsuccessrate(e.g.invivopatchrecordings
inbehavinganimals),ormaynotbeequallyapplicabletoallbrainareasorcelltypes.
Cellsindeepbrainareasandcellsthataresmall,orhavelowactivityrates,canbe
challengingtoaccessandidentifywithexistingrecordingmethods.Methodsthat
provideroutineaccesstoanyanatomicalstructureandneurontypeinthebrain,at
singlecellresolution,wouldbehighlyvaluable.

Compatibilitywithstimulationofneuralactivityatcellularresolution.Experimental
manipulationofneuralactivityisanimportanttoolfortestingcausalityinthe
characterizationofneuralcircuits,andisincreasinglyusedintherapeutics(see
SectionIII.4).Ideally,thecodinganddynamicpropertiesofneuronsinacircuit
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couldbecharacterizedwithlargescaleneuralrecording,andthenaparticular
spatialandtemporalpatternofstimulation,tailoredtothoseneuronsandthe
questionortherapyathand,couldbeappliedtothesystem.Thesegoalscanbe
metbythedevelopmentofcompatibleopticalimagingandstimulation
instrumentationandspectrallyseparatedopticalsensorsandeffectors;byimproved
highdensityelectrodeswithbothrecordingandstimulationcapability;orby
electrodearraysforusewithsimultaneousoptogeneticstimulation.
Abilitytoanatomicallyidentifytherecordedcells.Amechanisticunderstandingof
neuralcircuitfunctionwillbeaidedbycombininglargescalerecordingwith
methodsthatprovideinformationonthecelltype,anatomy,andsynaptic
connectivityoftherecordedneurons.Thisinformationcanobtainedduring
experimentsinrealtimebytargetinggeneticallyencodedsensorstospecificcell
types,orbyoptogeneticstimulationofgeneticallytaggedneurons,oritcanbe
obtainedposthocinfixedtissuesubjectedtohistologicalorconnectomicanalysis.
Abilitytoidentifyandrecordfromthesameneuronsoverlongperiodsoftime.The
developmentofmethodsthatprovidereliablecellidentificationbetweenrecording
sessionsandoverlongerandlongertimeintervalswillprovidenewcapabilitiesof
particularimportancetounderstandinghowneuralcircuitschangeoverthecourse
ofdevelopment,learning,ordiseaseprogression.
Minimaltissuedamageduetoinvasivenessofmethod,orchronictissuereaction.
Theseissuesarecriticalwhenrecordingsaremadeinhumans.Existingtechnology
leavesmuchroomforimprovementininvasivenessandbiostability,and
considerableimprovementisneededinminimizingtissuereactions.

ResolutionandfidelityofrecordingofactivitywithMRItechniques.VariantsoffMRI
havebeenshowntoreachthespatialscalesofcorticalcolumns,evenwithsome
degreeofcorticallayerdifferentiation.TheseMRIapproachescanprovide
informationconcerningtheaveragedactivityoftheseensemblesandtheirdynamics
overalargevolumeincludingtheentirehumanbrain.However,thesensitivity
neededforthesemeasurementsoftenrequiresextensivedataacquisitiontimes.
SignificantgainsinsignaltonoiseandspeedofMRIareneededtoachieverobust
detectionofactivityinsubcolumnarclusterswithbetterlayerresolutionandover
largevolumes.Withimprovementsininstrumentationaswellasimageacquisition
andanalysistechniques,MRIshouldaimtoreachvolumetricresolutionof0.1mm3
withhighfidelitytoneuronalsignalstriggeringtheMRIresponses.Suchacapability
wouldcomplementinformationobtainedthroughhighdensityelectricaloroptical
recordingswithinvolumesoftissueequivalentinsizetoMRIvoxels(fromfractions
tomultiplecubicmillimeters).AlthoughthemaingoaloffMRIworkishuman
neuroscience,validationofthesetechnologieswillrequireworkinnonhuman
animalsthatcombinessinglecellrecordingmethodswithMRImethod
development.
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Multiareapopulationrecordingatcellularresolution.Manycurrentlargescale
recordingtechnologies,suchasmicroelectrodearraysandcalciumimaging,are
typicallyusedtorecordfromonebrainareaatatime.Questionsabouthow
informationisconveyedfromareatoareainthebrainorhowmultipleareaswork
togetherforcognitivetaskslikedecisionmaking,wouldbenefitfromimproved
methodsbywhichseveralormanyseparatedareascanbesampledatthesame
time.

Subthresholdandsubcellularvoltagesignals.Extracellularlyrecordedspikesand
fieldpotentialsarethesignalscurrentlyemployedinlargescalerecordingswith
microelectrodes.However,dendriticactivityandsubthresholddynamicsbothhold
substantialinterest.Newapproachessuchasnanowires79,80andautomatedpatch
recordings81offeropportunitiestoexpandmultineuronrecordingtodirect
measuresofmembranepotential,whichwouldbeenormouslybeneficialin
characterizinghowsynapticinputsandintrinsiccelldynamicalpropertiessuchas
oscillationsandplateaupotentialscontributetoresponseproperties.Similarly,new
opticalprobessuchasgeneticallyencodedornanoparticlebasedopticalvoltage
sensors82,83offerprospectsfordendriticrecordingsandmaybringinvivooptical
imagingofmembranevoltageintoapracticalreality.

Chemicalandbiochemicalsignalsofbrainactivity.Currentmethodsformeasuring
neuropeptidesandbiogenicaminesareinsensitiveandspatiallycrude;theiractivity
isofteninferredindirectlyviameasurementsofelectricalactivity,leadingtoa
substantiallossofinformation.Yetthesesystemsarethetargetsofmostpsychiatric
drugsanddrugsofabuse,indicatingthattheyhavepotentbrainfunctions.
Improvedmethodsareneededfordirectmeasurementsofneurotransmittersand
neuropeptides,thereleaseofdifferentclassesofsynapticvesicles,andbiochemical
stateswithinneurons.

Effectivenessandefficiencyofdatacollection.Amajorbottleneckoflargescale
neuralrecordingtechnologiesisnotthesensorsperse,buthowtogettherecorded
informationfromsensortoanexternaldeviceforanalysisorarchiving.Forexample,
advancesinsiliconmultisiteelectrodesforlargescaleneuralrecordingwillrequire
advancesinonchipmultiplexing,filtering,digitization,andcommunication.
Similarly,nanoparticlebasedopticaldetectorsofvoltagewillrequiremethodsto
readoutallprobesindependentlyandsimultaneously84.

Compatibilitywithinterestingbehavior.Largescalerecordingmethodsoften
provideconstraintsonthetypeofbehaviorthatcanbestudiedduetorequirements
suchasheadrestraintandtethers.Twoapproachestoreducingtheseconstraints
showpromise.First,newbehavioralparadigmssuchasvirtualrealitysystems85and
voluntaryheadfixationsystems86provideagreaterrangeofbehaviors,suchas
navigationanddecisionmakinginpartlyrestrainedanimals.Second,wirelessly
poweredandtelemeteredminiaturizedelectrodearrays87andopticalimaging
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instrumentationcanbeusedforheadmountedsystemsonfreelybehavinganimals,
includinghumans.
3f.ImplementationandMechanisms
Thefuturedevelopmentofnewrecordingtechnologieswillincreasinglyrequirethe
participationofscientistsfromphysics,chemistry,molecularbiology,electricaland
neuroengineering,materialsciences,andcomputerscience.Oneratelimitingfactorfor
developmentofthistypeoftechnologyisasocialengineeringproblem.Neuroscientistsmust
beabletointeractwithscientistsandengineersfromthephysicalandinformationsciences,
anditmusthappenorganically.Indeed,humanMRItechnologyhasbeensuccessfully
developedingroupsspanningengineers,physicists,signalprocessors,mathematiciansand
neuroscientists,bothatthelevelofindividuallabsorinlargeconsortia(e.g.theHuman
ConnectomeProject).Morerecently,HHMIJaneliaFarmsResearchCampushashired
experiencedphysicists,chemists,engineers,andcomputerscientistswhoworkalongside
neuroscientists,withincentivestodevelopnewtechnologiesforbiology.Mechanismsmustbe
providedthatfacilitatethiskindofinteractionwithintheBRAINInitiativeatthelevelofasingle
universitylaborcenter,orinaconsortium.Inaddition,educationalprogramsthatallow
physicalandinformationscientiststolearnbiologywouldprovideanentrypointfornew
engineersandscientistsfromotherdisciplinestolearnabouttheopportunitiesprovidedbythis
initiative.
Itisalsohighlydesirabletoinvolveindustrypartnerswhohaveexperienceinmanufacturing
productsforuseinhumans,astheirresourcesandexpertiseoftencomplementthatofthe
academicresearcher.Manydevicespotentiallyhaveenormousdevelopmentandproduction
costs.Asingledeviceforhumanclinicalapplicationscantake$100200milliontobecomea
commercial,FDAapprovedproduct.Therateoftoolordeviceinnovationanddevelopmentis
linkedtotheamountoffundingavailable.Formingindustrypartnershipsisonewaytomitigate
thecoststotheNIH.
Ingeneral,newprogramsandfundingstrategiesareneededtobringtogetherpeoplewith
varyingexpertise(e.g.,physics,chemistry,molecularbiology,electricalengineering,
bioengineering,computerscience)andindustryorganizationscapableofcommercializingnew
recordingtechnologies.Smallgroupsofcollaboratorscanbeveryeffective,butlargermulti
milliondollarprojectsmayberequiredinsomecasesforengineeringandtechnology
developmentbeyondwhatisnormallypossibleinabasicresearchsetting.FutureBRAIN
leadershipcouldevaluatetheInitiativestechnologicalprogressinitsearlyyears,andthe
successorfailureoflargerscaleeffortspresentlyongoinginthefield,inordertogaugethe
importanceoffuturelargeprojects.Allmechanismsshouldoperateinawaythatdoesnot
isolatepotentialdevelopersandusersofthetechnologyfromoneanother,butratherdrives
innovationthroughconsortiaandcollaborations.
3g.TimelinesandMilestones
3gi.MicroelectrodeRecording
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Shorttermgoals(years15)
Highdensitypenetratingsiliconmicroelectrodearrays(100micronspacing,4x
increaseindensitycomparedtoexistingarrays88),withreliabilityandrecording
qualityappropriateforastandardizedlaboratorymethod.
Siliconprobeswithmultisiteelectrodescontaininghundredstothousandsof3D
distributedcontacts,withonprobeelectronicsforfiltering,amplification,
multiplexing,anddigitization,capableofrecordingandstimulatingcellsacrossall
layersinacorticalcolumn.
Flexible(electrocorticography/ECoG)surfaceEEGgrids(wirelesslypoweredand
reporting);mmandsubmmscaleelectrodespacing,designedprimarilyfor
primates,includinghumanapplications.
Proofofprincipledemonstrations,usinginvitropreparationsasafirststeptoward
invivoapplication,ofnovelelectronicdevicesusingnanowiresorother
nanofabricatedstructuresforneuralrecording.
Integratedtechnology,recordingandperturbation:fullyintegrated,robustwireless
duplex(twoway)electronicsonchipforremotepowering,recordingand
stimulationwithtransmissiondistancesof1meter.
Integratedtechnologyforhumanuse:practicalelectrodesfordeepbrainpopulation
recordingandstimulationatcellularresolution;methodstoreducechronictissue
reactionandimprovethereliability,biostability,andlongtermperformanceof
chronicelectrodes.
Longtermgoals(years610)
Practicalaccesstoanyareainanonhumanorhumanbrainwithminimum
invasiveness.Theimplantablebrainbuttonforhumanuse:aselfcontaineddevice
thatcanbesurgicallyimplantedwithnotranscranialconnectionsandthatallows
forrecordingandstimulationfromlargenumbersofneurons.
Practicaldevicesforinvivouseincorporatingnanowiresorothernanofabricated
structures;highdensityintracellularrecordinginvivo.
3gii.OpticalRecording
Shorttermgoals(years15)
Fast,sensitivegeneticallyencodedfluorescencevoltagesensorscapableofreliable
actionpotentialdetectioninneuralpopulationsinvivo.

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 Geneticallyencodedsensorsforopticaldetectionofneurotransmittersand
neuromodulators.
Sensorsthatreportthroughachangeinfluorescenceacombinationofphysiological
events,suchastheANDfunctionofneuralactivityandthetimeofalightpulse.
Thiswillallowcircuitsactiveatparticularepochsofabehaviortobehighlighted.
Reliable,highsensitivityopticalsubthresholdvoltagemeasurementsatcellular
resolutionformeasuringsynapticcurrentsanddendriticintegration.
Instrumentationplatformssuitableforwidedisseminationforrecordingfrom104
105neuronsinbehavingmammals.
Instrumentationforpopulationopticalrecordingatcellularresolutionfrom5
differentbrainareassimultaneously.
Integratedtechnologyrecording,behavior,andtheory:recordingtheactivityfrom
every(identified)neuroninthebrainofatransparentorganism(worm,flylarvae)
duringnaturalbehaviorastestcases:canwereallyunderstandfullrangeof
behaviorsfromnetworklevelneuraldynamics?(seealsoSectionsIII.5andIII.7)
Integratedtechnologyrecording,theory,andperturbation:simultaneousoptical
imagingandoptogeneticstimulationofneuralpopulationsatcellularresolution;
providingtailoredopticalstimulation(playback)tothesameordifferentpopulations
ofneuronsatcellularresolution.(seealsoSectionsIII.4andIII.7)
Longtermgoals(years610)
Instrumentationfor110millionneuronrecordingsinbehavingmammal.
Volumetricanddeepbrainimagingatmillisecondresolutioninnontransparent
species;reducedinvasivenessofopticalaccessforimagingapplications.
Highspeedvoltageimaging,inmultiplebrainareasofbehavingrodentsand
primates.
Integratedtechnology,recordingandperturbation:Multipleindependentspectral
channelsforbothimagingandstimulation,formonitoringandmanipulationof
multiplecelltypesconcurrently.
3giii.HumanNeuroimaging
Shorttermgoals(years15)
IncreasedspatialresolutionforfMRI(e.g.robustdetectionofsignalsonthespatial
scaleof~0.1mm3volumetricresolutionintheentirehumanbrain).
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 Quantitativeunderstandingofrelationshipsbetweenneuronal,glial,andmetabolic
signaldynamics(incombinationwiththeory,SectionIII.5).
fMRIdeployedincombinationwithEEGandMEGinmorenaturalenvironments,
withimprovedanalysismethods(SectionIII.5),allowingexaminationofagreater
rangeofhumanbehavior.
Integrationofexperimentwiththeory:Detailedunderstandingoftheproblemof
multiscaleaveraginginspecificneuralsystems(todeterminetheinformation
contentoftheMRIsignalsthataverageactivityacrossensemblesofindividualcells
thatarecontainedintheMRIvoxel).
Longtermgoals(years610andbeyond)
Innovativetechnologiesthatcansignificantlyexpandourabilitytodetectactivity
noninvasivelyinthehumanbrain.Thiswillrequirenew,unknownmechanismsand
techniques;nomilestonesortimelinesarepossible.Anoninvasiveorminimally
invasiveimagingmodalitywithcellularspatio/temporalresolutionthatcould
interrogatelargeportionsofthemammalianbrainwouldrepresentamajoradvance
forbothanimalandhumanstudies.Anysuchtechnologythatwassafelyapplicable
inhumanswouldrevolutionizeourunderstandingofhumanbrainfunction.

III.4.DEMONSTRATINGCAUSALITY
4a.ScientificGoal:Linkbrainactivitytobehaviorbydevelopingandapplyingprecise
interventionaltoolsthatchangeneuralcircuitdynamics
4b.OverallObjective
Precisecircuitlevelperturbationtechniquescan1)determinethecausalsignificanceofneural
activitypatternsincognition,emotion,perceptionandotherprocesses,2)probetheinternal
structureanddynamicsofnervoussystems,and3)serveasabasisfornewtherapeutic
interventions.Experimentalcontrolofcircuitactivity(orcircuittuning)ismostusefulwhen
integratedwithassessmentofnaturallyoccurringactivitypatterns,globalandlocalwiring
patterns,andmolecular/geneticidentityofthesamecellsthatarecontrolledorperturbed.
4c.Deliverables
1) Newandimprovedperturbationtechnologiessuitableforcontrollingcellsthathave
beenspecifiedbytype,wiring,location,andothercharacteristics(seeSectionIII.2).
Perturbationtechnologiesinthiscontextcouldincludetoolsforstimulation,inhibition,
ormodulationthatmimicnaturalactivity,andcouldspanoptical,chemical,
electromagnetic,biochemical,andothermodalitiesfordeliveryofcontrolsignals.
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2) Applicationofperturbationtoolstobehavinganimalstounderstandthecausallinkage
betweenneuralactivitypatternsandbehavior,inthecontextofsophisticatedand
quantitativebehavioralmeasurements.Playingbackactivitysequencesat
appropriatespatialandtemporalresolutiontotestthesufficiencyofcandidateactivity
patternsinelicitingorsuppressingnormalorpathologicalbehaviors.Inhibitingnatural
activitypatternstoaskiftheyarenecessaryfornormalorpathologicalbehaviors.
Perturbationisthecriticaltestofanytheorypurportingtorelatebrainactivityto
cognitionandbehaviordoesthetheorymakeaccuratepredictionsaboutcognitiveor
behavioralperformancefollowingprecisemanipulationsofspecificbraincircuits?At
thesametime,improvementsinquantitativeanalysisofbehaviorshouldincreasingly
movetowardtheprecisionofrecordingandperturbationmethods.
3) Applicationofperturbationtoolstoprovideamechanisticunderstandingofneural
dynamics.Combinedperturbation/recording/theoryexperimentsthatnudgesystems
outoftheirnaturaldynamicsinsimpleandcomplexways,toprobeinformationflow
andrevealtheorganizationallogicofcomplexneuronalnetworks.
4) Applicationofperturbationtoolstohumanstounderstandnormalnervoussystem
functionandmechanisms,causes,andtreatmentsofpsychiatricandneurological
disease.Clinicalstimulationdevicescanbeusedexperimentallytoexploremany
aspectsofhumanbrainfunction.Preciseinterventionsinthecontextofbehaviorcan
openthedoortounderstandingpathologicalprocesses,screeningfortherapeutic
agents,andidentifyingspecificactivityperturbationstorestore,regulate,andrepair
dysfunctionalcircuits.
Amongthescientificquestionstobeaddressedbythisgoal:
Howaremeasureableaspectsofperceptionandbehaviormodulatedbyalterationof
activitypatternsinunderlyingneuralpopulations?
Whatalterationsoftheseactivitypatternsgiverisetomaladaptiveorpathological
behavior?
Areprecisecorrectionsoftheseactivitypatternsatthecellularlevelrequiredtorestore
typicalbehavior,oraremoresimpleshiftsinregionalorprojectiondynamicssufficient?
Howdoshiftsinthebalanceofactivityamongdifferentbrainregions,projections,or
celltypesaffectcircuitfunction?
Whatisthecausalroleofspikerate,timingandsynchronyrelationshipsamong
neurons,projections,andbrainregions,incircuitprocessingandbehavior?
Arethereconsistentneuralactivitymotifsorpatternsthatperformcore
computationsindifferentbrainregionsthatperformdifferenttasks?

