PT Manual Version 3.0

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gel analysis interpretation sample process management
v3.0 user manual
Contents 1.0 Understanding the main Platinum functions. 1.1 Initial log on screen 1.2 Initial window 1.3 Active analysis window 1.3.1 Menu bar 1.3.1.1 File submenu 1.3.1.2 Edit submenu 1.3.1.3 View submenu 1.3.1.4 Validation submenu 1.3.1.5 Worklist submenu 1.3.1.6 Gel submenu 1.3.1.7 Comment submenu 1.3.1.8 Report submenu 1.3.1.9 Window submenu 1.3.1.10 Database Submenu 1.3.1.11 LIMS Submenu 1.3.1.12 Window Submenu 1.3.2 Tool bar 2.0 Performing Tasks in Platinum 2.1 Searching the Data base 2.1.1 Search terms 2.1.1.1 Default search terms 2.1.1.2 Demographic search terms 2.1.1.3 Samples/ whole gels 2.1.2 Display of search results 2.2 Setting up a worklist 2.2.1 Setting up a worklist before scanning a gel 2.2.1.1 Creating the worklist 2.2.1.2 Filling a worklist from ESH 2.2.1.3 Filling a worklist from LIMS or LIS 2.2.1.4 Saving the worklist 2.2.2 Setting up a worklist after scanning a gel 2.3 Scanning a gel 2.3.1 Selecting a gel type 2.3.2 Placement of the gel on the scanner 2.3.3 Scanning the gel 2.4 Aligning a gel template 2.4.1 Marking a gel 2.4.2 Aligning a gel 2.5 Editing a gel 2.5.1 Editing status indicators 2.5.2 Editing the base line 2.5.3 Editing peaks 2.5.4 Editing M-spikes 2.5.5 Adjusting gain settings 3 3 3 3 4 4 8 11 15 16 17 20 23 24 26 27 28 29 29 29 29 30 31 31 32 32 32 32 32 33 33 34 34 34 34 35 35 35 37 37 37 38 39 40
Platinum Software version 3.0 Manual
2.6 Linking results 2.6.1 Linking IFE images to scan results 2.6.2 Linking scan results to IFE images 2.7 Configuration of a gel 2.7.1 Gel configuration menu 2.7.1.1 Gel type 2.7.1.2 Geometry 2.7.1.3 Lanes 2.7.1.4 Bands 2.7.1.5 Smoothing and Filtering 2.7.1.6 Gains Settings 2.7.1.7 Lot ID 2.8 Creating and editing a report 2.8.1 Creating a new report 2.8.2 Editing an existing report 2.8.3 Template layout icons and menus 2.8.3.1 Standard Pt icons and menus 2.8.3.2 Page layout 2.8.4 How to create a template lay out 2.8.5 Producing a report 2.8.6 Selection of a report 2.8.7 Previewing a report 2.8.8 Printing a report 2.9 Performing statistics 2.10 Performing Levey-Jennings analysis 2.11 Configuration for ESH connection 2.11.1 Customise menu configuration 2.12 Configuration for LIMS connection 2.12.1 Customise menu configuration 2.12.2 Gel configuration 2.13 Specification of Communication between Platinum and LIMS Systems
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1.0 Understanding the main Platinum functions.

1.1 Initial log on screen. When the Platinum Software is started the user is given the choice to either log on or to change the password of a particular operator level. User level Password = helena Supervisor level Password = sr53xb
1.2 Initial Window After logging on the first screen that is displayed gives options that determine the main action of the session, either to start a new scan, search for previously scanned data or to continue editing a previously saved record.
1.3 Active analysis window

Menu options Whole gel image IFE display Comments Patient demographics Tool bar Scan image Scan trace Active sample bands list
Once a gel has been scanned or a stored scan opened then it is displayed in an active analysis window.
1.3.1 Menu Bar
There are eleven selectable options on the menu bar. 1.3.1.1 File Submenu
New Allows the opening of a new analysis window. Search This allows the operator to search for scan data which have been saved along with demographic information. For details on performing searches see section Searching the Database.
