Accelerating Lung Imaging Research

Through Open Science

Tom Baer
Sean Bagshaw
Optical Society of America
May 13, 2010 – Washington, DC
Interactive Science Publishing (ISP)

• Enhance traditional publishing with 3D

interactions and annotations
• Deliver open-data directly into the hands of
researchers
• Disseminate open-source tools to the
scientific community
ISP History

• Inspired by this meeting 5 years ago

– Identified critical need for system to share data
– Motivation was to accelerate development of CAD and protocols
for lung cancer drug development and early detection
• Demonstration project was funded by
– Optical Society of America
– National Library of Medicine
– Air Force Office of Strategic Research
• Fully integrated into OSA publications
• OSA is willing to collaborate with other interested
scientific societies
Interactive Science Publishing (ISP)
Authors

-Annotate Upload
-Render MIDAS
-Evaluate

high-res

Readers
low-res

- Visualize
- Interact
- Measure
Download
ISP MIDAS Server (midas.osa.org)
• Web-based digital repository
• Database of massive collections of Hi/Low Resolution Images
• Supports over 20 types of Medical and non-medical image
files
• Rich seachable metadata
• 20GB of open-access data
• Over 30 articles
• Offline archive download
ISP Viewer
• Full Scientific and Medical Viewer
• Graphic-accelerated volume renderer
• Measurement tools: bi-dimensional, linear, angular
• Support plug-ins: Lesion Sizing Toolkit
• 3D Annotations
• Snapshots
• MIDAS Communication
ISP Viewer
Lesion Sizing Toolkit
• The Lesion Sizing Toolkit (LST)
is a free and open source
software architecture designed
to accelerate the development
and evaluation of quantitative
lesion sizing algorithms.
• Integrated with ISP
• public.kitware.com/lesionsizingkit
First ISP Special Issues
Issue 1: Inaugural ISP issue (Nov. 2008)
7 articles
Imaging systems * Medical optics and biotechnology * Microscopy
* Vision, color, and visual optics

Issue 2: OCT in Ophthalmology (Mar. 2008)

18 articles
OCT in * Functional OCT * Visualization and Image Processing in OCT
Glaucoma * OCT in Retinal Disease * OCT Technology

Issue 3: Digital Holography (Oct. 2009)

5 articles
Information Processing * 3D Microscopy * Image Reconstruction
ISP Special Issue – Lung Cancer Detection
Issue 4: Imaging for Early Lung Cancer Detection
(April, 2010 – Issue is in progress)

– Ideal subject for ISP display and analysis tools (including

lung lesion sizing tool)
– First article:
• RECIST versus volume measurement in medical CT using
ellipsoids of known size
– Future Sample article topics:
• A resource of thoracic CT scans from an anthropomorphic
phantom containing synthetic lung nodules
• Cases of people who developed cancer after baseline scan was
negative
• Biomarkers as metrics of therapeutic responses
ISP Survey 2009
• 426 readers
• 81% of respondents said the data views enhanced
their experience of reading the OSA article.
• Researchers make up 50% of the overall
respondents for the survey. Students make up 24%
of the overall, and their satisfaction with the ISP
Software service is the highest.
• 83% would recommend ISP to a colleague.
ISP Statistics

• Most downloaded paper for the past 5 months in

Applied Optics is an ISP article.
Cumulative Downloads of ISP articles
ISP in Action (Live Demo)
ISP – Future Vision
Future Enhancements
 Server-based architecture option

 Rich web applications

 Client technologies

 Infrastructure to support user-supplied visualization

and analysis tools
 Move to Cloud Computing
ISP – What is “Cloud Computing”?
ISP – What is “Cloud Computing”?

On Demand Resources:
•Processing Power when YOU need it.
•Storage for all your data needs – structured and unstructured
•Tools for data analysis – Foundation for specialized tools
•Secure access over the Internet.
The cloud could change the way we do
research
Offers the promise of broadening participation
• The Rest of Us
– Use laptops.
– Got data, now what?
– And it is really is about data, not the FLOPS…
» Our data collections are not as big as we wished.
» When data collection does grow large, not able to
analyze.
– Tools are limited, must dedicate resources to build
analysis tools (and this doesn’t help us complete our
research).

• Paradigm shifts for research

– The ability to marshal needed resources on demand.
» Without caring or knowing how it gets done…
– Funding agencies can request grantees to archive
research data.
– The cloud can support very large numbers of users or
communities.
Cloud for Research
Seamless interaction
• Cloud is the lens that magnifies the power of
desktop;
• Persist and share data from client in the cloud;
• Analyze data initially captured in client tools, such
as Excel;
– Analysis as a service (think SQL, Map-Reduce,
R/MatLab).
– Data visualization generated in the cloud, display on
client;
– Provenance, collaboration, other ‘core’ services…
Some Examples of Microsoft’s
Azure Cloud Research
Engagements
AzureBLAST
BLAST is a very popular life sciences
algorithm used commonly in
bioinformatics research.

selects DBs
and
input
sequence

Web Input
Role Splitter
Worker
Role

BLAST BLAST
Execution Execution

…
Worker Worker
Role #1 Role #n

Azure
Blob Configurati
BLAST DB

on
.
Storage Geno
Geno
me me Combiner
DB 1 DB K Worker
Role
AzureBLAST

Seamless Experience
•Evaluate data and invoke computational
models from Excel.
•Computationally heavy analysis done close
to large database of curated data.
•Scalable for large, surge computationally
heavy analysis.
•Test local, run on the cloud.
Supporting Smart Sensors and Data
Fusion
The NSF Ocean Observing Initiative
• Hundreds of cabled sensors and robots exploring the sea
floor
• Data to be collected, curated, mined
• OOI Architecture plan of record, store this data in the cloud
Data collected from:
•Ocean floor sensors, AUV tracks,
ship-side cruises, computational
models
Data moves from ocean to shore
side data center to the Azure
cloud to your computer.
Role of collaborating scientific societies

 Define standards for data, metadata, and

visualization/analysis tools for their communities
 Encourage cross discipline interoperability of metadata
searching and data analysis algorithms
 Encourage cross disciplinary studies and collaboration
 Develop standards for data quality and provenance,
intellectual property, patient privacy safe guards, etc.
 Convince funding agencies to support the ISP
infrastructure
Get the Software

• Windows and Mac

• ISP 2.3 released in April
• http://www.opticsinfobase.org/isp
• http://midas.osa.org
QUESTIONS?

Enhance
Deliver
Disseminate