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 Whichactivitypatternsinspecificneuralcircuitscanpromoteorinhibitsocialbehavior,
allocationofbehavioralenergytoatask,orconsciousawareness?
Cantherapeuticinterventionbeproductivelyguidedinapatientspecificwayby
consideringbrainstructureoractivityalongsideapatientssymptoms,andthen
adaptinganactivityinterventiontothatpatientsuniqueclinicalsituation?
4d.RationaleandPrinciples
SeealsoSectionsII.3,II.4,andII.6ofthisreport.
Historically,perturbationssuchasanatomicallesions,behavioralpharmacology,andelectrical
microstimulationhaverevealedmanyimportantpropertiesofthebrain8993,andnewmethods
totuneneuralcircuitsareincreasinglypowerful.Electricalstimulationcontinuestobea
particularareaofimportancebecauseitprovideshightemporalresolutionandcanbeusedin
humansubjects,eitheracutelyorchronically,toprobeormodulatebrainfunctioninclinical
settings.Electricalstimulationdoesnottypicallyprovidesinglecellorcelltyperesolution,and
evenwhenelectrodesareplacedwithmillimeterscaleprecisiontheycanmodulatemuchmore
distantcellsbyactinguponfibersofpassage.Yetthesimplicityandflexibilityofelectrodeswill
ensureongoinguse,andtheirutilityshouldbeimproved.Specifically,electrodebased
perturbativetoolsshouldbelongerlastingwithenhancedbiocompatibility,biostability,
efficiency,compactness,spatialresolutionandmonitoringcapabilitiesforclosedloopcontrol.
StimulatingelectrodesshouldthereforebeanareaofBRAINInitiativetechnologydevelopment
andinvestigation.
Optogeneticsisapowerfulnewtoolformodifyingbrainactivity,inwhichtargetedgene
deliveryprovidescelltypeandregionalresolution,andtargetedlightdeliveryprovideshigh
temporalresolution.Currently,itsuseislimitedbylightscattering,typicallyrequiring
fiberopticsformostdeepbrainstructures9496.Neededimprovementstooptogenetictools
includenarrower(lightwavelength)actionspectra,increasedlightsensitivity,andtoolswith
newkindsofionconductionpropertiesorotherelectricalorbiochemicalmodulatory
capabilities.Optogeneticapproachesalsoneedtodevelopfurthertoenablenotjustcelltype
resolution,butsinglecellresolution,insystemsascomplexasbehavinganimals97.Amajor
goaloftheBRAINInitiativeshouldthereforebethedevelopmentofoptogenetictoolswithnew
kinetic,spectral,andeffectorfunctionproperties,andconcomitantdevelopmentofnewlight
deliverymechanismsthatareoperativeinbehavinganimalsandallowsparse,distributed,user
definedpatternsofcellresolution,millisecondscaleplayin/inhibitionofdynamicalmotifs.
Ifoptogeneticsrepresentsarefinementofelectricalstimulation,whatissometimescalled
chemogenetics98isarefinementofpharmacologyusinggeneticallyencodedeffectorproteins.
Regionalandcelltyperesolutionareprovidedbyeffectorgenedelivery,asforoptogenetics,
whiledeliveryofadrug(oftensystemically)triggerstheperturbativemanipulation.Thesetools
areoftenlimitedbyslowtimescalesforonsetandoffsetofdrugeffects(uptohourstodays,if
deliveredsystemically).Theyaretypicallyunsuitedforgeneratingspecificpatternsofneural
spikes,andofteninducesustainedperturbationsthatcanleadtocircuitleveladaptationsand
85

compensations.Nonetheless,theglobalreachofchemicalandchemogenetictools,theeaseof
drugdelivery,andthefactthattheycaneasilybecombinedwithoptogeneticsareadvantages
thatwilldriveinnovation.Newchemogenetictoolswithanexpandedrepertoireofeffectsand
bettercontrolledkineticpropertiesshouldbeagoaloftheBRAINInitiative.
Anewgenerationofbiologicalperturbationtoolscouldbeenvisionedbasedonadvancesin
naturalproductsbiochemistryandsyntheticbiology.Naturalproductscanprovideinsightinto
cellandcircuitlevelprocesses;muchhasbeenlearnedfromthepotentandspecificsnake
venoms(conotoxins)andplantmetabolites(capsaicin,opioids)thattargetpainpathways99,100.
Notableadvancesinsyntheticbiologyincludenanobodies,singlechainantibodiesfrom
camelidsthatcanbemolecularlytargetedtospecificcelltypesandreceptorstomodulatetheir
functionorincreasetheirsensitivitytodrugs101.Inanotherformofsyntheticbiology,the
biotechnologyindustryisdevelopinghybridproteinsthatcrossthebloodbrainbarrierby
combiningashuttleproteinsuchastransferrinwithapayloadtargetedtothebrain102.
Althoughthesetoolslacktemporalspecificity,theyarepromisingfortherapeuticusein
humans,andtheyhaveonlybeguntobeexploitedforneuroscienceatthecircuitandsystems
level.
Finally,nonchemical/optical/electricalenergydeliverymodalitiesforperturbationarea
speculativebutworthyavenueofinvestigation.Studiesinanimalshavedemonstratedeffects
ofmagnetic,acoustic/ultrasound,andthermalperturbationsonbrainactivityandbehavior,
andshouldbeexploredfurther.Inhumans,anexampleuseisprovidedbyTMSwhichisan
effectiveresearchtoolandalsoclearedforhumanclinicaltherapyindepression.Thereare
manypossibilities,butmostproposedmechanismsarelackinginspeed,safety,efficacyor
versatilesinglecomponenttargetability;itislikelythatmatureversionsofthesemethodswill
requirechemicalorgeneticsensitizingagentstoprovidespecificity.Newideasforperturbative
interventionareneededandwelcomedfromdiversefieldsofengineering,chemistry,and
physics.
Newperturbationtoolsshouldbeoptimizedandvalidatedbasedonthespatialandtemporal
specificityoftargeting,compatibilitywithsubsequentassessmentofwiringandmolecular
phenotypesofcontrolledcellsandsynapticpartners,andcompatibilitywithreadoutsof
behaviorandneuralactivity.Notalltoolsneedbeapplicabletoallsystems(forexamplesome
toolsmaybenotsuitableforprimatesorpeople)butgeneraluseacrossspeciesisdesirable,
andevenspeciesoptimizedapproachescanbeextremelyinformativeanduseful.
TofullycapitalizeontheincreasedunderstandingofcelltypesprovidedbytheBRAINInitiative
(SectionIII.1),newlydevelopedperturbationtoolsmustbereadilytargetedtocelltypes
definedbymultiplefeaturessuchasgenetics,wiring,spatiallocation,andactivityhistory.For
example,increasinglyadvancedintersectionalgenetictoolsorgenometargetingstrategies97,103
suitableforinvertebrates,fish,mice,rats,andprimateswillbecomeanessentialcomponentof
theperturbationtoolboxandwillneedtobedevelopedalongsidethesenewcontroltoolsto
ensurecompatibilityandsynergyacrossBRAINsubinitiatives.
4e.Implementation
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Weenvisiontwobroadphasesforthedevelopmentandapplicationofnewneuralperturbation
technologies:Phase1(years15)shouldemphasizerapidimprovementofrecentlyinvented
perturbationtechniques(e.g.optogenetics,chemogenetics),andinventionofnovel
approaches,especiallythosethatmaybeappliednon (orminimally)invasivelytohumanand
animalnervoussystems.Refinementofexistingelectricalstimulationmethodsshouldbe
supportedbecauseoftheiruniqueadvantagesinhumanneuroscienceandtherapeutics.As
always,technologydevelopmentwillproceedmosteffectivelywhenlinkediterativelyto
concreteapplicationsinneuroscienceresearch.
Phase2(years610)willadaptandapplyperturbationtechniquestoincreasinglylargeand
complexsystems,andwillcontinuetosupportongoingtechnologydevelopmentand
refinement.Phase2shouldemphasizeintegrationofmajorcategoriesofBRAINrelated
investigationintohownervoussystemactivityandbehaviorarisefromcircuitry,including
simultaneousperturbationofactivity,molecular/geneticandbiophysicalphenotypingofcells
andsynapses,mappingofwiringorconnectivitypatterns,observationofnativeactivity
patternsduringbehavior,quantificationofbehavioraloutput,andcomputationalanalysisof
circuitactivitypatterns.
Thedeepestunderstandingofnervoussystemfunctionwillbeachievedtotheextentthat
theseindividualtypesofinvestigationareintegrated,orallcarriedoutwithinthesamecircuit
(SectionIII.7).Theseintegratedmethodsshouldbeappliedtoscientificquestionsaboutbrain
function;onlythroughquestiondrivenresearchwillthestrengthsandlimitationsofeach
approachcomeintofocus.
Movinginvestigationalandinvasivemethodstowardthehumanbrainscalewillbepossible
withcertaintradeoffs.AstheBRAINInitiativeprogresses,newknowledgeaboutmacro and
mesoscalecircuitry(SectionIII.2)mayraisepossibilitiesforeffectivemacro andmesoscale
perturbations,asopposedtodemandingsinglecellspatialresolutionperturbations.
Assemblies,dynamictemporalmotifs,andlargerprojectionsortractsmayberecruitablein
principledfashionusingmacroresolutioninterventions,ashasbeenthecaseindeepbrain
stimulationtherapiesforParkinsonsdisease.
AdvancedinstrumentationwillbeessentialinPhase2.Forexample,atthesimplestlevel,laser
powerwillquicklybecomelimitingforlargescaleopticalperturbation.Newengineering,
physicalprinciples,andappliedsciencetoolswillberequiredtoguideperturbationenergyto
thetargetedvolumeofbraintissue,includingcorrectiveoradaptivestrategiestocompensate
fortissuedistortion,scattering,andabsorption.Collaborativeeffortsinvolvingscientistsand
engineersacrossfieldswillbeneeded.
Finally,theoryandcomputationalmethods(SectionIII.5)willbeanessentialandtightly
integratedpartofallperturbationwork.Forexample,inanimalstudiesinvolvingimagingof
activityfollowedbyperturbation,computationaltoolswillbeneededfordetectionof
statisticallysignificantdynamics,dimensionalityreductionofresultingdatasets,andrealtime
predictionofeffectiveinterventionsbasedonthiscomputationaloutcome.Inclinicalwork,
dynamicalmodelingoftheeffectofperturbationsonthebrainsofhumanpatients(basedon
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functionalconnectivityandtractography)maypredictoptimalsitesforintervention37,104,105,
especiallywithincreasedcausalunderstandingofneuralcircuitsandbehaviorarisingfrom
animalstudies96.
Behaviorandcognition.Theactivityofthebrainisexpressedinthebehaviorofananimalor
person.Correspondingly,thetoolsusedforanalyzingbehaviorshouldhavetheaccuracy,
specificity,anddiversityofthemethodsusedtomeasureandmanipulatethebraincircuitsthat
giverisetothosebehaviors.Theimprovementofexistingmethodsanddevelopmentofnovel
methodsforthequantitative,objectiveandautomatedanalysisofbehavioriscriticaltothe
BRAINInitiative.Standardmethodsofformalpsychophysics,principledapproaches
incorporatingsupervisedorunsupervisedcomputationalclassifiersfordetailedanalysisof
naturalbehaviorsinfreelymovinganimals,closedloopvirtualrealityenvironments,andother
techniquesformanipulating,trackingandanalyzinganimalbehavior,aswellasinternalbrain
statessuchasmood,emotionorattention,mustbedevelopedinpartnershipwithcompatible
longtermcapabilitiesforneuronalrecordingandperturbations.Theapplicationofmachine
vision,machinelearning,andothertechnologiesforidentifyingbehavioralmotifs,activitiesand
actionsislikelytobeasimportantforBRAINasthedevelopmentofmethodsforcapturing
neuralactivitymotifs106.Automatedbehaviorquantificationandclassificationisasteptoward
highthroughputandhighcontentanalysisofbehaviorasareadoutofbrainactivity.Itmay
alsohaveasignificantimpactonthedevelopmentofnewdrugsforthetreatmentof
neurologicalandpsychiatricdisordersinhumans.
4f.Mechanisms
Phase1(years15)shouldincludetoolsrelevanttolaboratoryanimalsaswellastohumans,
shouldincludeappropriateengineeringandcomputationaljustification,andshouldcapturethe
greatestdiversityofpossibleapproachesintheearlyyears.Thisphaseshouldemphasize
targetableperturbationtooldiversification/development/validation,aswellascelltype
targetingstrategiescompatiblewiththeseperturbationtools,andbasicinstrumentationfor
deliveryoftheperturbation(control)information.Itwillbeimportanttofundtherigorousand
quantitativecomparisonofdifferentperturbationmethodsinmultiplerealworldsystemsand
settings.
Phase2(years610)shouldincreasinglyaddressthepracticalrealitiesandeconomic
efficienciesofscalerequiredforbringingincreasingnumbersofcellsandcircuitsunder
perturbativecontrolusingreliableandreproducibletechniques.Thisphaseislikelytoinvolve
bothmoderatesizedcollaborationforsmallernervoussystemsandspecificscientificproblems,
andasmallnumberoflargerconsortiatomeetthegoalofmaximallyintegrated,large(e.g.
nonhumanprimateandhuman)nervoussystems.Fundedprojectsatallscalesshouldbuild
capabilityfor,orexperimentallyachieve,simultaneousintegrationofthemajorcategoriesof
investigationwithinthesystemofchoice.
4g.TimelinesandMilestones
Shorttermgoals(Phase1,years15)
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Identificationofnew,improved,andvalidatedperturbationtechnologies:
Spatialprecision:cellularoratleastcelltyperesolutionforexperimentalanimals;
identifiedcircuitlevelresolutionforhumans.
Temporalprecision:improvedtimescalesforonsetandoffset,matchedtothequestion
athandmillisecondresolutionisoneideal,andsustainedperturbationisanother.
Diversity:toolswithdifferentactivationproperties(e.g.photoactivationspectra),so
thatmultiplepopulationsorcelltypesmaybetargetedinthesamepreparation.
Scope:accesstoabroadanddeepvolumeofneuraltissueduringbehavior;atleast
hundredstothousandsofneuronsovermillimetersormore,withminimaltemporal
delaywithinanexperiment.
Compatibilityofperturbationtoolswithtoolsforobservationofnativeactivitypatterns,
wiring,andmolecularidentityoftheperturbedcircuitcomponents.
Integratedevolutionofquantitative,precise,highcontentbehavioralmethods
appropriateforfreelymovingandrestrainedanimals.
Longtermgoals(Phase2,years610)
Developmentandapplicationofperturbationtechnologiesinbehavior.Targetinglargeintact
primateorhumansystemsinadditiontosmallermodelsystems,buildingonadvanced
instrumentation,computation,datamanagementsandanalysis,andothertechnology
developedduringPhase1.
WithinexperimentintegrationofperturbationtechniqueswithotherkeyBRAIN
sponsoredtechnologies:celltypeidentification,anatomicalcircuittracing,largescale
recordingofnativeactivitypatterns,precisequantificationofbehavior,andtestsof
specifictheoriesofneuralcoding,computationanddynamics.
Advancethescaleofanalysisby~1orderofmagnitudeperyear:100cellscontrolled
independentlyalongwithmultipleparalleldatastreamsinthesamepreparation
(imaging,wiring,annotation,behavior,and/ormodeling)shouldbeachievableinyear6,
1000inyear7,10,000inyear8,andsoon.Accessto1millionneuronscouldbeheldas
anambitiousgoal.

III.5.IDENTIFYINGFUNDAMENTALPRINCIPLES
5a.ScientificGoal:Produceconceptualfoundationsforunderstandingthebiologicalbasisof
mentalprocessesthroughdevelopmentofnewtheoreticalanddataanalysistools
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5b.OverallObjective
Theoverarchinggoaloftheory,modeling,computationandstatistics(henceTMCS)in
neuroscienceistocreateanunderstandingofhowthebrainworkshowinformationis
encodedandprocessedbythedynamicactivityofspecificneuralcircuits,andhowneural
codingandprocessingleadtoperception,emotion,cognitionandbehavior.Powerfulnew
experimentaltechnologieswillproducelarge,complexdatasets,butrigorousstatistical
analysisandtheoreticalinsightwillbeessentialforunderstandingwhatthesedatamean.
Coherentlessonsmustbedrawnnotonlyfromtheanalysisofsingleexperimentsbutby
integratingacrossexperiments,scalesandsystems.Theoreticalstudieswillallowustocheck
therigorandrobustnessofnewconceptualizationsandtoidentifydistinctivepredictionsof
competingideastohelpdirectfurtherexperiments.Neurosciencewillmaturetotheextent
thatwediscoverbasicprinciplesofneuralcodingandcomputationthatconnectandpredict
theresultsofdiverseexperimentalmanipulationsofbrainandbehavior.
5c.Deliverables
1. Newtechniquesforanalyzingthelarge,complexdatasetstobeproducedunderall
goalsoftheBRAINInitiative(e.g.SectionsIII.14).Neededtechnicaladvancesinclude
methodsforfindinghighorderstructureinrecording,anatomicalandbehavioraldata
sets(dataexploration),methodsforbuildingmodelsthatcanidentifypotential
underlyingmechanisms,andmethodsforrigoroushypothesistestingbyfittingmodels
todata.
2. Multiscaleapproachesforintegratingdataobtainedfromdifferentexperimental
techniques.BRAINsponsoreddatasetswillcoverspatialscalesrangingfrommicronsto
meters,andtimescalesfrommillisecondstominutes,hoursoreventhelifetimeofan
organism.Newanalyticandcomputationalmethods,aswellasnewtheoretical
frameworks,arerequiredtounderstandhoworganismlevelcognitionandbehavior
emergefromsignalingeventsatthemolecular,cellularandcircuitlevels.
3. Discoveryofgeneralprinciplesofneuralcoding,computation,circuitdynamics,and
plasticity.Bysynthesizingresultsfromnumerousexperimentsthatexploredifferent
neuralcircuitsatdifferentlevels,theoreticalstudieswilluncovercommonthemesand
generalprinciples.Theseprincipleswillelucidatehowneuralcircuitswork,thatis,how
populationsofneuronscollectivelysupportcognition.
4. MakingTMCSperspectivesandtechniquesavailabletoallneuroscientists.Faculty
development,studenttraining,andcollaborativegrantswillgenerateincreased
quantitativerigorthroughoutthefield.
Amongthescientificquestionstobeaddressedbythisgoal:

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 Circuitstability:Howarecircuitsformedbygeneticandexperientialforces,andthen
maintainedovertheanimalslifespandespiteextensiveexperiencedependent
plasticity?
NeuralCoding:Whataretheneuralcodesusedbybrainsforsensoryinformation
processing,informationtransmission,andmotorcontrol?
NeuralDynamics:Howdointeractingneuronsindistributedcircuitsintegrateand
transforminputsonmultipletimescales?
Learning:Howareneuraldynamicschangedbylearning?Whatarethemodulatoryand
plasticitymechanismsresponsiblefordifferentformsoflearning?
Memory:Whatneuronal,synaptic,biochemicalandcircuitmechanismssupport
workingmemoryandlongtermmemory?Howarememoriesretrieved?
Decisionsandactions:Howdoneuralcircuitsreadoutthedynamicsofmultipleneural
populationstoguidebehaviorandcognition?
EachofthesefundamentalproblemsisanexampleoftheoverarchinggoalofTMCS:
understandinghowthenervoussystemproduceshighorder,flexiblebehaviorinthepursuitof
theorganismsgoals.
5d.RationaleandPrinciples
SeealsoSectionsII.5andII.7ofthisreport.
NewtechnologiesdevelopedbytheBRAINInitiativewillproduceopportunitiesfordeeper
understandingoftherelationshipsbetweendifferentformsofneuralactivityandthecognitive
andbehavioralfunctionsofthebrain.Exploitingthisopportunitywillrequirenewstatistical
andcomputationaltoolstoanalyzedatasetsthatarelargerandmorecomplexbyordersof
magnitudethanthoseofthepast,andthedevelopmentofnewmodelsofneuralcircuitsand
brainfunctionthatcanbetestedexperimentally.
TheBRAINInitiativeshouldincorporatesophisticatedstatisticalandcomputationalmethods
intoeverystageofresearch.TMCScollaboratorsshouldbeembeddedintheplanningand
designofexperiments,sothatexpensive,multidimensionaldatasetsareoptimalforanalysis
andinterpretation.Welldesignedandintelligentlyinterpretedexperimentscandrive
neurosciencetomovebeyondqualitativemodelstoprincipled,quantitativeanalysisof
nonlinearprocessesbyskilledapplicationofmathematicalandcomputationalmethods,
numericalsimulations,andformalstatisticalanalyses107.
Overthepasttwentyyears,theoreticalandcomputationalneurosciencehavebeenstimulated
bytherecruitmentofselectphysicists,engineers,mathematicians,computerscientists,and
statisticians108110,inpartthroughvisionaryinvestmentbytheSloanandSwartzFoundations.
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Nonetheless,theextenttowhichtheirexpertisehaspermeatedtheexperimentalcommunityis
uneven.Manytheoristsandmodelerswouldbenefitfromcloserinteractionswith
experimentalists,andmanyexperimentalgroupswouldbenefitenormouslyfromdirectaccess
tothistheoreticalcohort.TheBRAINInitiativeshouldfacilitatetheentryofTMCStrained
researchersintoneuroscience.
Atamorebasiclevel,manyexperimentalneuroscientistsarenottrainedinquantitative
methodstheywillneedinthefuture.Developmentanddisseminationofquantitativeexpertise
withintheneurosciencecommunityshouldbepursuedaggressively.
5e.Implementation
TheBRAINInitiativewillgeneratemanykindsofdata,including:
Functionalimaging:fMRI,PET,nearinfraredspectroscopy
Neurophysiology:EEG,MEG,andlocalfieldpotentials(LFP);singlecellandmultiplecell
spiketrains
Opticalrecordings:geneticallyencodedorchemicalreportersofvoltage(including
subthresholdvoltage),calcium,neurotransmitters,synapticactivity,biochemicalstates
Behavior:binaryobservations,processedvideodata,humanpsychophysicaldata
Cellleveldata:anatomy,connectivity,geneexpression,biophysicalproperties
Eachofthesedatastreamswillbenefitfromadvancesinthequantitativeanalysesdescribed
below,butthegreatestimpactwillcomefromcombininganalysisacrossthesemodalitiesa
relativelynewendeavorforneuroscience.
5ei.NewTechniquesforAnalyzingLarge,ComplexDataSets
StandardizedAnalysisMethodsforNeuralSpikeTrainData.Spikes,oractionpotentials,
aretheprimarymeansofinformationtransferoverlongdistanceswithinthenervous
system.Aseriesofspikes(orspiketrain)encodesthemessagethatagivenneuron
transmitstoitsdownstreamtargets.Analysisofneuralspiketrainshasbeenanactive
areainneuroscienceresearch,butmanyimportantquestionsremainunansweredand
thescaleoftheproblemwillgrowundertheBRAINInitiative107,111.Wemustdevelop
reliable,readilyaccessiblesolutionstotheproblemsofspikesorting,information
encoding,connectivityandinformationdecodingthatarecrucialforconfirmatory
statisticalanalysesindatasetsoftheexpectedsizeof100,000to1,000,000
simultaneouslyrecordedneurons.
NewMethodsforStatisticalModelingofNeuroscienceData.TheBRAINInitiativewill
needtodevelopnewstatisticalmodelsforneurosciencedata,bothforexploratory
analysiswhosepurposeistolearnaboutpotentialstructureinthedata,todevelop
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potentialhypotheses,andtoaidinthedesignoffuturedefinitiveexperiments112and
forconfirmatoryanalysiswhichentailsdefinitiveexperimentstotestexplicit
hypotheses,makeinferencesandeventuallydecisions107.Thesewillneedtobetailored
toeachkindofexperimentwithintheBRAINInitiative,andespeciallyintegrated
experimentscombiningmultipletechnologies(belowandSectionIII.7).
DimensionalityReduction.TypicalBRAINInitiativedatasets,consistingofrecordingsor
imagingofhundredstomanythousandsofneurons,willbefartoocomplextoanalyze
directly.Instead,dimensionalityreductionmethodsmustbeappliedtoextractasetof
significantindependentsignalsfromthesedata.Newapproachesmustbedeveloped
thatallowustoextractsignalsthatfaithfullyreflectthefulldataset,butarecompact
enoughforvisualizationandfurtheranalysis.Theimportanceofthisstepinthedata
analysispathwaycannotbeoverstated:extractingtheappropriate,meaningfulsignals
anddisplayingtheminilluminatingwaysisakeytodevelopinginsightintowhatneural
circuitsaredoingandhowtheyaredoingit.Dimensionalityreductionwillprovide
principledanswerstoaseriesofquestionsabouthowmuchdatashouldbegathered,at
whatlevelofdetail,inagivenexperiment.Forexample,ifonewishestounderstanda
specificcorticalcircuit,whatfractionofneuronsdoesoneneedtomonitortoextract
thenecessaryinformationaboutcircuitperformance?Isitappropriatetolump
differentcelltypestoobtainanoverviewofcircuitdynamics?Forinferringfunction
fromanatomicaldata,isitsufficienttoknowaveragepatternsofconvergenceand
divergenceofsynapticconnections,orisitnecessarytocapturethefullrangeofthe
distributionsandstrengthsoftheseconnections?
LevelsofDescription.Dimensionalityreductiontechniquesareequallyimportantfor
biophysicalmodelsofinformationprocessinginsingleneuronsandcircuits.Thereisa
tensionbetweenmodelsthatincorporatebiologicaldetailabout(forexample)the
distributionandkindofionchannelsandreceptorsonsingleneurons,andsimplified,
informativenetworkmodelsthatcapturetheessentialdynamicsoftheneuronsin
question113116.Wemustunderstandwhatlevelofdetailprovidesthegreatestinsight
foreachquestion.
DynamicSystemsAnalysis.Adynamicmodelisaformofdimensionalityreduction
becauseitpermitsanentiretimeseries,suchasasequenceofactionpotentials,tobe
derivedfromasetofinitialconditionsofadynamicsystem.Inotherwords,dynamic
modelingallowsustocompressdataconsistingofmeasurementsovermanytime
pointsintoasetofvaluesatasingletimepoint.Methodsexistforextractingdynamic
systemsdescriptionsfromdata,butthesemustbeextendedandspecializedfor
neuroscienceapplications.Advancesinthisareaareexpectedtohaveasignificant
impactonourabilitytounderstandBRAINInitiativedata.
5eii.MultiscaleIntegrationofDatafromDifferentExperimentalTechniques