Open.. This allows files to be opened that have been saved in previous sessions or to allow files to be imported from other instruments. This is used to open previous entered worklists that have not had a scan attached and are displayed as *.wl0 files.
Open Similar Data This allows the user to open any previous gel scans and data for the selected patient. The demographic that is used to call up previous results is set in the demographic configuration. Save This allows the operator to save the current scan data without exiting the program or closing the active window. At user level access there is no choice as to the file name or destination of the saved data. The scan image is saved with an unique number relating to the exact time and date the analysis was performed. Save as This allows the user to select an alternative file name and location when saving. Close This allows the current window to be closed and the data will be automatically saved. Print.. This allows the printing of a report for the current scan data.
Print preview.. This allows the operator to view a preview of the current report before printing.
Printer Setup This allows the configuration of the printer to be altered, the exact details of this are printer dependant.
Customise.. This submenu allows the user to configure the various settings of Platinum. These are;
File locations. Used to define the default directory for saving gel image and worklist files. Configure Demographics. Used to set up to ten demographic fields and identify which is to be used as the identifier in communication with a host system. Institution Data. Information relating to the user institution. Receiving from LIS. Configuration of Platinum to allow communication with a host system. Sending to LIS. Configuration of Platinum to allow communication with a host system and to define what information is sent to the host system from Platinum. Receiving from ESH Configuration of Platinum to receive information from ESH. Customise Tool bar This allows the user to select what icons are displayed on the tool bar. Operator.. This allows the operator to change the level at which they are logged on during a session.
Exit.. This allows the operator to exit the program and will automatically save any scan data that has not been saved and update any editing that has taken place.
1-5 File Listing The previous five files that have been open are kept displayed at the bottom of the File submenu.
1.3.1.2 Edit Submenu
Undo If any editing of scan data has taken place then this allows it to be undone. Redo If an editing operation has been undone then this allows it to be redone without performing the editing operation again. Select All It is the default that only one sample at a time is active and the scan data displayed. Using Select All the operator can select all scan data at once. Next lane This allows the user to advance to the next patient. Previous lane. This allows the user to return to the previous patient. Edit Baseline This allows the operator to edit the base line of the current scan data displayed as the scan trace. For further details see Editing scan data
base line
Edit Peaks This allows the operator to edit the peaks of the current scan data displayed as the scan trace. Peaks are defined by two trough markers, a trough marker is automatically placed at the lowest point between two peaks. For further details see Editing Scan Data.
trough markers
Skim Data
This allows the operator to skim out scan data, which is thought to be an anomaly. This could be in the form of an artefact spike on an otherwise smooth curve. When Skim Data is checked the cursor will show as active over the scan trace. The area to be removed is highlighted by keeping the left mouse button pressed whilst dragging over the required area. Slice Data
This allows the operator to slice out scan data, which is thought to be an anomaly. This could be in the form of an artefact spike on an otherwise smooth curve. When Slice Data is checked the cursor will show as active over the scan trace. The area to be removed is highlighted by keeping the left mouse button pressed whilst dragging over the required area. The trace is drawn to the base line rather than peak to peak as in Skim Data.
Stretch Data
This allows the operator to scale a selected trace to match that of another, i.e. a reference trace. When Stretch Data is checked the outer edges and centre of the trace will be highlighted. Using the left mouse button these markers can be dragged to the new position, the trace will be scaled to fit. Copy Copy allows any of the displayed scan data to be copied and pasted into other Windows applications.
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1.3.1.3 View submenu
Preferences.. This contains a table that allows alterations to the appearance of features of the analysis window, reports and tables.
Scan Plot
Gain Settings.. This allows the gain settings to be altered for the gel being analysed.
Set Scale.. This allows the operator to set the x and y axis scales on the scan trace image. Zoom Out If the operator has zoomed in on the gel image then this will allow them to zoom out in individual steps.