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 FusionofInformationFromHighlyDiverseDataStreams;LinkingActivityAcrossSpatial
andTemporalScales.TheBRAINInitiativewillproducenoveldatasetsofenormous
variety.Forexample,informationoncelltypes,anatomicalconnectivity,and
neurophysiologicalactivityandeffectsofperturbationduringbehaviormaybecollected
fromtheexactsameneuraltissueinsomeanimalsystems.Withinasingleexperiment,
spatialscalescouldrangefrommicrons(synapses)tomillimeters(shortrangecircuits)
totensofmillimeters(longrangecircuits).Inthesameexperiment,temporalscales
couldrangefrommilliseconds(spikes)toseconds(attractorstates)tominutesorlonger
(stablecircuitchangesrelatedtolearning).Identifyingappropriatewaystointegrate
datafrommultipleexperimentalsourcesacrossscalesisanunparalleledchallengeand
opportunityforTMCS.
UnderstandingtheBiophysicalBasisoffMRI,EEG,andOtherNeuralRecording
Technologies.Forseveralrecordingtechnologiescommonlyusedinneuroscience
experimentsparticularlythoughnotexclusivelyinhumanneurosciencethe
biophysicsofhowtherecordedsignalsrelatetoactivityintheunderlyingneuralcircuits
isanunsolvedquestion(e.g.EEG,MEG,LFP,fMRI).Collectivelythesetechniques
compriseourbestcurrentsourcesofinformationaboutneuralprocessinginthehuman
brain.Ourstatisticalmodelsofthesecriticalsignalsandwhattheymeancanbe
improvedsubstantiallythroughaccurateunderstandingoftheunderlyingbiophysics;
linkinglevelsinthismannerisanexampleofmultiscaleanalysis,animportantgeneral
problemthatmustbeaddressedintheBRAINInitiative.
SolvingHighDimensionalInverseProblemsforEEGandMEG.Inhumans,highdensity
EEGandMEGrecordingsareeasilyobtained,buttheirinterpretationislimitedbythe
inverseproblemofassigningthesourcesforsignalsmanyunderlyingpatternsof
brainactivitycangiverisetothesameobservedpatternofEEGorMEGsignalsatthe
scalp.EEGandhigherresolutionfMRIdataarenowbeingcollectedsimultaneouslyin
humans,providinganopeningforsubstantiveprogressontheinverseproblem.A
solutionwouldenablemoreincisiveinterpretationofhumanbrainsignalsandtheir
relationtoongoingcognitiveprocesses.
FunctionalConnectivityAnalysesinHumanBrainImaging.Largescale,simultaneous
recordingsofneuralsignalsleadtohypothesesabouttheconnectivityoflargescale
circuitsinthebrain.AsindicatedinsectionsIII.2andIII.3,forexample,simultaneous
fluctuationsinrestingstatefMRIsignalsmayallowreconstructionoffunctionallyrelated
networksofbrainareaseventhoughthoseareasarenotdirectlyconnected
anatomically.Considerabletheoreticalandstatisticalworkmustbedone,however,to
placetheseempiricalobservationsonfirmground.Becausemacroscalehumanbrain
networksarepotentiallyimportantasbiomarkersforpsychiatricdiseaseandfor
targetingtherapies,thisisaparticularlyconsequentialareaforTMCSanalysesin
neuroscience.
5eiii.IdentifyingGeneralPrinciplesofBrainFunction
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 TheoreticalInputonExperimentalDesign.Theoristsshouldbeinvolvedateverystagein
BRAINinitiativeexperiments,frominitialexperimentaldesigntothefinalextractionof
newconcepts.Theoreticalneuroscienceisaboutexperimentingwithideas.Althougha
theoreticalanalysiscanneverdeterminewhetheraparticularideaisactually
implementedinabiologicalsystemthatistheroleoftheexperimentitcancheckthe
consistency,viabilityandrobustnessofhypothesesataratethatishundredsoftimes
fasterthanexperimentation,savingmuchtimeandexpense.Furthermore,modeling
canhelpidentifythebestexperimentalapproachesfortestingaparticularhypothesisby
revealingthefeaturesthatareitsuniquesignatures.Theoristswillprovideanswersto
thebasicquestionsinexperimentaldesignsuchas:Howmanyneuronsshouldbe
recorded?Howmanytrialsarelikelytoberequired?Atwhatspatialandtemporal
scalesshouldthesystembestudiedandwithwhatresolution?Isthetaskbeing
consideredcomplexenough?Arethedataanalysismethodsbeingproposedoptimal?
UncoveringCommonThemesAcrossDifferentSystems.Theoristsareexpertat
integratingdatafrommultipleexperiments,techniquesandsystems.Byfocusingon
underlyingmechanisms,modelsallowparallelsbetweendifferentsystemstobe
identifieddespitedifferencesinimplementation.Inthisway,analogousoperating
principlesintheolfactorysystem,thecerebellum,othercerebellarlikestructures,and
corticalcircuitshavebeenrevealed.Thisintegrativeprocessshouldprogress
enormouslywiththedatathatemergefromtheBRAINInitiative.
SingleTrialDecodingTechniques.Decodingreferstoanumberofmethodsthatcanbe
usedtoeavesdroponthenervoussystembyreadingouttheinformationcontainedin
neuronalspiketrains117.TheBRAINInitiative,withitsgreatlyexpandedscaleof
neuronalrecording,offersanexcitingnewopportunitydecodinginformationfrom
singletrialdata.Thisisimportantbecauseitprovidesameanstoexploretheinternal
statesofthebrainthatarenotreliablylinkedtoexternallyobservableevents.Neural
activityassociatedwithobservablesensorystimuliormotorresponsescanbeidentified
inaverageddatabytemporallyaligningtrialsontheobservedevents.Thisisfarmore
difficultforactivityassociatedwithtransientinternalstatesthatareonlyloosely
associated(ifatall)withexternalevents.However,thestatisticalpoweroflargescale
neuronalrecordings,coupledwithanalysismethodssuchasstatespacemodelsor
hiddenMarkovmodels,canidentifyandclassifyinternalstatesonindividualtrials,
openingmanyaspectsofcognitiontoscientificinvestigationforthefirsttime117.
HumanBrainDisorders.Anotherareainwhichexperimentalresults,clinical
observations,andtheorycouldfruitfullybecombinedishumanneurologicaland
psychiatricdisease.Therewardpredictionerrormodelhasbeenusefulinreasoning
aboutdrugaddiction,andservesasanexampleofatheorythatlinksmolecules,cells,
andcircuitstoexperiencedependentbehaviorsandclinicalpathology.Building
theoriesofthisgeneralityandexplanatorypower,linkingdifferentfunctionaldomains,
shouldbeagoaloftheBRAINInitiative.Theoriesofemotionalprocessingcouldprovide
insightintomoodandanxietydisorders;theoriesofcognitioncouldmotivatenew
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experimentalinvestigationsofschizophrenia;andtheoriesofsocialcognitioncould
provokenewwaysofthinkingaboutautism.
5eiv.AccelerateAdoptionofTMCSPerspectivesandTechniquesinNeuroscience
Giventhecomingincreaseinlarge,complexdatasetsinneuroscienceandtheincreasing
relevanceofquantitativeapproachestounderstandingthesedatasets,theBRAINInitiative
shouldsponsorthedevelopmentofquantitativeexpertiseatalllevelsfaculty,postdoctoral
andgraduatestudent.
Faculty:Provideincentivestobiologyandneurosciencedepartmentssothattheoristsand
statisticiansareseenasimportantandintegralfacultyhires.Changethecompositionand
cultureofNIHstudysectionstorecognizethattheoryiscriticalfortheneuroscienceofthe
future.
Training:Ensurethatallneurosciencepostdocsandgraduatestudentsbecomeproficientwith
basicstatisticalreasoningandmethods,andareabletoanalyzedataatanappropriatelevelof
sophistication,forexamplebywritingcode.Encouragetraineestoconstructmodelsasaway
togenerateideasandhypothesesortoexplorethelogicoftheirthinking.
5f.Mechanisms
Combinedtheoreticalandexperimentalresearchinneurosciencecanbeaccommodatedunder
severalfundingmechanisms.Multicollaboratorinvestigatorinitiatedgrantsarewellsuitedto
intense,iterativeexchangesbetweenexperimentalandtheoreticalgroupsaddressingspecific
scientificproblemstogether.AnexpansionornewimaginingoftheNIHNSFCRCNSeffort,
whichencouragesclosecollaborationbetweenTMCSinvestigatorsandexperimentalists,would
beofgreatvaluetotheBRAINInitiative.TheBRAINInitiativeshoulddevelopstudysections
thatvalueTCMSbothinitsownrightandincollaborationwithexperimentalists;thereisa
widespreadsensethatthisperspectiveislacking.
ExperimentalbranchesoftheBRAINInitiative(seesectionsIII.14,67)envisionthepossibility
ofcollaborativeconsortiaorregionalcentersfordevelopingtechnologyandapplyingitto
fundamentalquestionsinneuroscience;itiscriticalthatTMCSinvestigatorsbeincludedinsuch
consortiafromtheirinception.
TheNIHBigDataToKnowledge(BD2K)initiativeoverlapsinsomeofitsgoalswiththisaspectof
theBRAINInitiative,withthestrongestoverlapindevelopingmethodsforanalysisoflarge,
complexdatasets.AclosepartnershipbetweenBD2KandtheBRAINInitiativewillaccelerate
thedevelopmentofquantitativemethodsinthisarea.
AcceleratingtheadoptionofTMCSapproacheswithinneurosciencedepartmentsand
educationalprogramsmayrequiremorecreativemechanisms,asoutlinedinthespecific
recommendationsbelow.Possibilitiesincludeadministrativesupplementstoexistingresearch
projectgrantsforcollaborationswithTMCSinvestigators,andjuniorfacultyhiringincentives
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likethosedeployedbyNIHundertheAmericanRecoveryandReinvestmentActof2009(ARRA)
severalyearsago.Avarietyofmechanismscanbedeployedtostrengthenquantitativetraining
amongpostdocsandgraduatestudents.
5g.TimelinesandMilestones
Shorttermgoals(15years)

Developnewtechniquesforanalyzinglarge,complexdatasets.
o Developdynamicversionsofprincipalcomponent,independentcomponent,
graphicalmodelsandcompressedsensingthatmaybeusedtodynamicallytrack
structureincontinuousdata,pointprocessdataandcombinationsofthetwo118.
o Developdimensionalityreductiontechniquestodetermine,forexample,how
denselyandunderwhatbehavioralconditionswemustsampletheelectricalactivity
oflargenetworkstounderstandtheirfunction;when,ifever,itisappropriateto
lumpcelltypes;whatlevelofanatomicaldetailismosteffectiveforconnectomics
analysis;andwhatbiologicaldetailsaremostimportantforusefulbiophysical
modelingofsingleneurons.
o Developautomated,dynamictechniquesthatwouldallowneuroscientiststotake
rapid,preliminarylooksattheirdatapriortoperformingformalanalyses.These
methodsmaytakeadvantageofgraphicaldisplays,deeplearningtechniquesand
graphicalmodels119,120.
o Implementsolutionstothespikesorting,informationencoding,connectivityand
informationdecodingproblemsthatareneededforconfirmatorystatisticalanalyses
of100,000to1,000,000simultaneouslyrecordedneurons121.
o Developrealtimesignalprocessingalgorithmsforeachofthemajortypesof
neurosciencedatalistedinsection5e.

Multiscalelinkages
o EstablishthebiophysicalsourcesofthemajorbrainrhythmsthatarepresentinEEG
andMEGrecordings,andthemorelocalsourcesthatgiverisetotheLFPindifferent
brainregionsanddifferentcorticallayers122.
o Developaformalstatisticalinferenceframeworktoconductnetworkconnectivity
analysesfromdifferenttypesofneurosciencedatasuchasfMRI,EEG,LFPand
multiplesingleneuronrecordings123.
o Exploretheoreticalandstatisticalframeworksforfusinginformationacrossdifferent
experimentaltechniquesanddifferenttemporalandspatialscalesinneuroscience
experiments.
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o Developcomputationallyefficientsolutionstohighdimensionalinverseproblems,
withparticularattentiontotheinterpretationofEEGandMEGdatainhumans.
o Developtheoriesandmodelsofcollectiveneuronalactivityonspatialscalesthat
spanindividualsynapses,neurons,circuits,networksandsystems;developtheories
ofdynamicalactivitythatspantimescalesofsynapses,actionpotentials,network
activity(includingattractorsandpersistentactivity)andinternalcircuitstates
(includingneuropeptidesandneuromodulatorysystems).

IdentifyingGeneralPrinciples
o Developtheoreticalinsightsintohowcircuitdynamicsdependonthepropertiesof
singleneuronsandtheirconnections.Identifyconditionsforwhichinsightsfrom
smallcircuitsscaletolargercircuits.Determinewhichgeneralrulesofcircuit
functiondependonspecificbiologicaldetailsofneuronalandsynapsefunction.
o Higherorderflexiblebehavior:Developsystematictheoriesofhowinformationis
encodedinthechemicalandelectricalactivityofneuronsandglia,howtheseare
usedtodeterminebehavioronshorttimescales,andhowtheyareusedtoadapt,
refineandlearnbehaviorsonlongertimescales108.
o Developadetailedunderstandingofthecircuitandplasticitymechanismsthat
supportdifferentformsoflearning.
o Constructamechanisticunderstandingofhowmotoractsareinitiated,controlled,
sequencedandterminated.
o Propose,studyandvalidatemechanismsthatallowinformationtobegated,
switchedandtransmittedbetweenspecificbrainregions.
o Developmethodsfordetectingandclassifyinginternalbrainstates;relatethese
statesdownwardtoneuromodulatorymechanismsandupwardtomemory
formation,motivation,andinternalmodels.
o Decisionmaking:Relatecellularlevelneuronalactivitytobasiccognitiveprocesses
underlyingdecisions,includingdopaminesystems,rewardpredictionerror,and
planning124.
o Goaldirectedbehavior:Theoriesforhowinteractionswithinandbetweenlarge
neuralsystemsandbrainareasencompassinginputsfrommultiplesensory
modalities,internalstates,memories,goals,constraints,andpreferencesdrive
behaviorinfreelybehavinganimalsincludinghumans125.

AcceleratetheincorporationofTMCSperspectivesandtechniquesinneuroscience
departmentsandprograms
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o Deployadministrativesupplementstoexistingexperimentalgrantstosupportthree
tosixmonthexploratorycollaborationsbetweenTMCSandexperimental
laboratories.
o DevelopincentivesfordepartmentstohiretenuretrackTMCSassistantprofessors.
o Increasethequantitativecapabilitiesofgraduatestudentsandpostdocsin
neurosciencetrainingprogramsbytailoringindividualandinstitutionaltraining
grantstoincludetraininginstatisticsandcomputationalmethods.
o ProvidefundingforsummercoursesinTMCSdisciplinesrelevanttoneuroscience,
andforinnovativenewmethodsforconferringexpertise.
Longtermgoals(610years)
Developnewtechniquesforanalyzinglarge,complexdatasets
o Integratestatisticalandanalyticapproacheswithmodelsofneuralcircuitsbasedon
connectivitymapsandcelltypes.
o Extendthesolutionsforspikesorting,encoding,connectivity,anddecodingtodata
setslargerthan1,000,000simultaneouslyrecordedneurons,andintegratewith
connectomicdataandothertypesofdata.
o Developprincipledmethodsforrealtimefeedbackcontrolexperimentsto
manipulateandanalyzeneuralcircuitsusingnovelperturbationandrecording
techniques.Includerealtimeapplicationstoneuraldevicesandprostheticsin
humans.
Multiscalelinkages
o Establishagenericframeworkforfusinginformationacrossdifferentexperimental
techniques,anddifferenttemporalandspatialscalesinneuroscienceexperiments.
o MakecomputationofhighdimensionalinversesolutionsfromMRI,EEGandMEG
recordingsfeasibleinrealtime.
o Identifytheessentialelementsofwidelydistributed,timevaryingneuronal
processesbybridgingbetweendetailedrealisticmodelsandqualitativebehavioral
models.Definetheprinciplesgoverningthecomputationateachspatialand
temporalscalethatareimportantforunderstandingthebehaviorofthesystemasa
whole.
Identifygeneralprinciples

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o Establishtheoreticalapproachestounderstandthegeneralprinciplesthatapplyin
bothlargeandsmallcircuits.Ofparticularinterestwillbetheoreticalstudiesthat
shedlightonhowcircuitsinteract,whichwilleventuallyprovideinsightintohow
complexhumancognitionemergesfrominteractingbraincircuits.
AccelerateincorporationofTMCSperspectivesandtechniquesinneuroscience
o ContinueincentivesforhiringTMCSfacultyanddisseminationofnewcomputational
methodsforpostdoctoralandgraduatestudentsthroughcoursesathomeinstitutions,
summercourses,webbasedcourses,andothermechanisms.