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Reset Scale This will allow any changes to the scale of the scan trace image to be returned to default. Gel Image
Full scale view This toggles the gel view to show the whole gel image. Detail view This toggles the gel view to the last zoomed in setting. View as gel This displays the whole gel image in the standard analysis window. View as traces. This displays all samples gel as traces. When a trace is selected editing is continued in the standard analysis window. Enhance contrast When this is selected the whole gel image and scan image are displayed in a single colour determined by the darkest pixel point on the gel scan. Intensity This is used to adjust the level of contrast that is used to display the whole gel and scan image.
Full colour spectrum When this is selected the whole gel image and scan image are displayed in false colour where black is darkest and blue is lightest. Maximise This displays the whole gel image in a new window at large scale.
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Restore This returns the whole gel image to the previous display scale in the standard analysis window. IFE
Full Scale View This displays the IFE total IFE image. Detail View This displays a magnified IFE image. Enhance contrast When this is selected the IFE image is displayed in a single colour determined by the darkest pixel point on the IFE image. Intensity This is used to adjust the level of contrast that is used to display the IFE image.
Full colour spectrum When this is selected the IFE image is displayed in false colour where black is darkest and blue is lightest. Helper Lines. When selected three lines are displayed on the IFE image to allow alignment of monoclonal bands.
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Bands
Show Peak Integral Value (IF) This allows the operator to select whether or not the peak integral values are displayed in the bands list table next to each band. Show Band Concentrations This allows the operator to select whether or not the band concentrations are displayed in the bands list table next to each band. Show Band Ranges This allows the operator to select whether or not the normal ranges are displayed in the bands list table next to each band.
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1.3.1.4 Validation submenu
Validation.. This allows the operator to enter into the validation window.
Levey-Jennings.. This allows the user to enter into the Levey-Jennings window. Control data can be searched and displayed in a Levey-Jennings plot.
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1.3.1.5 Worklist submenu
Set up Worklist This allows the operator to set up a work list of patient demographic information for a gel before or after it has been scanned. If this is done before a gel is scanned then the worklist can be stored for later attachment to a gel. For details on how to set up a worklist see the section Setting up a Worklist.
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1.3.1.6
Gel Submenu
Select Scanner.. This allows the operator to select the source scanner if more than one unit is connected. Select Gel This allows the operator to select the gel format that is to be used in the next scan.
Scan This starts the scanning of the gel. When selected an icon will appear to ensure that the gel is correctly placed for scanning.
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Align Gel.. When a gel is scanned a template mask is applied to the image and determines which data is to be analysed. These templates are set as defaults for different gel types but can be adjusted using Align Gel for individual gels to give a better fit. For further information see Aligning a gel template Re-Interpret Lane This allows any editing operations to be removed from the currently active sample scan data. The original data will be re-displayed. Re-Interpret Gel This allows any editing operations to be removed from the whole gel. The use of the function will return all displayed data to that of the original. Mark Gel This is used to indicate on the scanned image of the whole gel where the scan data template is being applied. Each lane is colour coded to indicate the editing status of each sample, this correspond to that of the sample number.
Search & Attach IFE This is used to search the database for any previously stored IFE scans for the currently active sample. Once found the IFE is attached so that when the scan data is retrieved the attached IFE is also displayed. For further information see Linking IFE and Scan results.
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Attach IFE to Scans This is used to search the database for any previously stored scan data and attach it to the current IFE image. Once found the scan data is attached so whenever the scan data is retrieved in the future the IFE image is also displayed.
Attached Scans When viewing an IFE sample this allows the user to retrieve any scans that have the selected IFE attached. Statistics.. This displays a table of means; standard deviations and C.V.s for any selected scan data. More than one sample at a time can be selected by keeping the Ctrl key pressed whilst selecting samples. Configure gels.. This allows the operator to configure the gel templates that are used to define the scan areas. There are factory set template configurations that correspond to commercially available gel types, these can be varied to allow for local variations. For more details see Configuration of gels.
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1.3.1.7 Scan Sub menu
Next Lane This allows the user to advance to the next patient sample. Previous Lane This allows the user to return to the previous patient sample. Enter Total Chemistry Value This allows the user to enter the chemistry value for a selected sample without selection in the patient demographics.
Mark as sample The selected sample is marked as a sample. Mark as Normal Control The selected sample is marked as a normal control. Mark as Abnormal Control The selected sample is marked as an abnormal control. Mark as Calibrator The selected sample is marked as a calibrator.
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Mark Automatically This is the default selection and all lanes are marked as samples either normal or abnormal dependant on the gel configuration. Mark as Normal This allows a patient sample marked as abnormal by the default method relative to the gel configuration to be marked as normal. For example if a serum protein were showing six bands rather than five it may be marked as abnormal. The actual sample may still be normal and so the sample could be marked as such without editing to remove one of the bands. Mark as Abnormal This allows a patient sample marked as normal by the default method relative to the gel configuration to be marked as abnormal. For example if a serum protein were showing five bands with a small monoclonal band in the gamma and the whole gamma region was still in range then the sample would be marked as normal. The sample could then be marked as abnormal without having to edit in the monoclonal band. Automatic Levey-Jennings This automatically marks a gel as having a control that is in range or out of range to within 2 SDs of the assigned mean. Suspect Levey-Jennings If a control is in range but there appears to be a trend taking the gel out of range then the gel can be marked as suspect. Accept Levey Jennings This allows the user to accept the results on a gel and mark it as such even if a control is shown to be out of range. Smoothing The use of smoothing allows the user to reduce the effect and display of noise shown on the scan trace. This is achieved through plotting a rolling average of results rather than individual points. The degree of smoothing used is on an arbitrary scale and increasing smooth too much can result in an adverse effect on quantitated values. Smoothing is set in the gel configuration but this function allows individual smoothing to be applied to each sample.
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Filtering The use of filtering alters the detection at which a trough marker is automatically placed on a scan trace. Filtering is set in the gel configuration but this function allows individual filtering to be applied to each sample.
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1.3.1.8 Comment Submenu
Add Comment This allows the operator to add a comment to the current sample from a list of predefined comments. This does not stop the operator from also adding free hand comments in the comments tile of the analysis window. Configure Comments.. This allows the operator to configure the comments that are held pre-defined in the Add Comments table.
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1.3.1.9 Report Submenu
New Report This allow s the operator to create a new report format. See Creating a report for further details
Load Report.. This allows the operator to load a previously saved report format. When selected the operator can browse all drives and directories and obtain the report format required.
Save Report This allows the operator to save an edited report template under the same file name.
Save Report As.. This allows the operator to save a new or edited report template under a new file name.
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Close Report This allows the operator to close the currently open report template without saving. Preview Report This allows the operator to preview a report lay out once it has been loaded into the program.
Edit Report This allows the operator to edit a previously created and saved report template.
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1.3.1.10 Database Submenu
Backup This group of functions allows data to be backed up to a location other than the main gel storage directory. New and Changed This function automatically backs up any new data created and any previously saved data that has been altered. All This function automatically backs up all data stored in the database Archive/Backup selected Data This allows specific data to be searched for and then only selected data to be archived. There is also the option to remove the backed up data from the database. Restore Data This function allows the import of new data or previously backed up data into the database. Compact Database This function reduces the size of the database through the removal of duplicate entries created during patient data retrieval. Clean Database This function cleans the database through the removal of any entries that do not have associated gel files.
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1.3.1.11 LIMS Sub Menu
Send Selected This function sends the data from any selected samples to the host system. The type of information sent from Platinum to the host system is set in the Customise function of the File sub menu. Send All This function sends the data from all samples on a gel to the host system. The type of information sent from Platinum to the host system is set in the Customise function of the File sub menu. Inspect This function allows the display of an inspection window that shows the progress of any communication between Platinum and the host system.
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1.3.1.12 Window Submenu
Cascade This allows all open windows to be viewed as a cascade. Tile Horizontal This allows all open windows to be viewed tiled horizontally.