III.6.ADVANCINGHUMANNEUROSCIENCE
6a.ScientificGoal:Developinnovativetechnologiestounderstandthehumanbrainand
treatitsdisorders;createandsupportintegratedhumanbrainresearchnetworks
6b.OverallObjective
EachgoaloftheBRAINInitiativehasanexplicitcomponentaddressinghumanbrainresearch,
andaccordingly,earliersectionsofthisreportaddresstechnologiestostudyhumancelltypes,
connectivity,largescaleactivity,functionalperturbation,andmodelsofbrainfunction.Beyond
thesetopics,however,therearescientific,experimental,andethicalissuesthatarespecificto
humanneuroscience,whetherfundamental,translational,orclinical.Clinicallyapproved
investigationaltechnologies,includingdevicesthataresurgicallyimplantedintothebrain,
provideauniqueresearchopportunitytoinvestigateneuralfunctionbystimulationor
recordingattheresolutionofcellsandcircuits.Researchinvolvinghumansubjects,however,
comeswithaspecialmandatetoensurethattheserareandvaluabledataarecollected
accordingtorigorousscientificstandards,curatedcarefully,andsharedamongsttheresearch
community.Specializedteamsofresearchersmustbeassembledandsupportedtoplanand
carryoutexperimentalstudiesinconcertwitheffectiveclinicaltreatmentprograms.
6c.Deliverables
1. Integratedteamsofclinicians,scientists,deviceengineers,patientcarespecialists,
regulatoryspecialists,andethicsspecialiststotakeadvantageofuniqueresearch
opportunitiesofferedbystudiesinwhichinformed,consentinghumansubjects
participate.Suchteamsmaybeassembledwithinasingleuniversityormedicalcenter,
ormaycompriseintegratedconsortiaacrossmultipleuniversitiesandmedicalcenters,
whichcouldfacilitatesharingofstandardizeddataandtraininginthisuniqueformof
research.
2. Astreamlinedpathfordeveloping,implementingandintegratinginnovativenew
technologiesforhumanneuroscienceresearch,throughcooperationofclinicaland
academicresearchteamsandprivatecompaniesinaprecompetitivespace.
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Technologieswouldincludeimplantabledeviceswithcombinedrecordingand
stimulationcapabilitiesthatbothadvanceclinicaldiagnosticortherapeuticapplications
andmaximizetheirscientificresearchvalue.Inthelongterm,advancesinelectrical,
optical,acoustic,geneticandothermodalitiesshouldbeintegratedinto
neurotechnologiesforhumanclinicalandresearchuse.
Amongthescientificquestionstobeaddressedbythisgoal:
Howdoesneuralactivityinspecificcircuitsrelatetotheconsciousexperienceofhumans
astheyperformacognitiveorbehavioraltask?
Whatneuralmechanismsunderlietheremarkablehumanabilitytorepresent
informationsymbolically(asinlanguage)andthenusethatinformationinnovel
situationsoutsidethecontextinwhichitwasoriginallylearned?
Whatneuralcircuitdynamicsenablementalmathematicalcalculations?

Whatpatternsofneuralactivityinwhichbrainstructurescorrespondtohuman
emotionalstates?Canwetreatemotionaldisordersbyapplyingneuromodulation
techniquestothesestructuresandcircuits?

Whatpatternsofneuralactivityinmotorareasofthebraincorrespondtospecificplans
tomovetheeyes,handorarmtowardparticulartargets?Canwedecodementalmotor
planswithsufficientspeedandaccuracytocontrolsupple,effectiveprostheticdevices
forparalyzedpatients?
6d.RationaleandPrinciples
SeealsoSectionII.6ofthisreport.
Certainquestionsaboutbrainfunctioncanonlybeansweredthroughstudyinghumans.Afew
examplesincludelanguage,higherordersymbolicmentaloperations,andindividualspecific
aspectsofcomplexbraindisorderslikeschizophreniaortraumaticbraininjury.Studiesof
humanbrainactivitypresentextraordinaryopportunitiesforbothclinicaladvancesand
research.Forexample,ourunderstandingofhowexperienceentrainsmemoryhasbeen
enhancedbyrecordingsinpeopleundergoingmonitoringpriortoepilepsysurgery126.
Similarly,aspartofanefforttorestorelostfunctionafterstroke,injury,orneurodegenerative
disease,researchershaveusedactivityrecordedwithinthenervoussystemofparalyzedpeople
todrivementalcontrolofcomputercursorsandroboticarms127.However,evenashuman
brainstimulationandrecordingincreasesinclinicalsettings,manyopportunitiespresentedby
thisvaluablepopulationofpeoplearemissedbecausetherearenoreadilyaccessible
mechanismstopreserveandsharethisdata.
Intherealmofbrainstimulation,therearelargepopulationsofpeoplewithimplanteddevices
usedforsensoryreplacementandneuromodulationapplications.Morethan200,000people
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havecochlearimplants.Studiesofsoundperceptionandlanguageinthesepeople,especially
thosewhoreceivethemforcongenitaldeafness,haveledtoinsightsintohumancognitionand
havealsoimprovedcochlearimplants128.Althoughtheynowrepresentasmallgroup,people
withstimulatingelectrodesintheeyetorestorevisionwillprovideagrowingopportunityto
studythehumanvisualsystemandcreatebetterdevices.Morethan100,000peopleare
implantedwithDBSsystemstotreatmotordisorderssuchasdystonia,essentialtremor,and
Parkinsonsdisease.Stimulatingsystemsarealsobeingusedinthespinalcordtotreatchronic
pain,andelectrodesarebeingplacedinmanydifferentbrainregionsforexperimental
treatmentofdisorderssuchasdepression,obsessivecompulsivedisorder,orcognitivedecline.
Theseindividualsprovideauniquesettingforresearcherstostudycircuitfunction,whilealso
learninghowstimulationcanovercomemovement,behavioralandcognitivedisorders.
Atthesametime,theabilitytorecordelectricalactivityatthecellularscaleinhumansis
expanding,providingauniqueopportunitytomakeessentialcrossscalelinksbetween
neuronalactivityandmoreglobalsignalsfromnoninvasiveimagingmethodslikefMRI.Both
cellularlevelandglobalsignalscanthenbelinkedtohumanbehavior,thoughtandemotion.
Mosthumanstudiesatthecellularlevelareperformedintraoperativelyforbrieftimes(acute
studies)orintermittentlyforafewweeksinassociationwithclinicallyindicatedinvasive
mapping(subacute).Morerecently,withtheadventofbraincomputerinterfaceresearch,
chronicallyimplantedelectrodearrayshavemadeitpossibletostudypopulationsofneurons
fordurationslongerthan5years.Thenumbersofpeopleengagedinresearchtrialsislikelyto
expandconsiderablyinthenextdecade.
Inmanycases,theindividualswhohavestimulationorrecordingdevicesarealsotreatedwith
drugs,providingopportunitiestoadvanceanunderstandingofpharmacologicalmechanismsas
well.
Theimportantopportunitytocarryoutresearchonhumanbrainfunctionwhileadvancingthe
clinicalcapabilitiesofemergingneurotechnologiescreatesspecialissuesforhumanresearch,
including:
Clinicalsupportnetworks:Ameanstoensuresupportoffundamentalhumanbrain
researchinclinicalsettingsandwithinclinicaltrials.
Training:Ensuringunderstandingofthespecialrequirementsforhumanresearch.
Traininganewgenerationofhumanneuroscientistswhoarerigorousresearchers,
compassionateclinicians,creativeengineers,andcompetentadministratorsofcomplex
scientificteams.
Datacaptureandsharing:Ameanstocapturehumandatainstandardizedformatsand
tocurateandsharethatdatawithintheframeworkofprotectingprivateinformation.
Effectivehumanneurotechnology:Ameanstoadvancethedevelopmentofsafe,but
innovativetechnologysuitableforresearchinhumanbrains.

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Ethics:Strongethicalframeworks,reviewandoversightofhumanresearch.

6e.Implementation
6ei.ClinicalSupportNetworks
Humanresearchusinginvasiverecordingsorimplanteddevicescanincludefundamental
neuroscience,translationalresearch,andappliedworktoevaluatesafetyandefficacyofnew
clinicaltechnologies.Bothinvestigationalandapprovedmedicaldevicesenablebasicresearch
thatcanbeperformedduringclinicaldiagnosticprocedures(e.g.epilepsymonitoring),in
clinicaltrialsettings(e.g.implantedinvestigationaldevices),orinconjunctionwithclinically
indicatedtherapies(e.g.deepbrainstimulation).However,muchofthisexceptionallyvaluable
humandataarenotcaptured,curatedormadeavailableforresearch.Achangeofculturein
neurosurgeryandachangeinsupportbyNIHcoulddramaticallyexpandourknowledgeof
humanbrainactivity.Itisdisappointingthatofthehundredsofpeoplewhoexperiencebrain
stimulationandrecordinginsurgery,onlyahandfularestudiedsystematically.
Therangeofissuesassociatedwiththisresearchrequiresintegratedresearchteams.Aclose
workingrelationshipbetweencliniciansandinvestigatorsisneededsothatrigorous
experimentscanbeperformedwithoutcompromisingclinicalcare.Theteamshouldinclude
engineerstokeepequipmentfunctionalforthelimitedtimeavailableforresearch,andmonitor
thesafeandeffectiveoperationofresearchlevelequipment.Efficientresearchrequiresclinical
trialmanagementbyprofessionallytrainedindividualswhomaintaincloseinteractionswith
institutionalandfederalregulatorybodiestoensureproperadherencetohumanresearch
requirements,safetymonitoring,andtimelydocumentationandreporting.Becausethis
researchcanprovideacriticalassessmentoftechnologybeingusedinhumans,theteammust
haveseamlessmechanismstocommunicateregularlywiththeFDAtoprovideongoing
feedback.
Supportingresearchindevicetrialsisparticularlychallenging.Pilotstageclinicaldevicetrials
performedinacademicsettingsshouldbedesignedandsupportedtopermithypothesisdriven
neurosciencewhilepursuingclinicalsafetyandorefficacygoals.Inthiscontext,fundamental
neurosciencecanonlybepursuedonasolidfoundationofcarefullydesigned,concurrently
performedclinicalresearchrequiringparticipantrecruitment,surgery,inpatienthospital
stays,deviceassessment,clinicaldatacollection,andsafetyandregulatorymonitoringby
specialistswithspecifictrainingintheseareas.Partnershipsbetweenresearchteamsand
industryareexceptionallyvaluablefortechnologydevelopment.Industryiswellversedin
controlleddesign,processmanagement,andregulatorycompliancerequiredofdevices,while
academicresearchershavedeepknowledgeaboutthesignificanceandmeaningofthedata.
Industryinputandcollaborationinresearchteamswillaccelerateprogressintranslating
technologytotheclinicalpopulationandprovidingprocessmanagementnecessarytogenerate
devicesthataremaximallyusefultothelargestpossiblepopulation.
6eii.HumanDataCapture,Curation,andSharing

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MakingdataavailabletotheresearchcommunityisageneralprincipleoftheBRAINinitiative
(SectionIII.8),butgathering,curating,anddisseminatinghumandataiscomplex.Evenwhere
humandataexists,inmanyinstancesitisnotavailableforresearchuse.Straightforward
changesinmechanisms,supportedbytheNIH,couldchangethisreality.Forexample,
intraoperativebrainfunctionmappinginneurosurgeryshould,wherepossible,bestoredand
fullyannotatedandmadeavailabletoresearchers.Humanswithimplantedsensorsor
stimulatorsshould,whereverpossible,bestudiedsystematicallywithformalcollectionof
information.Forexample,whendeepbrainstimulationprotocolsareadjustedinParkisonian
patients,systematicinformationshouldbecollectedontheeffectsondiseasestate,cognitive
ability,andmood.Achievingdatacollectioninabroadrangeofsettingsinvolvingclinicalbrain
recordingandstimulationwillhavecosts,whichshouldberecognizedandsupported.Patient
advocacyorganizationsshouldbemobilizedtoencourageparticipationoftheirmemberbasein
researchstudies.Patientgroupsarealsoapowerfulforcetoencouragedatacollectionand
datasharing.
Thecomplexityandexpenseofexperimentaltherapiesmeansthatmostneurotechnology
devicestudiesincludejustasmallnumberofparticipants,andsimilartrialsmaybeconducted
atmultiplesites.Whereverpossible,thepowerofthesestudiesshouldbeincreasedbymaking
anearlyinvestmentindatastandardsandmechanismstocollect,storeandsharedataamong
differentgroups,beginningwithpilottrialsthattestandevaluatedifferentcollaborative
structures.Onesuccessfulexampleistheinternationalepilepsyelectrophysiologyportal
(IEEG),aNIHfundedcollaborativeinitiativetosharedata,tools,andexpertisebetween
researchers;thisgrouptranslatesrecordingsmadeusingdifferentsitesandinstrumentsintoa
commondataframeworktofacilitatecomparisonandcollaboration.Severalotherdata
collectioninitiativesarecurrentlyinoperation;theyneedamechanismtolinkthemseamlessly,
makeusercommunitiesawareoftheirexistenceandcapabilities,andmostimportantly,to
assessandcommunicatetheireffectiveness.
Computationalspecialists,asdescribedinSectionIII.5,willbeneededtoensureproper
collectionandtimelyprocessingofhumanneurosciencedata.Standardizationchallenges
abound.Forexample,studiesofseizurepatientswithsubcranialsensorsandstimulatorsvary
byclinicalspecialties,referralpatterns,thepopulationsizeofthemedicalcenter,andthe
particulartechnologyusedtoobtainthedata.Humansalsoposeaparticularchallengeinthat
theparticipantsalmostalwayshaveanexistingdiseaseprocess(e.g.,Parkinsons,ALS)orinjury
(stroke,spinalcorddamage)thatmustbeconsideredinexperimentsrelatedtonormal
function.Clinicalassessmentsofthenatureandformofthedisordershouldbestandardizedto
allowcrosspatientandcrosslaboratorycomparisonsanddatapooling.Itwouldbeimmensely
valuabletoidentifywaystomergeall(deidentified)clinicalandresearchdatacollectedfrom
humansintoasingleresearchrecord(e.g.genetics,recordings,imagingdata).
6eiii.AdvancingEffectiveTechnologyforHumans
Whenadeviceisimplantedorusedinahuman,itisessentialthatthedevicefunctions
effectivelyandsafely,andwillmaximizethequalityandquantityofthedatacollected.FDA
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approveddeepbrainstimulationelectrodes,intraoperativerecordingandstimulating
electrodes,andsubacutesurfacegridsanddepthelectrodesarecommerciallyavailable.
However,currenttechnologiesdonotmeettheclinicalandresearchneedsforhighdensity
samplingandstimulationandbroadspatialcoverage,andarenotproventobereliableor
stableoverlongdurations(SectionIII.3).Specialissuesofmaterialsdevelopment,device
longevity,andsafetymustbeconsideredbeforepreclinicalinnovationsfromanimalstudiescan
beappliedtohumans;implantfailures,shortdevicelifetimes,andsignalinstabilityare
unacceptableforhumandevices.Solvingtheseproblemswillrequireacloseworking
relationshipbetweenengineers,cliniciansandneuroscientiststoovercomethesechallenges.
Untilnow,mostdevicesusedinhumanshavebeendesignedforasinglegoalforexample,
eitherstimulationorrecording.Themostdramaticimprovementthatcouldbemadefor
implanteddeviceswouldbetocombinemultiplemeasurementandmanipulationcapabilitiesin
asingledevice.Withtechnologicalminiaturizationandcostreduction,itshouldbepossibleto
buildsophisticatednewdevices,collectdataabouttheiroperation,andprovideinvestigational
accesstothebrainwithoutcompromisingthesafetyorefficacy.Verynewdevicescombine
DBSwithsensorsthatallowEEGscalemeasurementsofchangesinbrainactivitythatresult
frommacroscalestimulation.Incombinationwithcarefulclinicalassessment,suchhybrid
deviceshavegreatpotentialtohelpusunderstandexactlyhowstimulatingcurrentsinteract
withhumanbraintissue,whyoutcomesvaryfrompatienttopatient,andhowwecanachieve
moreconsistenttherapeuticresults.NewBRAINsupportedtechnologiescreatedforresearch
inanimals(SectionsIII.3,III.4)willinspirenextgenerationdevicesforhumanbrainmonitoring
andtherapiesusingoptical,acousticandmagneticmodalities.
6eiv.ConnectingtoBrainStructure
Humanbraintissueisaprecious,limitedresource,whetherfromnormalordiseasedbrains,
frompostmortemtissuesorbiopsies.Brainbanksarecostlytomaintainandrequireskilled
technicaloversight.Thoughtfulimprovementscouldincreasethevalueoftheseresources.For
example,itwouldbeinvaluabletoexaminehumanbrainstructurepostmortemwithmeso
scaleconnectomictechniquesinindividualswhohadbeenstudiedpreviouslywithmacroscale
diffusionandfMRItechniques(SectionIII.2).
NIHshouldconsiderhowbesttobuildinfrastructurethatprovidesanintegratedrecordof
functionalandstructuraldatafromhumanbrains.Movementinthisdirectionisalready
happening,asNIHhasrecentlyfundedtheNeuroBioBank(https://neurobiobank.nih.gov/),a
federatednetworkofbrainandtissuerepositoriesthatcollects,evaluates,andstoreshuman
brainsandmakesthemavailabletoqualifiedresearchers.
6ev.HumanResearchEthics
Whiletherearewellestablishedlawsandproceduresforhumanresearch,studiesinhumans
thatinvolvesensingorstimulatingthebrainrequireongoingoversight.Thisneedisbestserved
byacontinualdialogbetweentheresearchersandethicaloversightbodies.Ethicscommittees
mustincludestrongrepresentationfrommemberswhoareinformedinclinicalandbasic
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neuroscience,andwhoareawareofthehistoryofbrainmanipulationsandrecordings.
Studentsandscientificstaffmustbetrainedinethicalhumanresearch;meetingsdealingwith
humanbrainresearchmustaddressethicalconsiderations.Ethicistsshouldalsobeexposedto
theuniquenatureandpotentialofhumanneurotechnology.
6f.Mechanisms
Research:NIHcouldleadanewscientificerainhumanbrainresearchbysupportingintegrated
teamsofclinicians,scientists,deviceengineers,patientcarespecialists,regulatoryspecialists,
andethicsspecialiststotakeadvantageofuniqueresearchopportunitiesofferedbybrain
stimulationandrecordinginhumanswithclinicallyindicateddeviceswhohavevoluntarily
giveninformedconsenttoparticipateinresearch.TheNIHClinicalandTranslationalScience
Awards(CTSAs)areonemechanismthatcouldprovideresourcesandincentivesforthese
interdisciplinarystudies.Newmechanismscouldbedevelopedthatpromoteincreased
engagementofneurosurgeons,neurologists,neuroradiologists,andanesthesiologistswith
scientists,andsupportthecostsassociatedwithperformingresearchinthecontextofclinical
activity.Aclinicaltrialnetworkfordeviceswouldbeavaluablemechanismtocoordinatetrial
design,datacollection,sharing,andanalysis.Inaddition,itcouldaddtotheefficiencyof
humandevicetrials,acceleratingboththeaccumulationofknowledgeandthetranslationof
devicestoendusers.Engagementofhumansthemselvesasvoluntary,informedparticipants
isofprimaryimportance.
Training:Humanresearchrequiresspecializedknowledgeandtrainingintheabilitytoworkin
interdisciplinaryteams,knowledgeofIRBandcomplianceprocesses,andattentiontodata
security,datahandling,andconfidentiality.Researchaimedatcreatingnewhumandevices
anddrugsmusttakeaccountofFDAprocessesandprocedures,andultimatelymustrespondto
policiesforreimbursement(e.g.CentersforMedicareandMedicaidServicespolicies),because
aproductthatcannotbepaidforcannotbeused.Ethicstrainingisessential.NIHshould
supporttrainingprogramsfortheentireenterpriseofhumanresearch,bothfundamentaland
applied(seealsoSectionIII.8).Ideally,thistrainingcouldbeincorporatedintoclinicaltrial
networkstohelpensureuniformityandcompliance.
6g.TimelinesandMilestones
Shorttermgoals(15years)
Technology:Establishasupportpathfordevelopinginnovativetoolstranslatableto
humanapplications(coordinatedwithneurotechnologyadvancesinanimals);pipeline
todevelopoveryears35.
TrialNetworks:Establishpilotprojectsforcollaborativehumanneurosciencetrial
networks,thenexpandtheprogramwithinCTSAsorotherentitiestoformlargescale
clinicaltrialnetworkstofacilitatebasicresearchanddevicedevelopment.
Training:Establishtraininggrantsforhumanresearch,ethics.
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 Humandatacapture:Supporthumandatasharingforelectrophysiologicaland
structuralstudies,andcommonplatformdevelopmentforelectrophysiologicaland
clinicaldata.
Ethics:Neuroscience/ethicstrainingprograms,meetingsandinteractionstoestablish
guidelinesandprinciplesforhumanneuroscienceresearch.
Longtermgoals(612years)
Technology:Applicationofhighresolutionrecordingandstimulationforhuman
researchandforabroadrangeofclinicalapplications;supportongoingpipelineofnew
technologyinnovationinvolvingelectrical,optical,acousticandmagneticmodalities.
TrialNetworks:Establishinternationalcollaborativenetworksbasedonthemost
successfulwithinUnitedStatesmodelfromyears15;generalizeUnitedStatesmodelto
manymajorclinicalresearchinstitutions.
Training:Corenetworksprovidetrainingtoadditionalresearchersandphysiciansin
humanneuroscienceresearchrequirements;disseminationtootherinstitutions.
Humandatacapture:Routinecaptureofdatainsurgicalsettingsanddeviceuse;
curatedhumanneurophysiologicaldataavailabletoresearchcommunity.Integrate
knowledgewithanimaldata.
Structure/Function:Correlationofhumancircuits,electrophysiologyandanatomy.
Ethics:Allresearchcarriedoutandmonitoredunderagreeduponethicalprinciplesfor
humanneuralinterfaces.

III.7.FROMBRAININITIATIVETOTHEBRAIN
7a.ScientificGoal:Integratingnewtechnologicalandconceptualapproachesproducedin
goals#16todiscoverhowdynamicpatternsofneuralactivityaretransformedinto
cognition,emotion,perception,andactioninhealthanddisease
7b.OverallObjective
Thebrainisthemostcomplexbiologicalsystemweknowofinnature.Unlockingitsmysteries
willrequireasystematiceffortthatcoordinatesandfocusesalltechnologiesdevelopedunder
theBRAINInitiative.Tomaximizetheirabilitytoanswercriticalquestionsaboutbrainfunction,
thenewtechnologiesmustbecombinedinanintegratedwayanddevelopedusingprinciplesof
systemsengineering.Theoverallobjectiveistodevelopandusetheseintegratedplatformsto
provideacomprehensive,mechanisticunderstandingofneuralcircuitsandsystems.Wemust
understandhowcircuitsgiverisetodynamicandintegratedpatternsofbrainactivity,andhow
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theseactivitypatternscontributetonormalandabnormalbrainfunctions.Ourexpectationis
thatthisapproachwillanswerthedeepest,mostdifficultquestionsabouthowthebrainworks,
providingthebasisforoptimizingthehealthofthenormalbrainandinspiringnoveltherapies
forbraindisorders.
7c.Deliverables
1.) Integratedmethodsandinstrumentationthatcombineactivitymeasurements,
perturbation,behavioralanalysis,celltypeinformation,connectionmaps,andtheory.
Integratedexperimentationrequirescarefulcoordinationandcoevolutionofindividual
technologies,butwillyieldgreatbenefits.Whenmature,thesetechnologiesshouldbe
disseminatedwidelyinbasicandclinicalneurosciencesettings.
2.) Applicationoffullyintegratedsystemstodiscoverbrainprocessesunderlyingcognition,
emotion,perception,decisionmaking,andmemory;answerstofundamentalquestions
abouthowthebrainworks,andstartingpointsfornewtherapeuticcapabilities.By
analyzingneuralcodinganddynamicsinrelevantbrainregionsandcellpopulations,in
thecontextofconnectivitydiagrams,behavioralanalysis,andsophisticatedtheoretical
andquantitativetools,wewillacquiremechanisticandconceptualinsightintothe
relationshipsbetweenneuralsystemsandmentalfunctionsinhealthanddisease.
7d.RationaleandPrinciples
AguidingprincipleoftheBRAINInitiativeisthateachnewtechnology,beitsensors,
connectomicanalysis,neuralrecordingorperturbation,shouldbedevelopedwiththegoalof
answeringfundamentalquestionsinbrainfunction.Insomecases,particularlyintheearly
phasesoftheinitiative,agiventechnologywillbeappliedinisolationtoprovideimportant
knowledge.Forexample,newmethodsofcellidentificationcouldproduceanunderstandingof
allcelltypesintheneocortex,ornewconnectomicsmethodscouldyieldtheprojectomeofthe
humanbrain.However,manyofthemostexcitingandpowerfulapplicationswillcomefrom
combiningthenewtechnologiesintoanintegratedwhole,agoalwehavepointedtoineach
precedingsection.
Handinhandwiththesenewcombinationsofexperimentalmethodswillcomeintegrated
workfromtheory,modelingandstatisticsthatproviderigortoobservations,newmethodsof
visualizationandunderstandingofthedata,and,mostimportantly,newconceptual
frameworksforinterpretationofthedata(SectionIII.5).Thesenewconceptualframeworks
willgeneratetestablehypothesesframedintermsofmeasurableparametersthatinturnwill
stimulatenewexperimentalwork.Whenverified,thesehypothesesandtheorieswillprovide
themechanisticunderstandingofneuralcircuitfunctionthatistheprincipalgoalofBRAIN.
SuccessfulintegrationofneurosciencetechnologiesintheBRAINInitiativeshouldemphasizea
systemsengineeringapproach,inwhichoneoptimizesthecollectiveperformanceofthefinal
system,ratherthanoptimizingindividualcomponents129.Forexample,asystemsengineering
approachtodevelopingfluorescentindicatorsofneuralactivityshouldfocusnotonlyonthe
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propertiesoftheindicatormoleculebutalsoonparameterssuchaswavelengthcompatibility
withotheropticalsensors,optogeneticprobes,detectorsorilluminationsources,orrobustness
tofixationprocessesusedinpostmortemanalyses.Thiswouldbeimportantwhencombining
targetedrecordingwithposthocconnectomicanalysis.Similarly,designersofnewlasers,
lensesordetectorsfordeeptissueimagingshouldconsiderthecapabilitiesofimportant
molecularsensorsandprobes.
Achallengeinthedesignofintegratedsystemsariseswhenmultiplecomponenttechnologies
areadvancinginparallel.Ongoingprogressinlasers,microscopes,optogeneticprobesand
opticalindicatorsshouldbecoordinatedacrossthesedomains.Coordinationbetweenteams
workingincomplementaryareascanhelptechnologiescoevolvesuccessfully.Ingeneral,
integrateddesignoftenrequiresmultipledomainsofexpertiseworkingtogether,andforthis
reason,technologyintegrationwillrequirefundingmechanismsthatencouragecollaborative
teamsofinvestigators.
7e.ImplementationandMechanisms
StartingintheearlystagesoftheBRAINinitiative,andprogressingsteadilyoveritsduration,we
expectagrowthintheintegrationandcombinationofnewtechnologies.Thecombinationswill
firstbepairwise(e.g.recordingwithstimulation),butwilllateroccurwithincreasing
sophisticationascombinationsofmanyorallofthetechnologies.Weanticipatethat
integrationwillalmostalwaysinvolveconcomitantdevelopmentofbridgetechnologiesthatgo
beyondthedevelopmentofeachcomponenttechnology.Forexample,performing
connectomicanalysisafterlargescalerecordingrequiresaccuratemethods(i.e.fiducialmarks)
thatcoregisterrecordedcellswithanatomicallyidentifiedcells.Similarly,thecombinationof
largescaleopticalrecordingwithpatternedopticalstimulationrequiresnewformsof
integratedinstrumentationthatcanbeusedinbehavingsubjects,andthedevelopmentof
molecularsensorsthatallowindependenttargetingandspectralseparation.Thuscontinued
technologydevelopmentwillbeintrinsicallylinkedtoapplicationinthemiddlestagesofthe
BRAINInitiativeascombinationsoftechnologybegintoemerge.Theapplicationofintegrative
technologiestospecificquestionbasedprojectswillgrowoverthelateryearsoftheBRAIN
Initiative.
CollaborativeConsortia:Weanticipatethatintegratedconsortiacombiningseveralapproaches
willcometogetherasgroupsofBRAINInitiativeresearchersfocusonansweringspecific
questionsinneuroscience.Inanidealconsortium,weimagineexpertiseandintegrated
instrumentationinquantitativeanalysisofbehavior,largescaleneuralrecording,cell
identificationandtargeting,connectomicandstructuralanalysis,perturbation/stimulation
technology,statisticalanalysisofhighdimensionaldata,andtheoreticalmodelingand
simulation.Groupsofresearcherswithsharedinterestsinthesameneuralcircuitoranimal
modelwillbenefitfromintegratedapproachesthatcreatestandardizedtechnologyplatforms
forneuroscienceexperimentation.
Thisbreadthofexpertiseisdifficultorimpossibletoachieveinsinglelab,butcanbedeveloped
inselforganizedconsortia.Althoughsomeofthisworkwillhappenthroughpartnershipswith
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foundationsandprivateinstitutesthathavebroadinhouseexpertise(e.g.themousevisual
cortexprojectatAllenInstituteforBrainScience130,andflyworkatHHMIJaneliaFarm
ResearchCampus53,131),mechanismsshouldbedevelopedthatencourageteamsof
investigatorsatacademicresearchcenterstoorganizearoundspecificresearchprojects.A
teammightbelocatedatanindividualinstitution,oratasetoflabsdistributedacrossmultiple
locations.
Onceintegratedtechnologiesaremature,appropriatemechanismsformaximizingtheirimpact
mayincludefundingstateoftheartinstrumentationfacilities,accessibletoresearchersfrom
acrossthecountry(SectionIII.8b).
7f.TimelinesandMilestones
Examplesofintegratedtechnologies(years15)
Geneticaccesstocelltypescombinedwithopticalstimulationandopticalorelectrical
recording.Recordingscanbetargetedtowardspecificcelltypesthathavebeen
geneticallytaggedaccordingtotheirneurotransmitters,anatomicalconnections,or
morphologicalcharacteristics.
Geneticaccesscombinedwithconnectomics.Forexample,differentiallabelingofcell
typescombinedwithlightmicroscopeorEMconnectomicswillprovideconnectivity
statisticsofindividualcellclasses.
Quantitativebehavioralanalysisintegratedwithlargescalerecordingandfunctional
perturbationinthecontextofanatomicallyorgeneticallycharacterizedcelltypes.The
neuralmechanismsunderlyingasophisticatedbehavioraltaskcanbecastintermsof
circuitfunction:cellidentities,inputs,projections,andneuromodulatoryinfluences.
Simultaneousopticallargescalerecordingandopticalstimulation:replayofnatural
activitypatternsfirstmeasuredwithrecordingtechniquesduringcontrolledbehavior.
Forexample,thisapproachcouldtesttheideathatspecificneuralactivitysequences
encodeelapsedtimeinepisodicmemory.
Posthocconnectomicsofaneuralcircuitfollowinglargescalerecording.Recordings
alonetypicallypermitmultiplemechanisticaccountsoftheobservedactivitypatterns.
Posthocreconstructionoftheunderlyingcircuitswillprovideessentialinformationfor
identifyingtheactualmechanismsofneuralcodinganddynamics.Forexample,this
combinationoftechnologiescantesttheideathatpersistentneuralactivityinshort
termmemory(likethememoryofeyepositionintheoculomotorintegrator)is
producedbyarecurrentconnectivityinthenetwork.

Advancedopticalhelmetsforinterrogatingbraintissueinfreelybehavinganimals,
miniaturizedtobewornduringactivebehavior,integratingmultiplecolorchannelsfor

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recordingandmanipulatingneuralactivity,advancedsignalprocessingcapabilities,and
wirelessconnectivity.
Applyingthesemethodstofundamentalquestionsaboutthehealthybrainandbraindisorders
(years110)
IntegratedexperimentationliesattheheartoftheBRAINInitiative.Applicationofcombined
technologieswillbefarmorepowerfulthanapplicationofanynewtechnologyalone,andthe
realpayoffofBRAINwillcomeasweapplythesepowerfulintegratedtechnologiestoaddress
fundamentalproblemsofbrainfunctioninhealthanddisease.Thusweenvisionrelatively
modestfundingforintegrated,collaborativeexperimentationinyears15oftheBRAIN
Initiativethatwillincreasesubstantiallyinyears610.Examplesofspecificquestionstobe
addressedareprovidedintheConclusions(SectionIII.10)ofthisreport.

III.8.SUPPORTINGTHECOREPRINCIPLESOFTHEBRAININITIATIVE
InadditiontothescientificgoalsoftheBRAINInitiative,theworkinggroupidentifiedcore
principlesthatshouldapplytoresearchconductedinthisprogram.Theseare:
1. Pursuehumanstudiesandnonhumanmodelsinparallel.
2. Crossboundariesininterdisciplinarycollaborations.
3. Integratespatialandtemporalscales.
4. Establishplatformsforpreservingandsharingdata.
5. Validateanddisseminatetechnology.
6. Considerethicalimplicationsofneuroscienceresearch.
7. CreatemechanismstoensureaccountabilitytotheNIH,thetaxpayer,andthe
communityofbasic,translational,andclinicalneuroscientists.
Principles13areexplicitlyembeddedwithineachindividualgoaldescribedinthisReport.For
example,eachofthescientificgoalsdescribedinSectionsIII.1 III.5andSectionIII.7includes
bothresearchinhumansandresearchinnonhumananimals(Principle1)withtherecognition
thatthesetwostreamsofresearchwillcomplement,challenge,andcompleteeachother.
Similarly,interdisciplinarityandintegrationacrossscales(Principles2and3)areincludedinall
goals,andareattheheartofSectionIII.7.
Technologyvalidation(Principle5)shouldalsobeembeddedwithineachindividualgoal.In
overview,theBRAINInitiativeshouldsupportmaturationoftechnologiesthathavealready
achievedproofofprinciple,buthavepromiseforfurtherdevelopment.Metricsofvalueduring
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thisphaseofmaturationandvalidationincludeeffectiveness,robustness,practicality,
applicabilitytoawiderangeofsystems,andminimizingcost.Eachnewtechnologyshouldbe
rigorouslycomparedtoothertechnologiesusingthesemetricsduringtheprocessofvalidation,
withtherecognitionthatthesearenothardandfastrules.Forexample,insomecasesa
particularapproachwillhavegreatvalueinasingleexperimentalanimal,andshouldbe
pursuedevenifitdoesnotapplyacrossmanyspecies.Theprocessofvalidationshould
emphasizeiterativecommunicationbetweentooldevelopersandexperimentalistsinbiological
systems.
AspectsofPrinciples47,however,arenoteasilysubsumedwithinaparticulargoalandwill
requirededicatedresources;wethereforediscussthemhere.Aninfrastructurefordata
sharing(Principle4)willcontributetoeachgoaloftheBRAINInitiative,andshouldbe
developedwithallgoalsinmind.DisseminationofnewtechnologydevelopedundertheBRAIN
Initiative(Principle5)willcontributetosomegoalsmorethanothers,butatthispointwe
cannotforeseewhereitseventualcostswillbeconcentrated.Wethereforepresentamore
generaldiscussionoftechnologydissemination.Ethicalconcerns(Principle6)aresocentralto
humansubjectsresearchthattheyarediscussedspecificallyinSectionIII.6;hereweconsider
broaderethicalissuesthatapplyacrosstheBRAINInitiative.Finally,accountabilityisaprinciple
towhichweallsubscribe,butwedonotalwaysstateitexplicitly(Principle7).Itisan
appropriatetopiconwhichtoendthisreport.

8a.Principle:Createandsupportaninfrastructureforpreservingandsharingdata
8ai.OverallObjective
Acceleratescientificprogressbyestablishingplatformsforsharingdata(SectionII.8)anddata
analysistools.Makeexpensive,hardwondatasetscollectedundertheBRAINInitiative
availabletoalargecommunityofresearchers.
8aii.Deliverables
1. Integratedrepositoriesfordatasetsanddataanalysistools,withanemphasisonuser
accessibilityandexpertcuration.
2. Aninfrastructureforopensharingofarchivaldataandtoolsfordataanalysisthat
improvereproducibilityofpublishedresults,makesnewanalysespossible,and
facilitatescomparisonstodatafromfutureexperiments.
8aiii.Rationale
TheBRAINInitiativewillproducelargedatasetsthatshouldbedesignedandcollectedwiththe
goalofwidespreaddissemination.Goodexamplesofaccessible,welldesigneddatasharing
platformsinneuroscienceincludetheAllenBrainAtlasandtheHumanConnectomeProject.
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Morebroadly,theNationalCenterforBiotechnologyInformation(NCBI)andtheProtein
DataBank(PDB)aregoldstandardexamplesingenomicsandstructuralbiology,respectively.
TheBRAINInitiativewillfacesubstantialchallengesinfacilitatingdatasharing,including:
BRAINdatawillbeheterogeneousinnature,includinganatomicalandconnectomic
data,physiologicalrecordingsofdifferentkinds(e.g.electrical,optical,andfMRI
obtainedunderdifferentconditionsindifferentformats)andgeneticinformation;new
kindsofdatabaseswillbeneeded.
Experimentalprotocolsandreagentsvarywidelybetweenlabs,presentingachallenge
fordatastandardization.
Datapreparation,annotation,andmetadatacollectionwillhaveassociatedcoststhat
requirefinancialsupport.
Anatomicalnamesforbrainareasandstructuresareofteninconsistentbetweenspecies
andlabs132,andwillneedtranslationintocommonframeworks.
Privacyisaconcernforsharinghumandata.
Despitethesedifficulties,itisimportantthatpreparationsfordatasharingbeginassoonas
possible,sinceamajordataplatformforBRAINislikelytotakeseveralyearstoplanandbuild.
Indeed,experienceingenomicssuggeststhatthedepositionofdataincommondataplatforms
willrevealwhichofthechallengeslistedabove(ornotyetconsidered)aremostserious.
ThesegeneralguidelinesshouldhelptospeedthedevelopmentofdatasharingfortheBRAIN
Initiative:
Standardsfordataformats,metadataandnomenclatureshouldbeestablishedthrough
consensusinvolvingallmajorstakeholders.
Computerprogramsfordatapreprocessingandanalysisshouldroutinelybeprovided
alongwiththedatasothatpublishedresultscanbereplicatedand,ifnecessary,re
evaluated.
Policiesfordepositinganddisseminatingdataandprogramsshouldbeestablished,
includingwhohasaccessandunderwhatconditions.
Dataplatformsshouldmakeiteasyforresearcherstostandardizetheirdataandmakeit
public,andeasyforotherresearcherstoaccess,analyze,andvisualizethedata.
Expertcurationandotherresourceswillbeneededfordatadeposition,access,and
updating.Thesewillhaveassociatedcoststhatshouldbesupported.

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 Analysistoolsshouldbedevelopedtointegrateacrossdatasetsandspandifferent
typesofdata.Likegenomeanalysistools,theseshouldrunontheserversthatmaintain
thedata,sincesomedatasetswillbetoolargetodownload.
Welldesigneddataplatformswilldirectlybenefitresearchinindividuallabs,providingan
incentivefortheiruse.EvenwithoutaBRAINInitiative,thesizeandcomplexityofemerging
datasetsmakeitdifficultforindividuallabstoanalyzeandbackuptheirdata.The
developmentofwelldesigneddataplatformscanprovideconvenientsolutionswithinthelab
astheirfirstuse.Atthenextstage,theplatformswillmakeiteasierforlabstocollaboratewith
otherresearchersanddatascientists.Bydesigningplatformswithdifferentlevelsof
permissionandagreementsondatause,theseinlabresourcescanbeseamlesslyexpanded
intoshareddataresourcesatappropriatetimesandlevels.
Thecallfordatasharingexpressedhereisabottomupmandatefrommuchoftheresearch
community.Forexample,itwasstronglyvoicedbytheresearcherswhoparticipatedinour
workshoponhumanneuroscienceinthesummerof2013.Thisgrouphasalreadybenefited
fromthesharingoflargebrainimagingdatasetsgeneratedbytheHumanConnectomeProject,
andseesitsfuturepotential.
Thequestionofwhichdataareshared,when,andhowcreditisassigned,shouldbeanswered
byNIHandBRAINInitiativeparticipants.Experiencefromotherfieldssuchasgenomics
suggeststhatdatashouldbesharednolaterthanthedateoffirstpublication;forresource
projects,datashouldbesharedonaregular(e.g.quarterly)schedulepriortopublication.
Communityrecognitioncanbeconferredbycitingdepositeddata;newjournalsarebeing
foundedtopublishandenablecitationofdatasets(http://www.nature.com/scientificdata/).
Neurosciencecanlearnnotonlyfromgenomicsbutfromotherareasofsciencesuchas
astronomyandparticlephysicswheretheseissueshavebeenresolved.Halfofthearticles
publishedfromtheHubbleSpaceTelescopearebasedonwellcuratedarchivaldata,not
includingtheoriginalteamthatdesigneddatacollection133.
Inadditiontosharingofdata,perse,researchcouldbespeededinmanylabsthrough
development,validationanddisseminationofgenerallyusefulsoftwaretoolsfordataanalysis.
ExamplesofhighimpactsoftwaretoolsincludeBLAST,developedattheNationalCenterfor
BiotechnologyInformationforcomparingbiologicalsequenceinformation;ImageJ,developed
atNIH,asuccessfulopensourceprogramforgeneralimageprocessing;andtheInsight
SegmentationandRegistrationToolkit(ITK),developedwithNIHsupport,anopensource
imagesegmentationandregistrationprogramthatfacilitatedthehighsuccessfulVisibleHuman
Project.Tomaximizetheirutility,softwaretoolsmustbedesignedwithcarefulconsideration
ofbothscientificneedsandlongtermsustainability.VirtuallyallmajorgoalsoftheBRAIN
Initiativeresearchcouldbenefitgreatlyfromdevelopmentofrobust,widelysharedsoftware
tools.
Mechanismsforsharing,preservationandanalysisofdatafortheBRAINInitiativemaybe
developedinpartnershipwithotherNIHprogramssuchastheNCBIandtheBigDatato
Knowledge(BD2K)Initiative,andwouldalsorepresentanopportunityforinteractionwith
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otherorganizationswhohaveexpertiseinthisarea,suchasInternationalNeuroinformatics
CoordinatingFacility,theNeuroscienceInformationFramework,andtheAllenInstitutefor
BrainScience.
8aiv.TimelinesandMilestones
13years:Identifydatatypesandestablishstandardsforeachdatatype.
35years:Createdatasharingplatformsformajordatatypes.
35years:Supportdevelopmentofdataanalysissoftwaretoolsthatarewellvalidatedand
valuabletolargesegmentsofthecommunity.
510years:Scaleupdatabases,maintainsoftware,curatedata,supportcontinued
developmentofanalysistools.