Tile Vertical This allows all open windows to be viewed tiled vertically.
Close All This allows all open windows to be closed automatically saving any scan data and demographic information. 1- Gel Scan This lists all open windows and allows the operator to switch between them.
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2.0 Performing Tasks in Platinum 2.1 Searching the Data Base Previously stored scan data can be retrieved from the data base using the search facility. This can be accessed from all windows by either using the Menu Bar under File | Search or using the search icon . Both routes will activate the search window that displays all of the searchable fields available. Those fields are based upon the configured demographic fields as well as those relating to the type of gel and sample scanned.
Search terms
Function Keys Default search terms
Demographic configured search terms
Search results
2.1.1 Search Terms 2.1.1.1 Default search terms Default search terms are those terms that are the determined by the type of gels that are scanned and the type of samples, which are present on those gels. Scan type The Scan type describes the type of scan data that is to be searched for.
Sample This is used to describe a patient specimen regardless of the type of test that was performed. Using this term only scan data with patient demographics attached will be returned by the search. Normal control This is used to described controls with normal values that are run along side patient specimens. Using this term will return scan data for all normal controls regardless of the type of gel was scanned.
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Abnormal control This is used to described controls with abnormal values that are run along side patient specimens. Using this term will return scan data for all abnormal controls regardless of the type of gel was scanned. IFE This is used to describe scan data that were saved as IFE images only. Using this term only IFE scan data with patient demographics attached will be returned by the search. Gel name This is the name of the gel that is to be searched for. Only gel names which have had data stored are searchable.
Analysis type This describes the type of test that is to be searched for. Only analysis types, which have had data stored are searchable. The use of analysis type instead of gel type ensures that all data for one type of analysis are returned, I Measurement time This describes the date on which a scan was performed. It is possible to put in a low and high value to search for all scans performed in a certain time frame. Measurement status This describes whether normal, abnormal or both types of sample are to be returned in the search results. Levey-Jennings This describes whether the results to be returned from a search are from gels that have either passed, failed or both Levey-Jennings QC. 2.1.1.2 Demographic search terms Demographic search terms are those that are set in the configuration of the demographics at the initialisation of the software. These are used to search for specific individuals using terms such as their name or hospital identification number.
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2.1.1.3 Samples/ whole Gels The operator can choose between searching individual scan data or whole gels. This is achieved through the use of the two radio buttons at the top right of the search window. When searching for samples both default and demographic search terms are available whilst when searching for whole gels only default search terms are available. 2.1.2 Display of search results
All search results are displayed in the search data base window. This is used to check the validity of the returned results and the required items are selected. When this is done selection of the OK key will bring up the results in an analysis window where they can be compiled as standard scan data. It is important however, to note that it is not possible to edit scan traces when they have being retrieved from the data base. To do this it is necessary to access the original gel and edit the trace as normal. When this is done the data base and any active display containing the result will be up dated. Any search results that have been previously saved as independent files will obviously not be updated with the new editing. To access the original gel simply activate the sample require editing and right click on the mouse. A menu will appear and offer the choice to load the original gel that will be displayed, this can then be tiled so that both windows are displayed.