8b.Principle:Disseminationandtraininginnewtechnologies
8bi.OverallObjective
AsdiscussedinSectionII.8,itisaprincipleoftheBRAINInitiativethatnewlydeveloped
technologiesandreagentsshouldbemadebroadlyavailabletohavethegreatestpossible
reachandimpact.Thisprincipleismostimportantforthecomplexintegratedtechnologies
(SectionIII.7),butappliestoindividualtechnologiesaswell.
8bii.Deliverables
1. Mechanismstoenablesharingandwidespreaddisseminationofbiologicalreagents,
instruments,andcomputationaltoolsdevelopedundertheBRAINInitiative,to
maximizetheirimpactacrossbasic,translational,andclinicalneuroscience.
2. Practicalcoursesintheuseofnewneurosciencetechnologiesthatallowresearchersto
applythemskillfullyandrigorously.
8biii.Rationale
Disseminationoftechnologywillhavespecialneedsandcoststhatarenotincludedinthe
individualgoals.WeexpecttheBRAINInitiativetodevelopnewinstrumentation,possibly
includingnewkindsofmicroscopes;newclosedloopelectricalrecording/stimulatingsystems
fornonhumananimalsandhumans;entirelynewinstrumentationappropriatefor(for
example)useofnanotechnologyinthebrain;andnewintegratedinstrumentsystemsthat
enablestudiesofneuronalactivity,celltype,connectivity,perturbation,andbehaviorwithin
thesameindividual.WeexpecttheBRAINInitiativetodevelopnewbiologicalreagents,
possiblyincludinggeneticallymodifiedstrainsofrodents,fish,invertebrates,andnonhuman
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primates;recombinantvirusestargetedtodifferentbraincelltypesindifferentspecies;
geneticallyencodedindicatorsofdifferentformsofneuralactivity;andgenetictoolsfor
modulatingneuronalactivity.ItisaprinciplethatsuchreagentsdevelopedundertheBRAIN
Initiativebeaccessibletothebroadestpossiblecommunityofscientists,whoshouldalsobe
trainedintheiruse.
8biv.ImplementationandMechanisms
Forbiologicalreagents,appropriatemechanismsofsharinghavebeendeveloped,butmay
needtobeexpandedandfurthersupportedbyBRAINInitiativesupportofvirologycentersand
geneticstockcenters,forexample.
Forinstrumentation,advancescanbepromotedbythoughtfuldevelopmentofdissemination
policiesbythescientificcommunity,aswellasspecializedsupportmechanismsandprivate
publicpartnerships.Forexample,forcomplexinstrumentation,commercializationcouldbe
supportedthroughtheSmallBusinessInnovativeResearch(SBIR)programorother
partnerships.
SomenewBRAINtechnologiesmaynotbeaffordablebyindividuallabsorsmallconsortia,and
thereuniqueissueswillarise.Themultiphotonmicroscopes,superresolutionmicroscopes,
multielectrodearrays,multibeamelectronmicroscopes,andvirtualrealitybehavioral
chambersalreadyinuseinneuroscienceareexpensive,andintegratedsystemswillbemoreso.
Oncetechnologiesaremature,appropriatemechanismsformaximizingtheirimpactmay
includefundingstateoftheartinstrumentationfacilities,perhapsatafewlocationsat
universitiesorresearchinstitutes,thatcouldbeusedbyresearchersfromacrossthecountry.
Visitingscientistsmightbeinresidenceforseveralweeksormonthswhiledevelopinga
researchgoal.Hostinstitutions,whichwouldclearlybenefitfromproximity,couldcoinvestin
equipmentandsupportpersonnel.Asoneexample,weanticipatethatexpensive,complex
technologiessuchasnextgenerationhighfieldMRIinstrumentsmightneedtobecentralized,
likethecentralizedXraybeamlinesusedbystructuralbiologists,butweemphasizethatthose
technologiesdonotcurrentlyexist.
AnyplannedBRAINInitiativefacilitiesshouldbeevaluatedfortheirimpactonthebroad
scientificcommunity,notsmallgroupsofresearchers.AnyfacilitiesfundedbytheBRAIN
Initiativeshouldhavetheclearlystatedgoalofdemocraticaccessandwidespreadavailability
oftechnology,notjustinthehostinstitution.Groupsthatarefundedmustbeheld
accountableandwillingtoacceptcloseoversightfromtheNIH.
TraininginnewmethodsandtheirrigorousapplicationshouldbeacomponentoftheBRAIN
Initiative.Arelativelysmallinvestmentinhandsonpracticalcoursescanprovideimmense
addedbenefitinthereachoftechnologies.ThiscouldoccurattraditionalcoursesiteslikeCold
SpringHarborandWoodsHole,oratuniversitiesthatinviteoutsideresearchersfortraining.
8biv.TimelinesandMilestones

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Shorttermgoals(15years)
Expandexistingresourcesforsharingbiologicalreagentstoaccommodatetheprojected
needsofBRAINInitiativeresearch.
SupportcommercializationanddisseminationofnewinstrumentsthroughtheSBIR
Programorotherpartnerships.
Supportsharedinstrumentationforconsortiaofinvestigatorswithinoracross
universitiesandresearchinstitutions.
Trainingcoursesforresearcherstomasternewresearchtechnologies.
Longtermgoals(610years)
Continuetosupportresourcesforsharingofreagentsandinstrumentation;continue
trainingcoursesfornewtechnologies.
Withappropriateoversightandevaluationofneed,createfacilitiesforintegrated
instrumentationwhosecostisbeyondthescopeofanysinglelaboratoryormost
institutions.Ensurebroadaccesstothesecentersfrommultipleuniversitiesand
researchinstitutions.

8c.Principle:Considerethicalimplications
8ci.OverallObjective
Asolidethicalframeworkisapathforensuringthatscientificresearchisoftheutmostvalueto
thepublicitintendstoserve.Therefore,theresearchsupportedbyandtheknowledge
generatedthroughtheBRAINInitiativeshouldberegularlyassessedfortheirethical,legal,and
societalimplications.
8cii.Deliverables
1. Carefulandbroadlybasedconsiderationoftheuniqueethicalissuesraisedbyhuman
neuroscienceresearch.Jointneuroscience/ethicsmeetingsandtrainingprograms;
resourcesforcollectinganddisseminatingbestpractices.
2. Vigorousdialogueamongethicists,educators,governmentandcorporate
representatives,patientsandtheiradvocates,lawyers,journalists,scientistsandother
concernedstakeholdersaboutsocialandethicalissuesraisedbynewknowledgeand
technologiesgeneratedundertheBRAINInitiative
8ciii.RationaleandPrinciples
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EthicalissuesimplicitintheBRAINInitiativefallundertwobroad,equallyimportantcategories:
1)ethicalconductofresearch,and2)ethicalandsocietalimplicationsofnewtechnologiesand
scientificdiscoveries.
Ethicalconductofresearch.
Societystandstobenefittremendouslyfromneuroscienceresearch,butitisimperativethat
thisresearchisconductedinaccordancewithhighethicalstandards.Establishingethical
guidelinesearlymakesitpossibletoaddressfuturehurdlesanddilemmasinadvance,
preventingunnecessarycostsanddelaysaswellasadverseconsequences.Manylawsand
oversightsystemsarealreadyinplaceforresearchonhumansubjects,butstudiesinvolving
monitoringandstimulatingthehumanbrainrequireparticularsensitivityandongoing
oversight.Humanparticipantsareinvaluableresourcesforneuroscienceresearch,and
protectingtheirinterestsisoftheutmostimportance.Informedconsentandprotectionof
privacyarecriticalcomponentsofhumanneuroscienceresearch.BRAINInitiativeprojects
shouldstriveforcompletetransparencyabouttherisksandbenefitsofparticipationinthese
studies.
TheBRAINInitiativeaimstounderstandhowlivingbrainsworktogeneratecognitivefunctions
andbehavior.Asaresult,inevitably,manyscientificstudiesmustbeconductedinliving
animals,notintissueslices,cellculturesorcomputersimulations.Thisresearch,too,should
adheretorigorousethicalstandards.Bothourownsenseofethicsandthelegalandregulatory
frameworkofscientificresearchintheUnitedStatesrequireastrongcommitmentto
performingsuchexperimentswithminimalsufferingtoanimals,andarespectforanimal
cognitionandlife.
Ethicalandsocietalimplicationsofnewtechnologiesandscientificdiscoveries.
AssuggestedinSectionII.8f,mysteriesunlockedthroughtheBRAINInitiative,andthrough
neuroscienceingeneral,arelikelytochangehowweperceiveourselvesasindividualsandas
membersofsociety.Manyofthesediscoverieswillraisemorequestionsthantheyanswer.
Wemayneedtoconsider,asasociety,howdiscoveriesintheareaofbrainplasticityand
cognitivedevelopmentareusedtomaximizelearningintheclassroom,thevalidityof
neurosciencemeasurementsforjudgingintentoraccountabilityinourlegalsystem,theuseof
neuroscienceinsightstomountmorepersuasiveadvertisingorpublicservicecampaigns,the
issueofprivacyofonesownthoughtsandmentalprocessesinanageofincreasingly
sophisticatedneuraldecodingabilities,andmanyotherquestions134.Questionsofthis
complexitywillrequireinsightandanalysisfrommultipleperspectives,andshouldnotbe
answeredbyneuroscientistsalone.
ManyoftheseethicalconsiderationsarenotuniquetotheBRAINInitiativeorneuroscience.
Butresearchersmustremaincognizantofthematallstagesofresearchandshouldhave
appropriateavenuesforseekingguidancewhenapplicable.
8civ.ImplementationandMechanisms
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ThePresidenthaschargedhisBioethicsCommissiontotakeabroadviewofethicalimplications
ofneuroscienceresearchthatextendbeyondtheBRAINInitiative.TheBRAINworkinggroup
endorsesthisactionenthusiastically.TheBioethicsCommissionshouldengageneuroscience
relatedissueswhenevertheyariseunderthepresentandfutureadministrationsandthe
Commissionshouldbeabletocountontheparticipationandsupportofneuroscientistswhen
ourexpertiseisneeded.
Nosinglecommission,however,canexploretheseethicalissueswiththedepthanddiversityof
perspectivesthatmirrorsoursociety.Abroaderconversationisnecessary.Stakeholders
shouldbeengagedthroughavarietyofadditionalmechanisms,includingacademicresearchin
bioethics,trainingprogramsforabroadarrayofpractitionersandstudentsinthemedical
professions,conferencestargetedtoaudienceswithdifferentlevelsofscientificexpertise,and
mediaoutreach.
AssummarizedinSectionIII.6,oversightforneuroscienceresearchwithhumanvolunteer
subjectsisbestservedbyacontinualdialogbetweentheresearchersandethicaloversight
bodies.Ethicscommitteesmustincludememberswhoareinformedinclinicalandbasic
neuroscience,andwhoareawareofthehistoryofbrainmanipulationsandrecordings.
Studentsandscientificstaffinvolvedintheprojectsmustbetrainedinethicalhumanresearch,
andethicistsshouldbeeducatedabouttheuniquenatureandpotentialofhuman
neurotechnology.
8cv.TimelinesandMilestones
Goals(years110)
Jointneuroscience/ethicstrainingprogramsandmeetingstoconsidertheuniqueissues
raisedbyhumanneuroscienceresearch,andtoestablishasharedvisionfortheethical
conductofsuchresearch.
Resourcesforcollectinganddisseminatingbestpracticesintheconductofethical
scientificresearch,particularlyfortheconductofclinicalresearch.
SupportfordatadrivenresearchtoinformethicalissuesarisingfromBRAINInitiative
research,ideallywithintegratedactivitiesbetweenethicistsandneuroscientists.
Opportunitiesforoutreachactivitiesfocusedonengaginggovernmentleaders,
corporateleaders,journalists,patientsandtheiradvocates,educators,andlegal
practitionersindiscussionofthesocialandethicalimplicationsofneuroscience
research.

8d.Principle:AccountabilitytoNIH,thetaxpayer,andthebasic,translational,andclinical
neurosciencecommunities
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8di.OverallObjective
EnsurethatresearchconductedundertheBRAINInitiativeistargetedtowardthescientific
prioritiesestablishedbytheNIH,makesefficientuseoftaxpayerfunds,andresultsintechnical
andconceptualadvancesthathaveahighimpactonthepaceandqualityofneuroscience
research.
8dii.Rationale
AccountabilitytotheNIHandthetaxpayer.
TheBRAINInitiativehasenormouspotentialforsolvingpersistentmysteriesofbrainfunction,
spinningofftechnologiesthatseednewindustries,andopeningthedoortonewtreatmentsfor
diseasesanddisordersofthenervoussystem.ToensurethattheInitiativeremainsontrack
scientificallyandismakingefficientuseoftaxpayerdollars,theprogressandaccomplishments
oftheBRAINInitiativeshouldbeanalyzedregularlybytheNIHleadership,theNIH
neuroscienceleadership(directorsofneurosciencerelevantinstitutes),ascientificadvisory
board(seebelow)andrepresentativesofthepublicsuchasmembersofpatientadvocacy
groupsforbraindisorders.Thisprocesswillrequireactive,highleveltrackingofInitiative
progress,overandabovethetypicalannualevaluationofinvestigatorinitiatedresearchgrants.
Scientificaccountability.WhiletheproposedscientificgoalsfortheBRAINInitiativearefocused
onenhancingourabilitiestostudyandunderstandbraincircuits,theultimatevisionisthatthis
knowledgewilltransformallofbasic,translational,andclinicalneuroscience.Toachievethis
aim,NIHshouldencourageandfacilitatethedisseminationandutilizationofBRAINInitiative
advancesthroughouttheneuroscienceenterprise,movingcreativelytobringnewtoolsand
discoveriesintoareasofopportunity.
Breakthroughsinmodernsciencearetypicallyachievedthroughcascadingadvancesmadeby
manyresearchersandcliniciansovertime,notbyisolatedgroupsatasinglemoment.Inthe
shortrun,simplyensuringwidespreadaccesstonewreagents,technologies,anddataisasure
waytomaximizeimpact,andalsodemonstrateaccountabilitytothescientificcommunityand
theNIH.Manyprinciplesenunciatedinthisreportwillcreateapathforaccountability.
Atintermediatetimescales,highqualitydatamovesthefieldforward.Thesuccessof
cooperativeandopenaccessprojectssuchastheHumanConnectomeProjectortheHuman
GenomeProjectcanbemeasuredbythereleaseanduseofthedata.Shareddataarea
productavailabletomanyresearchers,notjustthosefundedbytheBRAINInitiative,andthe
externaluserscanprovideunbiasedevaluationofdataquality.Ifthedataarevaluable,the
datasharingpolicywillincreasesupportfortheBRAINInitiativeinthecommunity,justasthe
depositionofDNAsequencesintocommondatabasesledtoincreasedgrassrootssupportfor
theHumanGenomeProject.Conversely,Balkanizeddataininaccessibleformatswithreluctant
sharingleadstoresentmentanddiminishedscientificreturn.Annualrenewalofgrantfunds
couldbecontingentontimelydepositionofdatasetsintosharedresources.Disseminationof
powerfulexperimentaltoolsandtechnologiestothecommunityisanotherclearcut
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demonstrationofscientificbenefitprovidedbytheBRAINInitiative.Theuseofsuchtools
outsidethelabthatdevelopedthemisthemostpotentindicatoroftheirvalue.
Inthelongrun,scientificandmedicaladvanceswillbetheultimatemetricsofthesuccessof
theBRAINInitiative.ThesecanandshouldbetrackedbytheNIH,withinsightintotheareas
thathavemadeprogress,thosethatrequireadditionalsupport,andthosethatshouldbe
terminated.
8diii.ImplementationandMechanisms
CoordinationandevaluationofresearchundertheBRAINInitiativeposesspecialchallenges
duetotherapidlyevolvingneurosciencelandscape,thehighlyinterdisciplinarynatureofthe
research,andtheneedtoleverageeffortswiththeexistingNIHneuroscienceresearch
portfolio.Accountability,integration,andtransparencycanbegreatlyenhancedthroughthe
formationofascientificadvisoryboard,whichwouldbecomposedofscientistswhoare
expertsinthemanydisciplinesrelevanttotheInitiativeandpossessanunderstandingofthe
breadthoftheNIHneuroscienceresearchportfolio.Acohesiveandrigorousscientificadvisory
boardwould:
1. EnsurethatthescientificvisionoftheBRAINInitiativeisupdatedinresponsetonew
technologicalandconceptualadvancesthatwillbemadeoverthecourseofthenext10
years.Aparamountresponsibilityofthisboardwillbetohelpidentifyandrespondto
thesedynamicandexcitingchanges.
2. GuideandfacilitatetheintegrationofthediversedisciplinesundertheBRAINInitiative
asenvisionedinthisreport.Nosingleentityisaccustomedtointegratingneuroscience
withengineering,physics,statistics,appliedmathematics,chemistry,genetics,
molecularbiology,andtheclinicalsciences,anditwillbecrucialthatcommunication
acrossthesedisciplinesisachievedandmaintained.
3. ProvidecohesionacrosstheNIHInstitutesandCentersresponsibleforsupporting
neuroscienceresearchintodiseasespecificareas.Ultimately,theintentisthat
advancesundertheBRAINInitiativewillspurnewbreakthroughsinourunderstanding
ofthesediseasesanddisorders,andBRAINeffortsmustbemaximizedtoachievethis
aim.

III.9.COSTESTIMATES
TheBRAINInitiativeWillRequireNewandDistinctFundingof$300500MillionperYear.
Aspartoftheplanningprocess,theworkinggroupwasaskedtoestimateabudgetforthe
BRAINInitiative.WhilethescientificprogramoftheBRAINInitiativehasbeeninformedbythe
professionalexpertiseoftheworkinggroupmembersandmanyothercontributingscientists,
wedidnotconductadetailedanalysisofcosts.Instead,weconsideredthescopeofthe
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questionstobeaddressedbytheInitiative,andthecostofprogramsthathavedevelopedin
relatedareasoverrecentyears.ThecostestimatesfortheBRAINInitiativeshouldthusbe
viewedasprovisional,butinformedbythecostsofrealneuroscienceatthistechnologicallevel.
EachscientificgoaloftheBRAINInitiativeiscriticaltoitsintegratedpurpose,butdifferentgoals
requiredifferentkindsofinvestmentandresources.Instrumentationandtechnologycostsare
expectedtobeparticularlyhighindevelopingnewrecordingmethods(Goal3)andimproving
anatomicalmethods(Goal2).Allresearchwithhumansubjectsrequiresclosesupervisionand
associatedcosts,whetheritinvolvesstructuralandfunctionalimaging(Goals2and3),
perturbation(Goal4),orintra orperioperativerecording(Goal6).Theory,computation,and
statisticsrequirerelativelylittleequipment,butwillrequirestrongsupportforpersonnel(Goal
5).Infrastructurefordatascienceandtechnologydisseminationwillprovideaddedvalueto
theentireInitiative(SectionIII.8).
ThefirstyearoftheBRAINInitiative,FY14,wasseededbyanew$40millioncommitmentfrom
theNIH;inthesecondyear,FY15,NIHwillcontribute$100milliontonewandcontinuing
grants.Theworkinggroupbelievesthattheprogrampresentedintheprecedingsectionscould
rampupto$400millionperyearoverthenextfiveyears(FY1620),andcontinueatroughly
$500millionperyearforthelastfiveyears(FY2125).Intotalthismightrepresentaround5%
ofthebudgetforbrainrelatedresearchatNIH.Apossibletrajectoryofcostsperfiscalyearis
diagrammedbelow.

Figurecaption.Proposed12yearbudgetfortheBRAINInitiative.Collaborativetechnology
developmentisemphasizedthroughFY2019,whilediscoverydrivensciencereceives
prioritybeginninginFY2020.Infrastructureisforfacilitiesandcapabilitiesthatwillbenefit
researchersacrosstheentirenation,withemphasisondatasharingresources,trainingin
theuseofnewtechnologiesandquantitativemethods,andpossibleregional
instrumentationcentersduringthelasthalfoftheBRAINInitiative.

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AsdescribedearlierinthisSection,thefirstyearswillemphasizetechnologydevelopmentand
validation,withalargeremphasisonproblemdrivenneuroscienceafterFY20.
RampingupsupportfortheBRAINInitiativeovertimeisimportanttodriveitssuccess.A
structurethatbuildsupoverfivetosevenyearswillencouragetalentedscientiststoenter
interdisciplinarycollaborationstosolveimportant,difficultproblems,becausetheywillseea
longtermcommitmentoftheNIH.TheBRAINInitiativeshouldbeacatalystthatwilldrive
outstandingyoungpeopletoenterthisareaattheirmostcreativecareerstage.
WeenvisionthefollowinggeneralmechanismsforsupportingBRAINInitiativeresearch.This
listisnotmeanttobeprescriptiveorcomprehensive;note,forexample,thatdetailed
mechanismsforsupportingtheoryandhumanneuroscienceresearchareaddressedwithin
SectionsIII.5andIII.6.
1.Collaborativetechnologydevelopmentandvalidationgrantswith25PrincipalInvestigators
representingseveralareas(forexample,tooldevelopersandtoolusers,oropticalmicroscopy
andbiologicalsensordevelopment).
2.Technologyinnovationgrantsfordevelopmentofnew,blueskytechnologies,with12
PrincipalInvestigators.
3.Integratedscientificgrantsaddressingafundamentalquestionsuchasperception,memory,
cognition,oraction,with25PrincipalInvestigatorsrepresentingdifferentdisciplinary
approaches,experiment,andtheory.
4.Multisitegrantstoaddresscomplexintegratedsystemsandprimateorhuman
neurotechnologies,withmultiplecollaboratorsacrossfields,includingclinicalresearchers.
5.InfrastructuresupportforBRAINInitiativeresearch.Datainfrastructuregrants;practical
traininginfrastructureinquantitativemethodsandexperimentalmethods;technology
disseminationinfrastructureforprovidingbroad,democraticaccesstonewneurotechnologies.
Ourcostestimatesareextremelyoptimistic.Developingasinglenewstimulatingorrecording
deviceforhumansupthroughFDAapprovalmightcost$100millionor$200million,andthisis
notrepresentedinourbudgetestimates.WebelievethattheBRAINInitiativecancatalyzethe
firststepsofthisprocess,butthatclinicaladvancescanthenbestmoveforwardthrough
partnershipwithotherclinicalandindustrialaspectsoftheresearchenterprise,whichshould
shouldersomeofthecost.Weexpectcoinvestmentfromgovernmentagencies,private
foundations,internationalefforts,andindustryinsupportingBRAINInitiativegoals.
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ThesecostestimatesassumethatthebudgetfortheBRAINInitiativewillsupplement,and
notbetakenfrom,existingNIHeffortsinproblembasedbasic,translational,andclinical
neuroscience.ThemajorityofNIHinvestmentinbrainresearchisappropriatelydirected
towardessentialquestionspertainingtohealthanddisease,aninvestmentthatwillremainas
importantinthefutureasitisnow.Forexample,whilewebelievethatBRAINInitiative
technologieswillaccelerateourunderstandingofcircuitsinvolvedinlearningandmemory,and
willsuggestpossibleapproachesforcircuitlevelinterventionsintomemorydisorderssuchas
Alzheimersdisease,wealsostronglysupporttheentiresuiteofongoingNIHAlzheimers
researchthatstudiesproteinfoldingofthetoxicbetaamyloidpeptide,cellbiologyofaffected
neurons,humangeneticsofdiseaseriskfactors,developmentofnewPETligandsfordiagnosis,
andclinicaltrialsbasedonourmolecularunderstanding.Itwouldbeinappropriate,even
unethical,toplacethesetargetedquestionsasideascircuitlevelneuroscienceisdeveloped
throughBRAINtechnologies.Thusourbudgetplanningassumescontinuedstrongsupportof
theNIHcommitmenttoneurologicaldisordersandstroke,mentalhealth,addiction,aging,and
basicmolecular,cellular,developmentalandsystemsneurosciencewhicharenotindividually
includedintheBRAINInitiative.

III.10.CONCLUDINGREMARKS
TheApplicationofIntegratedTechnologiestoStudyFundamentalQuestionsinNeuroscience.
Numerouslongstandingproblemsinbrainsciencewillbenefitdramaticallyfromtheintegrated
experimentalapproachmadepossiblebytheBRAINInitiative.Itisdifficultifnotimpossibleto
identifyonesetofproblemsthatismoreimportantthanothersthebrainfunctionsasa
whole,notasthesumofitsparts.Nevertheless,weoutlinebelowfiveoutstandingquestions
inunderstandingthebraininhealthanddisease,andhowtechnologyandbasicneuroscience
developedundertheBRAINInitiativewilladdressthesequestions.
Perception
Perceptionmediatesoursenseoftheexternalworldandinitiatesmuchofourinteractionwith
theworld,providinganessentialfoundationforcognitionandbehavior.Ourunified,subjective
perceptionoftheworldemergesfromcoordinatedelectrochemicalactivityofbillionsof
neuronsinthebrain.Whilethefirstlevelsofsensoryprocessinghavebeenmuchstudied,the
BRAINInitiativewillmakeitpossibletoaskincreasinglysophisticatedquestionsabouthigher
levelperceptionandmultimodalintegration.Howdocircuitdynamicsperformcomputations
ontheinformationateachlevelofsensoryprocessing?Howissensoryinformationfrom
multiplemodalities(vision,audition,touch)integratedtogenerateacoherentperceptof,for
example,aspecificperson?Theabilitytomonitorthedynamicactivitypatternsoflarge
populationsofneuronsinareasofthebrainspecializedforsensoryprocessing,theabilityto
relatethosepatternstotheunderlyingcircuitstructures,andtheabilitytomeasurethe
perceptualconsequencesofperturbingthosepatternsinprecisewayswillberevolutionary.A
criticalchallengewillbetodeveloppowerfultheoriesofsensorycoding,computation,and
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multimodalsynthesisofsensoryinformationthatbuildonknownmechanismstomake
testablepredictions.Progressinthisareawillsuggeststrategiesfortreatingsensorydeficits
suchasblindnessormaculardegeneration,andstrategiesforunderstandingtheperceptual
distortionsinbraindisorderssuchasschizophrenia.
EmotionandMotivation
Ourreactionstoinformationfromtheexternalworldarecriticallyshapedbyinternalbrain
statessuchasemotion,motivation,andarousal.Perceptualrecognitionofaparticularperson
mayelicitawarmgreetingorfurtiveavoidancedependingupononesemotionalstate.Cell
typespecificaccesstoneuralsystemsinthehypothalamusandamygdalaareuncovering
intermixedneuralcircuitsunderlyingemotionalstatessuchasfearandaggression,butata
deeperlevel,theintegrationofthisinternalinformationwithexternalinformationisamystery.
Howareinternalstatesgeneratedinthebrain,atthelevelofneuralcircuitsandbrain
chemistry?Howdothesestatesinfluencecognitiveprocessessuchaslearningandmemory,
decisionmakingorattention?Howarethedifferenttimescalesofcognitiveprocessesand
emotionalprocessesintegrated?Understandingmotivationandcognitionisamultilevel
processinwhichnoonebrainareawillprovideafullanswer.TheBRAINInitiativewillprovide
morepreciseaccesstothesubcorticalcircuitsthoughttohaveimportantrolesingenerating
brainstates,andtothecorticalareasthatareinfluencedbythemandinfluencetheminturn.It
willprovidetoolstomanipulateactivitywithinthosecircuitsandmeasurebehavioral
outcomes.Anunderstandingoftheneuralbasisofemotionalandmotivationalstatesis
criticallyimportantinunderstandinghowgenes,theenvironment,andexperienceinteractin
thebraintocausepsychiatricdisorderssuchasdepression,anxiety,andposttraumaticstress
disorder.
Cognition
Cognitionliesatthecoreofourinternalmentallives,comprisingourthinking,planning,and
understandingoftheworld.Forexample,forhumanstocarryoutaconversation,understand
eachothersneedsandpriorities,andworktogetherasagrouporteam,remarkablefeatsof
cognitionarerequiredinvolvingsocialandemotionalprocessing,modelsofthementalstates
ofothers,andpredictionsaboutthefutureovermanytimescalesofteninconstantlychanging
situationswithmanyuncertainties.Basicformsofcognitioncanbestudiedinanimalsaswell,
includingdecisionmaking,planningoverarangeoftimescales,navigatingpathsand
performingspatialcomputations,andmakingpredictionsaboutfuturerewards.Whilepast
experimentshaveopenedthedoortomechanisticstudiesofcognition,theBRAINInitiativewill
introduceanewera.Cognitionintegratestheexternalworld,internalemotionalstates,
memories,goals,andsocialcontext,andthusthecircuitsunderlyingcognitiveprocessingare
likelytospantheentirenervoussystem.Morethananyotherarea,perhaps,thestudyof
cognitionwillbenefitfromthefarreachingandhighresolutionanatomical,recording,and
perturbationmethodstobedevelopedundertheBRAINInitiative.Cognitioniscentralto
clinicalconditionsaswell,sincekeysymptomsofcripplinghumandiseases(including
degenerativebraindisorders,schizophrenia,andautism)lieintherealmofcognition,asdo
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sometreatments.Forexample,thecognitivebehavioraltherapiesfordepressionandanxiety
disordersarewidelyusedandeffectivepresumablybecausecognitionisheavilyinfluencedby
(andpowerfullyinfluences)emotion.TheBRAINInitiativewillprovidetoolsforusebothin
humansandinanimalmodelstounderstandcognitivedisorders,thesystemiceffectsof
complexandvariedgeneticfactorsthataffecttheriskofthesedisorders,andthemechanistic
effectsofcognitive,pharmacological,andelectricaltherapies.
LearningandMemory
Ourmemoriesprovideuswithoursenseofourlivesandselves;theyareourconnectionwith
thepastandthefuture.Learningandmemoryarenearmiraculouspropertiesofthebrainthat
permitittoencode,store,andrecallanyevent,associatingfeaturesfromallofthesenses,
linkingthemintoasequencethatincorporatesrecentanddistantinformation,andinfusing
themwithmeaning.Thehippocampusisonebrainregioncriticaltotheformationofnew
episodic,explicitmemories,butitismysterioushowthevastassortmentofassociationscanbe
assembledorroutedthere.Itisequallymysterioushowthatinformationiseventually
transferredtootherbrainareas,asitisduringlongtermmemory.TheBRAINInitiativewill
providethetoolsforunderstandingthehippocampusandthemanyotherbrainareasinvolved
inlearningandmemory.Thesetoolswillhelpunravelthedynamicneuronalmechanismsthat
storeinformationlikeaphonenumberforjustafewseconds(perhapspersistentneural
activity?),andthestablemechanismsthatcanstoreamemoryforalifetime(perhaps
modificationstosynapticstructures,butwhich,andwhere?).Abetterunderstandingof
memorysystemsinthebrain,andtheircircuitproperties,isurgentlyneededforaddressing
learningdisabilitiesinchildrenandforaddressingthetragedyofmemorylossinAlzheimers
diseaseandotheradultdementias.
Action
Motorsystemsgenerateoursophisticatedlearnedbehaviors,ourskills,ourlanguage,and
manyofourpleasuresinlife.Anyimpactwehaveontheworldhappensultimatelythrough
action,yettheneuralprocessesthatgenerateactionaremysterious.Anapparentlysimple
goalpickingupacoffeecupinvolvesdozensofmusclesandmultipledegreesoffreedom
aboutseveraljoints.Whilecomputerprogramscanroutinelybesthumanchessgrandmasters,
robotscannotmovewiththesupplenessofachild.Motorplanningandexecutionisawhole
brainprocess,withessentialcontributionsofscatteredregionsincludingthecerebralcortex,
thebasalganglia,thepons,thebrainstem,andthecerebellum,aswellasthespinalcord.
Theseareashavegenerallybeenstudiedinisolation,buttheyfunctiontogether,anddamage
toanyoftheseareas,forexamplefrominjuryorstroke,resultsinmotordeficits.Experimental
andtheoreticaltoolstobedevelopedundertheBRAINInitiativewillenablecomprehensive
analysesofmovementpreparationandgeneration.Motorstructuresthataretypicallystudied
individuallywillbestudiedincreasinglyascouplednetworks,resultinginaclearerpictureofthe
signaltransformationsthatoccurbetweenselectionandexecutionofamovement.
Perturbationtoolsshouldenableincisivetestsoffunctionformotorloopsthroughthebasal

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gangliaandcerebellum.Theseadvanceswillbehighlyrelevanttounderstandingmovement
disorderslikedystoniaandneurodegenerativediseasessuchasParkinsonsandALS.
Insummary,weseeimmensepotentialinBRAINInitiativetechnologyappliedtocompelling
neurosciencequestions.Weseegreatopportunitiesinprovidingnewtoolstobasic
neuroscientists,translationalresearchers,neurologists,psychiatrists,radiologists,and
neurosurgeons.Atthesametime,werecognizethattheseinitialgoalswillberefined,thatnew
goalsmayemerge,andthatobjectivesandprioritiesarestillcrystallizing.Wehaveattempted
torepresentthebestcollectivescientificwisdomofthefield,withtheadviceofourcolleagues
inneuroscience,medicine,psychology,biology,chemistry,andthequantitativesciences,and
withtheadviceofpatientadvocatesandthepublic.TheBRAINInitiativeisachallengeandan
opportunitytosolveacentralmysteryhoworganizedcircuitsofcellsinteractdynamicallyto
producebehaviorandcognition,theessenceofourmentallives.Theanswerstothatmystery
willnotcomeeasily.Butuntilwestart,theprogresswedesirewillalwaysbedistant.Thetime
tostartisnow.

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135

APPENDIXAHOWTHEBRAININITIATIVEWILLADVANCECLINICALRESEARCH

Theburdenofhumanbraindisordersissobering,andthereisanurgentneedforbetter
approachestotreatandcuretheseconditions.Asanexample,over5millionAmericans
currentlysufferfromAlzheimersdisease
(https://www.alz.org/alzheimers_disease_facts_and_figures.asp#quickFacts).Thecostof
caringforthesestrickenindividualsisover$200billionperyear,including$150billionfrom
MedicareandMedicaid.Greatstrideshavebeenmadeinuncoveringthegeneticriskfactors
thatpredisposetoAlzheimersdisease,butincurrentmedicalpracticewelackevenasingle
effectivedrugforreversingitssymptoms,muchlesscuringit;wecanonlyslowtherateof
decline.
Similarly,welackeffectivetreatmentsformanypsychiatricdisorders.2.4millionAmericans
sufferfromschizophrenia,aterrible,lifeshorteningmentalillnessforwhichexisting
medicationsareonlypartlyeffective
(http://report.nih.gov/nihfactsheets/ViewFactSheet.aspx?csid=67).Therehasnotbeena
fundamentallynewdrugdevelopedforschizophreniainthepast20yearsofintenseeffortsby
thepharmaceuticalindustry.
Theclassicalapproachtakentosolvebraindisordersistofocusoneachdisorderindetail,
examiningitssymptoms,pathology,causes,andresponsestointerventions.Insomecases,
therehavebeengreatsuccessesfromthisfocusedapproach.ThedevelopmentofLdopaasa
Parkinsonstreatmentfollowingtherealizationthatdopaminergicneuronsdegenerateanddie
inthisdisease.However,inmanyothercases,wedonotunderstandthesymptomsorcauses,
andevenwhenwedo,wehavenotbeenabletodevelopeffectiveinterventions.Theearly
successeswithParkinsonshavebeenreplicatedtoofewtimes.
Onereasonthattherearenotbetterdrugsandtreatmentsforbraindisordersisthatwedonot
knowenoughaboutthebrain.Ourfragmentaryunderstandingofbrainfunctionsmeansthat
wearestumblinginthedarkwhenweattempttotreatpatientswithbraindisorders.
Neuroscienceprovidesawaytoturnonthelights:abetterunderstandingofallbraincircuits
andnetworks,andtheirrelationshipswithoneanother,hasthepotentialtoshedlighton
disordersofbraindevelopment,function,andaging.Whetherbraindisordersresultfrom
injury,orfromenvironmentalandgeneticinteractions,theyaffectthesameorgan.Untilwe
understandwhatthebraindoesandhowitdoesit,wewilllackthejudgmenttorepairorassist
itwhenitmalfunctions.
Evenbraindisordersthathavemolecularorcellularcausesareultimatelyexpressedatthe
levelsofcircuitsandnetworks.Thisistruebothforneurologicalandforpsychiatricdisorders.
Forexample,specificionchannelmutationscanleadtoseizuredisorders(epilepsy),butthese
effectsexpressthemselvesasadisruptionoftheratioofexcitationtoinhibitionthatleadsto
widespread,aberrantneuralactivity.Rectifyingtheactivitystatemayprovetobeasimportant
andusefulascorrectingtheaberrantchannelsperse.Similarly,Parkinsonismbeginswiththe
degenerationofdopaminergicneurons,butthisdisruptstheentirecircuitsformotorcontrolin
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whichtheseneuronsareembedded,andcan,tosomeextent,bemitigatedbytargetingremote
brainsites.Psychiatricdisorderscanalsohavemolecularorenvironmentaltriggers,buttheir
symptomsarisefromdefectsinthecircuitsthatcontrolcognition,emotionandmotivation.
Psychiatricdisordersinparticularhavewaxingandwaningtrajectoriessuggestiveofabnormal
networkstates.Electroconvulsivetherapyisoneofthefastestactingandmosteffective
treatmentsfordepression;thecurrentexplorationofdeepbrainstimulationfordepression
representsthesearchforamorefocalandrationallydesignedcircuitbasedintervention.A
deepknowledgeofbraincircuitswillprovideafoundationforunderstandingallbraindisorders
intheperspectiveofwholebrainfunction,andthisinturnwillsuggestnewapproachestotheir
treatment.
ThetechnologiestobedevelopedbytheBRAINInitiativewillalsomotivatenewclinical
applications.TheBRAINInitiativeshoulddevelopwaystotargetparticularcelltypeswith
chemicalorgeneticagents,providingpreciseandlocalcontroloftherapeuticdelivery.The
BRAINInitiativeshouldincreasethepowerofstructuralandfunctionalimagingandrecording
methodsforthehumanbrain.Itshouldleadtoanewgenerationofimplantabledevices.
Here,wedescribeafewclinicaladvancesindiagnosing,treatingorrestoringbrainfunctionthat
canadvanceusingtheknowledgegainedundertheBRAINinitiative.
Neuromodulationtorestorecircuitsinneurologicalandpsychiatricdisorders:Theuseof
implantabledevicesasclinicalinterventionsbeganwiththeelectricalpacemakersthat
regularizeaberrantrhythmsoftheheart1.Implantabledevicesinthebrainarethe
basisofdeepbrainstimulation(DBS),whichtreatsbraindisordersbymodulating
dysfunctionalcircuitswithelectricalcurrent.Basicsciencestudiesthatexplainedhow
clinicalsymptomsemergefrombasalgangliacircuitimbalanceledtotheeffectiveuseof
DBStoovercomerigidity,slownessandtremorinParkinsonianpatientswhocouldnot
useLdopa2,andDBShasalsobeensuccessfulinothermovementdisorders3.
Understandingthecircuitsinvolvedinpsychiatricdisordersmayhelptodevelop
effectiveDBSstrategiesfortheirtreatment,asisalreadybeginningfordepression4.It
mayevenbepossibletointerveneinmemorydisorderssuchasAlzheimersdisease,at
leastintheirearlystages,bystimulatingthedisabledcircuits5.Moresuccessful
implementationofDBSshouldarisefromknowledgeofconnectionsandcircuitfunction
thatemergefromBRAINinitiativeresearch.
Epilepsypreventionandintervention:TechnologiesdevelopedundertheBRAIN
Initiativeshouldalsobevaluableinthetreatmentofepilepsy,wherethereisparticular
promiseintheuseofdevicesthatcanbothrecordandstimulatebrainactivity.Many
patientswithintractableseizuresaretreatedbyirreversiblesurgicalablations,but
reversible,tunableinterventionwouldclearlybefarmoredesirable.Wecanenvision
sensitiveimplantedmeasurementdevicesthatcandetectanimminentseizureevent
andimmediatelymodulatethecircuittorestorenormalfunctionbeforeaseizure.
Indeed,afirstversionofsuchafullyimplantablesystemhasbeenapprovedforhuman
usebytheFDA.Abetterunderstandingofthecomplexinteractionsofexcitatoryand
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inhibitorycelltypesinbraincircuitsshouldenableadvancesintheseandotherformsof
seizureprevention.
Restorationoflostsensoryfunctions:Thecochlearprosthesis,implantedinmorethan
200,000people,isaneffectivetreatmentforprofounddeafness6andacompelling
modeldemonstratinghowstrongunderlyingscienceandmedicinecanleadto
commercialdevicesforhumanuse7.Devicestorestorevisionforthosewithprofound
blindnessareatanearlystageoftechnologicaldevelopment,withonesystemrecently
approvedforhumanusebytheFDA.Byunderstandinghowtheneuronsintheretina
andbrainprocessstreamsofinformationfromthevisualworld,itshouldbepossibleto
deviseintelligentretinalorcorticalprosthesesorotherdevicestorestoresight.Active
workisalreadyunderwayonelectricalstimulationoftheretina8,theopticnerve9the
lateralgeniculatenucleus10,andtheprimaryvisualcortex11.Newtechnologiessuchas
optogeneticsmayprovideotherwaystorestorelostvision.
BrainandperipheralnerveInterfacestorestoremovementafterparalysisor
amputation:BrainComputerInterfaces(BCI)areatechnologicalapproachtorestoring
volitionalcontrolofexternaldevicestopatientsparalyzedbyinjuriesorstrokes,
impactinghundredsofthousandsofAmericans11withlifelongdisabilityandaneedfor
supportivecare.BCIshavetheaimof(a)accessingvolitionalintent,byrecordingfrom
surgicallyimplantedmicroelectrodesinthebrain,(b)translatingtheneuralcode
representingintentintoaspecificcommandsignaland(c)couplingthatcommand
eithertoanassistivedevicesuchasaroboticarmorcomputer,ortoelectrodesdirectly
implantedinperipheralnerves12.BCIshavehadafewpromisingsuccesses,butthe
speed,reliabilityanddexterityofcontrolarestillintheirinfancy.Abetterunderstanding
ofthebrainscodefortargetedmovementhasthepotentialtomakethisexperimental
technologyapracticalreality.Anotherkindofbraindeviceinterfaceisrepresentedby
aspirinsizedmicroelectrodearrays,implantedintotheseverednervesofamputees,
thatcanrecordvolitionalmotorcommandsignalsandusethemforclosedloopcontrol
ofactuatorsinprototypeprostheticdevices.Newinsightsintomovementcircuitsmay
helpdevelopsuchdevicestothelevelthatprostheticdevicesareeventuallyregardedas
self.
Newbrainimagingmethodsfordiagnosisofbraindisordersandevaluationof
treatments:Humanbraindisordersarenotoriousfortheircomplexsymptomsand
trajectories:itcanbedifficultevenforaskilledcliniciantoassessthecourseofan
illnessorsignsthatatreatmenthassucceeded.ThetoolsdevelopedundertheBRAIN
Initiativeprovideapproachestounderstandingthecircuitcausesofthesedisordersas
wellastheeffectsoftreatments.Forexample,certainpatternsofbrainactivitysuchas
highactivityofthesubcallosalcingulategyrushavebeenassociatedwithdepressed
statesinpatients,andcanresolvewhendepressionbeginstolift.Thismarkercanhelp
toassesstheeffectsofcommontherapeuticagentssuchasSSRIinhibitors,whichcan
takeweekstowork.ImprovementsinhumanbrainimagingthroughtheBRAIN
Initiativemayextendthisprinciplebyallowingthediscoveryofbiomarkersofdifferent
138