Original gel window Search results window
Active sample
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2.2 Setting up a worklist 2.2.1 Setting up a worklist before scanning a gel 2.2.1.1 Creating the worklist To create a worklist before a scan has been performed is sometimes required and can save time whilst a gel is being processed. From the initial screen select the new icon that will open up a new analysis window. Then select the set up worklist icon and this will open a worklist window with no entries in it. Patient demographic information can now be entered into the blank table. To insert new lines select the Add Blank button. It is possible to navigate through the table by using either a mouse or the cursor direction keys. The column headers are; Line this denotes the sample position on the gel, Sample/Control by default all positions are set as samples but these can be changed to either controls or calibrator on a sample-by-sample basis, Total Chemistry column and External Chemistry column Patient Demographics. 2.2.1.2 Filling the worklist from ESH To fill a worklist from ESH the ESH button should be selected and then the Query ESH option. This will bring in data from the ESH as the worklist ID and/or the worklist information. The worklist information transferred will fill the worklist under the demographic heading that has been selected as the LIS identifier in the customise submenu. 2.2.1.3 Filling the worklist from LIMS or LIS system. When filling the worklist from a host system there are two possibilities for accessing data. Both are found by selecting the LMS button. Option 1, Query LIMS. In this option the demographic field identified as the LIS identifier should be completed. These data are then sent as requests to the host system. The host system returns the matching demographics and chemistry values. Option 2, Fill worklist. In some instances a worklist may be available complete on the host system and in this case a LIS identifier is not required to be sent to the host system. If the main worklist is larger than can be accommodated on a single Platinum worklist then a partial subset can be imported by selecting the number in the list at which to start.
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2.2.1.4 Saving the worklist Once a worklist has been set up then it may be required to save it before the appropriate gel can be scanned. To save use the close button to exit the Set up Worklist window and display only the new analysis window, either select Save in the File submenu or close the new analysis window. Both actions will activate the Save As window for worklists. Enter the name of the worklist in the File name box and the select the Save button. The worklist will be saved until retrieved. 2.2.1.5 Retrieving the worklist and scanning a gel Once a worklist or worklists have been saved then it will be required to open these work lists and scan gels to attach to them. From the initial window select the open icon or File | open.., this will activate the open window and display all of the saved worklists. The selection can then be made and a new analysis window will be opened ready to scan a gel. Once the gel has been scanned then the worklist will no longer be available to be attached to other scan data. 2.2.2 Setting up a work list after scanning a gel After scanning a gel select the set up worklist icon and this will open a worklist window with a series of blank entries equal to the number of samples set in the gel configuration. See section 2.2.1 for functions.
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2.3 Scanning a gel This section deals with the placement of a gel in the scanner unit in the correct orientation. 2.3.1 Selecting a gel type Before scanning a gel it is necessary to select the type of gel that is to be scanned. To choose a gel, open the Gel sub menu from the menu bar and select gel. A menu will be displayed showing a list of all gels that are contained in the gel configurations.
2.3.2 Placement of the gel on the scanner Once the correct gel type has been selected then the gel should be placed face down in the top right hand corner of the scanner. All gels should be placed on the scanner so that the top left and bottom right corners when the gel is face up remain so when the gel is face down. 2.3.3 Scanning the gel When the gel is in place on the scanner close the lid and select either the scan icon or Scan from the Gel submenu. Before the scan begins a window will display how the gel of choice should be placed on the scanner. This should be checked and then click OK to continue. Before the scan takes place a dialog box may appear requesting the gel lot number to be entered. This will only appear is positive patient ID is selected in the customise menu and communication with an ESH is required. It does not need to be entered for normal scanning. The scan will take place and the whole gel image will be displayed in the analysis window.
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2.4 Aligning a gel template When a gel type is selected and a gel scanned a template is applied to the gel image. The template represents the areas of the gel image from which scan data will be analysed. These areas should correspond to each sample on the gel. The area of analysis of each sample should include all stained material from the beginning to the end of the sample lane and 75% of the lane width. There are numerous templates pre-set in the gel type menu all corresponding to particular gel configurations of gel size and sample number. These templates however, may require slight adjustments to account for individual variations. The steps below indicate how this is done. 2.4.1 Marking a gel To see that a template fits correctly on the scanned image a feature call Mark Gel can be used. This is selected in the Gel submenu as Mark gel. When this is selected a template mask is applied to the gel image and the alignment with the samples on the gel can be checked. If is out of line then this is adjusted with the align gel function.
2.4.2 Aligning a gel If after marking the gel it is found that the template needs adjustment then this is done by selection of the align gel function either in the Gel submenu as Align gel or the align gel icon . When the align gel function is active the mask will be removed from the gel image and is replaced by a set of three markers for each sample row. There are two
vertical markers that represent the left and right hand limits of each row and a single horizontal marker that indicates the centre position of the first sample in a row. Each of these markers can be positioned either by clicking and dragging with the cursor or by
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altering the values that are in the displayed table. These values indicate in mm the distance of the marker from the appropriate axis. Once any adjustments have been made then the new position of the template can be verified by deselecting the align gel icon and the template mask will be reapplied to the gel image. Before editing continues the mask can also be removed by un-checking Mark gel in the Gel submenu.
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2.5 Editing a gel When first a gel image is displayed it is likely that the scan data will require some form of adjustment so that the correct interpretation of the results can be reported. 2.5.1 Editing status indicators When the whole gel image is displayed the sample index is also displayed next to each sample. This index is in a coloured circle and it is this colour that indicates the editing status of each sample. The same colour scheme is used when the gel template mask is displayed. There is a default colour scheme that is used and is dependant on the mode that is set for detection of different bands. Recognise bands by tops. In this mode bands are recognised by the top of each peak. Each lane is marked red until some form of editing takes place. Red Orange Yellow Lane is unedited. Lane has been viewed but remains unedited. Lane has been viewed and edited.
Fixed Fraction mode. In this mode the expected number of bands is entered in the gel configuration along with either the expected relative percentages of each band or the expected concentration of each band, both are set as ranges. Red Orange Yellow Green Lane has incorrect number of bands or values are out of range. Lane has been viewed but not edited, still incorrect number of lanes or values are out of range. Lane has been edited but there are an incorrect number of bands or values are out of range. Lane has the correct number of bands and all are within range.
Using the fixed fraction mode this colour scheme allows the operator to easily see the status of all of the samples on the gel. After editing in this mode all normal samples should be green and the reportable samples will be yellow. 2.5.2 Editing the base line When the base line is set on the scan trace it is automatically set at the lowest point and therefore should only require editing if there is an anomaly in a particular trace. To edit the base line select either Edit base line in the Gel submenu or the Edit baseline icon . Whilst the edit base line unction is active it is possible to click and drag the base line with the cursor to the desired position. Once this is done all of the band values will be automatically re-calculated.
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2.5.3 Editing peaks When a scan trace is displayed the different peaks are marked automatically by trough markers that, are placed at the minimum points that divides peaks. In some instances an extra peak may be inserted or two peaks may not be differentiated. The operator can alter this using the edit peaks function. This can be activated by, selecting Edit peaks in the Gel submenu or the edit peaks icon . When peak editing is active the cursor will change to a horizontal double pointed arrow when placed over a trough marker. The markers can then be clicked dragged into position using the left mouse button. The marker can be removed by pressing the right mouse button and selecting Remove Trough in the menu that appears.
Move Trough
Remove Trough
2.5.4 Editing M-spikes M-spikes are spikes that appear within other peaks and require quantification whilst the peak they are a part of is also quantified as a whole. These spikes are not marked automatically and it is up to the operator to define where M-spikes lie. To introduce an M-spike the cursor is moved to where the peak is to be added by clicking the right mouse button and selecting either Add Skimmed M-spike or Add Sliced M-spike from the menu. The Sliced M-spike is calculated to the base line whereas the Skimmed M-spike is calculated to a base line taken between the intersections of the peak and the trough markers. Once inserted an M-Spike can be switched between the two types. The M-spike can be positioned by clicking and dragging the boundary markers.
Spike
Skimmed M-Spike
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The M-spike can be removed by clicking the right mouse button and selecting Remove M-Spike from the menu. In some instances multiple M-spikes are apparent and these can be included or removed in the same way as a single spike. The value of each Mspike is displayed in the band list table along with information as to which band the spike is associated.