braindisorders.Moreover,improvedimagingandrecordingmethodsmayhelpaddress
theheterogeneityofbraindisordersbyidentifyingbrainactivitychangesassociated
withdiseasestatesinasingleindividual,creatingatrulypersonalizedbrainmedicine.
OtherBRAINInitiativetechnologiesmayalsobedeployedforuseinpatients.For
example,combiningfunctionalbrainimagingwithimprovedversionsofperturbation
technologiessuchastranscranialmagneticstimulationcouldbeusedtoassessaltered
functionalconnectivityinpatientswithbraindisorders,allowingmoreprecisetargeting
oftherapiestofunctionallycompromisedpathways.
Newpharmaceuticaltreatmentsbasedoncellularandcircuittargets:Mosteffective
drugstargetseveralmoleculesandmanyorallbrainregions.Manydrugsareeffective
onlyinanunpredictablesubsetofaffectedpatients.Manydrugsthatcouldbe
successfulintreatinghumanbraindisordersarediscardedbecauseofsideeffectsthat
compromisetheirusefulness.Targetingpharmacologicalagentstoaspecificbrain
regionorcellpopulationmaybecomepossiblewhentherearemolecularmarkersfor
thoseregionsorcells,oneofthegoalsoftheBRAINInitiative.Forexample,hybrid
deliverysystemsinwhichadrugiscoupledtoanantibodythatrecognizesaparticular
cellpopulationmayeffectivelydeliverthedrugwhileminimizingitslevelinother
locations.
Newapproachestolinkinggeneticriskfactorstobrainfunction:Thepowerofhuman
genomicshasledtotheidentificationofmanysinglenucleotidepolymorphisms(SNPs)
thatincreasetheriskofbraindisorderssuchasschizophrenia,autism,bipolardisorder,
andmentalretardation.MostoftheseSNPsfalloutsidethecodingregionsofthe
genes,suggestingthattheyaffectgeneregulation,buttheaffectedcelltypesand
regionsareunknown.Asaresult,therelationshipbetweengeneanddiseaseprocesses
isunclear.TheBRAINInitiativewillprovideinformationaboutbraindisordersthat
complementsthisgeneticinformation.First,theidentificationofthecelltypesinthe
humanbrain,andtheirgeneexpressionpatterns,shouldhelptoidentifythecellularsite
ofactionofsomegenesimportantinbraindisorders.Anelegant,perhapsextreme
exampleofcelltypespecificityisthe20,000orsoneuronsinthehumanhypothalamus
thatproducetheneuropeptideorexin/hypocretin;theimmunedestructionofthistiny
populationofneuronsleadstonarcolepsy/cataplexy,asystemichumansleepdisorder.
Atthispointwedonotknowhowmanysuchspecializedcategoriesofneuronalcells
remaintobediscovered.Attheotherextreme,manygenesnearriskassociatedSNPs
areexpressedverybroadlyinthebrain,raisingquestionsabouthowtheypredisposeto
selectivecognitiveandemotionaldisorders.Examiningbrainactivityinpatientsbearing
theseSNPscanhelppinpointtheaffectedbrainsystems,pointinginvestigationtoward
celltypesinwhichtheSNPsmaybeactive.
ACalltoAction
Thepathfromsciencetotherapeutictreatmentsisarduousandslow,alongbattle.However,
biomedicalsciencecanpointtonotablesuccesses.Studiesinthe1970sand1980sintheUS,
139

theWarinCancerledtotheidentificationofmoleculesthatcontrolcelldivisionandgrowth,
andthentherealizationthatthesemoleculesweremutatedincancercells.Onlyinthelate
1990swerethefirstcancerdrugsdevelopedthatcoulddirectlytargetthosetumorcausing
mutations;atthiswriting,theyrepresentoneofthefastestgrowingareasforeffectivecancer
treatments.Inanothercase,whenHIV/AIDSfirstappearedintheUnitedStatesinthe1980s,
lifeexpectancywasmeasuredinmonths.ScientificstudiesoftheHIVvirusandtheimmune
systemsincethen,fundedbyfederalinvestmentintheNIH,havegeneratedtreatmentsthat
raiselifeexpectancyafterdiagnosisto30yearsormore.Thebrainisthemostcomplexsystem
inthebody,andmovingfrombrainsciencetotreatmentswillnotbeeasy.Wemustrealize
thatitmaytake20yearsfordiscoveriesinbasicneurosciencetoleadtotreatmentsandcures
forbraindisorders.Itmaytaketenyearstoelucidatethefunctionsofthebraintoadegree
thatprovidesaclearpathforourcolleaguesinmedicine,engineering,andthebiotechnology
andpharmaceuticalindustries.Itmaytaketenadditionalyearsforthemtotransformthis
knowledgeintopracticalandeffectivemedicaladvances.Butthehistoryofbiomedical
research,andofvisionarysupportbytheNIH,provideshopefortreatingbraindisorders
throughadeeperunderstandingofthebrain.

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Lillehei,C.W.,Gott,V.L.,Hodges,P.C.,Jr.,Long,D.M.&Bakken,E.E.Transitor
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Farris,S.&Giroux,M.Retrospectivereviewoffactorsleadingtodissatisfactionwith
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Panov,F.etal.DeepbrainstimulationinDYT1dystonia:a10yearexperience.
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Mayberg,H.S.etal.Deepbrainstimulationfortreatmentresistantdepression.Neuron
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Alzheimer'sFactsandFigures,<www.alz.org/alzheimers_disease_facts_and_figures.asp>
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Mudry,A.&Mills,M.Theearlyhistoryofthecochlearimplant:aretrospective.JAMA
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(2013).
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Clark,G.Themultichannelcochlearimplantandthereliefofseveretoprofound
deafness.CochlearImplantsInt13,6985,doi:10.1179/1754762811Y.0000000019cim77
[pii](2012).
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Caposecco,A.,Hickson,L.&Pedley,K.Cochlearimplantoutcomesinadultsand
adolescentswithearlyonsethearingloss.EarHear33,209220,
doi:10.1097/AUD.0b013e31822eb16c(2012).
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[pii](2003).
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APPENDIXBEXPERTCONSULTATIONS

MAY29,2013MOLECULARAPPROACHES
EdwardCallaway,PhD,AudreyGeiselChairandProfessor,SalkInstituteforBiologicalStudies
NathanielHeintz,PhD,JamesandMarilynSimonsProfessor,RockefellerUniversity
EhudIsacoff,PhD,ProfessorandHeadofNeurobiology,UniversityofCalifornia,Berkeley
LorenLooger,PhD,GroupLeader,JaneliaFarmResearchCampus
LiqunLuo,PhD,ProfessorofBiology,StanfordUniversity
ClayReid,PhD,SeniorInvestigator,AllenInstituteforBrainScience
GeraldRubin,PhD,VicePresidentandExecutiveDirector,JaneliaFarmResearchCampus
MichaelStryker,PhD,WFGanongProfessorofPhysiology,UniversityofCalifornia,San
Francisco
AliceTing,PhD,EllenSwallowRichardsAssociateProfessorofChemistry,Massachusetts
InstituteofTechnology
HongkuiZeng,PhD,SeniorDirector,AllenInstituteforBrainScience
FengZhang,PhD,CoreMember,BroadInstitute;Investigator,McGovernInstituteforBrain
Research;andAssistantProfessorofNeuroscience,MassachusettsInstituteofTechnology
JUNE26,2013LARGESCALERECORDINGTECHNOLOGIESANDSTRUCTURALNEUROBIOLOGY
EdwardBoyden,PhD,BenesseChair,NewYorkStemCellFoundationRobertsonInvestigator,
andPaulAllenDistinguishedInvestigator,MassachusettsInstituteofTechnology;Associate
Professor,MITMediaLabandMcGovernInstitute
GyrgyBuzski,MD,PhD,FAAAS,BiggsProfessorofNeuralSciences,NewYorkUniversity
WinfriedDenk,PhD,Director,MaxPlanckInstituteforMedicalResearch
FlorianEngert,PhD,ProfessorofMolecularandCellularBiology,HarvardUniversity
MichaleFee,PhD,Professor,McGovernInstitute,MassachusettsInstituteofTechnology
JeffLichtman,MD,PhD,ProfessorofMolecularandCellularBiology,HarvardUniversity
MarkusMeister,PhD,ProfessorofBiology,CaliforniaInstituteofTechnology
PavelOsten,MD,PhD,AssociateProfessor,ColdSpringHarborLaboratory
HongkunPark,PhD,ProfessorofChemistryandPhysics,HarvardUniversity
KristinScott,PhD,AssociateProfessor,UniversityofCalifornia,Berkeley
KarelSvoboda,PhD,GroupLeader,JaneliaFarmResearchCampus
RafaelYuste,MD,PhD,Professor,ColumbiaUniversity
JULY29,2013COMPUTATION,THEORY,ANDBIGDATA
KwabenaBoahen,PhD,ProfessorofBioengineering,StanfordUniversity
KristinBranson,PhD,LabHead,JaneliaFarmResearchCampus
142

JenniferChayes,PhD,DistinguishedScientistandManagingDirector,MicrosoftResearch
ToddColeman,PhD,AssociateProfessorofBioengineering,UniversityofCalifornia,SanDiego
UriEden,PhD,AssociateProfessorofStatistics,BostonUniversity
JackGallant,PhD,ProfessorofPsychology,UniversityofCalifornia,Berkeley
SuryaGanguli,PhD,AssistantProfessorofAppliedPhysics,StanfordUniversity
StephanieJones,PhD,AssistantProfessorofNeuroscience,BrownUniversity
NancyKopell,PhD,WilliamFairfieldWarrenDistinguishedProfessorandCoDirectorofthe
CenterforComputationalNeuroscienceandNeuralTechnology,BostonUniversity
MaryannMartone,PhD,ProfessorinResidence,UniversityofCalifornia,SanDiego
BrunoOlshausen,PhD,DirectoroftheRedwoodCenterforTheoreticalNeuroscienceand
Professor,UniversityofCalifornia,Berkeley
PatrickPurdon,PhD,AssistantProfessorofAnaesthesia,HarvardMedicalSchool,andAssociate
Bioengineer,MassachusettsGeneralHospital
SebastianSeung,PhD,ProfessorofComputationalNeuroscience,MassachusettsInstituteof
Technology
AUGUST29,2013HUMANNEUROSCIENCE
KrystofBankiewicz,MD,PhD,ProfessorofNeurosurgeryandNeurologyandKinetics
FoundationChairinTranslationResearch,UniversityofCalifornia,SanFrancisco
SydneyCash,MD,PhD,AssociateProfessorofNeurology,HarvardUniversity
TimothyDenison,PhD,DirectorofCoreTechnologyandTechnicalFellow,Medtronic
Neuromodulation
RainerGoebel,PhD,ProfessorofCognitiveScience,MaastrichtUniversity
BrianLitt,MD,ProfessorofNeurology,UniversityofPennsylvania
HelenMayberg,MD,ProfessorofPsychiatry,Neurology,andRadiology,andDorothyCFuqua
ChairofPsychiatryNeuroimagingandTherapeutics,EmoryUniversity
AlvaroPascualLeone,MD,PhD,ProfessorofNeurologyandDirectoroftheBerensonAllen
CenterforNoninvasiveBrainStimulation,HarvardUniversity
BruceRosen,MD,PhD,ProfessorinRadiology,HarvardMedicalSchool,andDirectorofthe
AthinoulaAMartinosCenterforBiomedicalImaging,MassachusettsGeneralHospital
NicholasSchiff,MD,DirectoroftheLaboratoryofCognitiveNeuromodulation,Cornell
University
StephenSmith,PhD,AssociateDirectoroftheCentreforFunctionalMRIoftheBrainand
ProfessorofBiomedicalEngineering,UniversityofOxford
DorisTsao,PhD,AssistantProfessorofBiologyandComputationandNeuralSystems,California
InstituteofTechnology
DavidVanEssen,PhD,ProfessorofAnatomyandNeurobiology,WashingtonUniversity

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NOVEMBER13,2013SOCIETYFORNEUROSCIENCE
StevenHyman,MD,PresidentElectoftheSocietyforNeuroscience,andDirectoroftheStanley
CenterforPsychiatricResearch,BroadInstituteoftheMassachusettsInstituteofTechnology
andHarvardUniversity
CarolMason,PhD,PresidentoftheSocietyforNeuroscience,andProfessorofPathologyand
CellBiology,Neuroscience,andOphthalmology,ColumbiaUniversity
LarrySwanson,PhD,PastPresidentoftheSocietyforNeuroscience,andMiloDonandLucille
ApplemanProfessor,UniversityofSouthernCalifornia
NOVEMBER13,2013OTHERBRAININVESTORS
MiyoungChun,PhD,ExecutiveVicePresidentofSciencePrograms,KavliFoundation
KathyHudson,PhD,DeputyDirectorforScience,Outreach,andPolicy,NationalInstitutesofHealth
AllanJones,PhD,ChiefExecutiveOfficerAllenInstituteforBrainScience
GeoffreyLing,MD,PhD,DeputyDirectoroftheDefenseSciencesOffice,DefenseAdvancedResearch
ProjectsAgency
GeraldRubin,PhD,VicePresidentandExecutiveDirector,JaneliaFarmResearchCampus
JohnWingfield,PhD,AssistantDirectorfortheDirectorateforBiologicalSciences,NationalScience
Foundation
CLINICALCONSULTATIONS
RobertBrown,Jr,MD,President,AmericanNeurologicalAssociation
WilliamCouldwell,MD,PhD,President,AmericanAssociationofNeurologicalSurgeons
JeffreyLieberman,MD,President,AmericanPsychiatricAssociation
DanielMarson,JD,PhD,NationalAcademyofNeuropsychology
JohnMazziotta,MD,PhD,ExecutiveViceDean,DavidGeffenSchoolofMedicine,Universityof
California,LosAngeles
TimothyPedley,MD,President,AmericanAcademyofNeurology
StanleyPrusiner,MD,Presidentelect,AmericanNeurologicalAssociation
AliRezai,MD,President,CongressofNeurologicalSurgeons
DavidRubinow,MD,AssadMeymandiDistinguishedProfessorandChairofPsychiatry,
UniversityofNorthCarolina
MatthewState,MD,PhD,DirectorofLangleyPorterPsychiatricInstituteandChairof
Psychiatry,UniversityofCalifornia,SanFrancisco
GordonSze,MD,President,AmericanSocietyofNeuroradiology

144

APPENDIXCACRONYMLIST
ALS
AIDS
ATUM
BCI
BD2K
BOLD
cAMP
C.elegans
CLARITY

CMOS
Cre
CRCNS
CRISPR
CTSA
DARPA
DBS
DNA
DREADD
DWMRI
EEG
EM
FDA
FIB

Flp

fMRI
FY

GABA
Genesis
GRASP
HHMI
HIV
IDPRIME
iPS

IRB
Ldopa
LFP
MCell
MEG
ModelDB
MR

AmyotrophicLateralSclerosis
AcquiredImmunodeficiencySyndrome
AutomatedTapeUltramicrotomy
BrainComputerInterface
BigDatatoKnowledge
BloodOxygenLevelDependent
CyclicAdenosineMonophosphate
Caenorhabditiselegans
Clear,LipidExchanged,AnatomicallyRigid,Imaging/Immunostaining,
Compatible,TissueHydrogel
ComplementaryMetalOxideSemiconductor
CarbapenemResistantEnterobacteriaceae
CollaborativeResearchinComputationalNeuroscience
ClusteredRegularlyInterspacedShortPalindromicRepeat
ClinicalandTranslationalScienceAward
DefenseAdvancedResearchProjectsAgency
DeepBrainStimulation
DeoxyribonucleicAcid
DesignerReceptorsExclusivelyActivatedbyDesignerDrug
DiffusionWeightedMagneticResonanceImaging
Electroencephalography
ElectronMicroscopy
FoodandDrugAdministration
FocusedIonBeam
Flippase
FunctionalMagneticResonanceImaging
FiscalYear
GammaAminobutyricAcid
GeneralNeuralStimulationSystem
GFPReconstitutionAcrossSynapticPartners
HowardHughesMedicalInstitute
HumanImmunodeficiencyVirus
InteractionDependentProbeIncorporationMediatedbyEnzymes
InducedPluripotentStem
InstitutionalReviewBoard
Levodopa
LocalFieldPotential
MonteCarloCellSimulator
Magnetoencephalography
ModelDatabase
MagneticResonance
145

MRI
mRNA
NSF
PALM
PCR
PET
RASSL
rfMRI
RNA
RSN
SBF
SBIR
SeeDB
SNP
STED
STORM
TALEN
TEM
TMCS
TMS

MagneticResonanceImaging
MessengerRibonucleicAcid
NationalScienceFoundation
PhotoactivatedLocalizationMicroscopy
PolymeraseChainReaction
PositronEmissionTomography
ReceptorActivatedSolelybyaSyntheticLigand
RestingStateFunctionalMagneticResonanceImaging
RibonucleicAcid
RestingStateNetwork
SerialBlockFace
SmallBusinessInnovativeResearch
SeeDeepBrain
SingleNucleotidePolymorphism
StimulatedEmissionDepletion
StochasticOpticalReconstructionMicrosopy
TranscriptionActivatorLikeEffectorNuclease
TransmissionElectronMicroscopy
Theory,Modeling,Computation,andStatistics
TranscranialMagneticStimulation

146