2.5.5 Adjusting gain settings When ever a scan trace is displayed there are three ways in which to control the y-axis scale. To alter the gain settings select either Gain Settings in the View submenu or right click whilst the cursor is over the scan trace and select Gain Settings from the menu. Auto gain Auto gain sets the y-axis at 100% and this is the highest point on the trace, therefore regardless of the actual value the maximum point will always be 100% of the scale. Manual gain In manual gain the scale is displayed as a percentage but the scale is fixed by setting the maximum O.D. value. The scan trace is displayed relative to this scale. Constant gain In constant gain the maximum O.D. value of the yaxis is set and the scale displays this. The trace is displayed relative to this value.
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2.6 Linking results It is normally the case that if an IFE gel is to be run on a patient sample then a scan of the original patient sample will already exist. In the software it is possible to link many IFE images to many scan results so that when ever a patient scan is retrieved the IFE is also displayed. 2.6.1 Linking IFE images to scan results To link an IFE to a scan result the IFE image should be active and the patient demographic information filled in. Then in the Gel submenu select Attach IFE to Scans, the database search menu will be opened and the patient demographics of the scan will be automatically inserted. Select Search and the details of all the scans for the patient will be displayed. Select the correct scan result or results and the IFE will be linked to the result or results. When the scan result is opened in the future the IFE will also be displayed.
2.6.2 Linking scan results to IFE images To link a scan to an IFE result the scan result should be active and the patient demographic information filled in. Then in the Gel submenu select Search & Attach IFE, the database search menu will be opened and the patient demographics of the scan will be automatically inserted. Select Search and the details of all the IFEs for the patient will be displayed. Select the correct IFE image or images and the scan will be linked to the image or images. When the scan result is opened in the future the IFE will also be displayed.
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2.7 Configuration of a Gel In Platinum it is necessary to configure the templates that are used in the scanning of gels. These templates are used to indicate how large a gel is, how many samples there are and where they are located. This feature is only accessible at the supervisor level. 2.7.1 Gel Configuration menu. From the Gel menu select Configure gels and this will bring up the configuration table for editing. It is possible to import gel configurations using the Import gel definitions function. This function will import and merge or replace gel definitions from other gels.gel files.
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2.7.1.1 Gel Type In the Gel Type table the following can be set:-
Standard Gels This is where the gel name is entered. Analysis Type This is where the type of gel is entered i.e. Serum Protein, Urine Protein etc. Gel Type This is where the type of gel is entered i.e. Normal Gel for any gel that requires densiometric measurement, Validation Gel for validation gel formats and IFE Gel for gels that require an image to be captured. Scanning Mode This is where the mode of the scanner is selected. For transparent gels then Transparent should be selected whilst for opaque gels or membranes Reflective should be chosen. Total Chemistry Value Name This where the name of the total chemistry is entered i.e. Total Protein or Total Haemoglobin etc. and is used for the main imported chemistry value External Compound chemistry value This is the imported chemistry value that can be used in addition to the total chemistry value i.e. External Albumin. Concentration unit This is where the units that are to be applied to the chemistry values are entered. The units are only used as a title and not in any calculations. LIMS Name This is where the LIMS name for the chemistry value should be entered. Platinum uses this to identify the correct value to use from returned patient results.
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2.7.1.2 Geometry In the Geometry table the size and position of the total scan area is set.
Right edge This is the distance along the top edge of the scanner from the origin that the scan area will start. Upper edge This is the distance along the right hand side of the scanner from the origin that the scan area will start. Width This defines the scan area distance on the x-axis Height This defines the scan area distance on the y-axis
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2.7.1.3 Lanes In the lanes table the number and positioning of the samples is set.
Number This is the number of lanes on the gel. Samples per lane This is the number of samples that are in each lane Spacing This is the distance in mm between the centre point of two different samples when on a gel. Height This is the width in mm of the section of a lane that is included in the scan data i.e. if a lane is 6mm and the height is 4mm then 75% of the lane height has been included. Left and Right This is the distance in mm of the left and right hand edges of each lane from the right hand edge of the scanner Start This is the distance in mm on the first sample centre in a row from the upper edge of the scanner.
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2.7.1.4 Bands In the bands table the expected band positions and names are entered. In addition the mode by which peaks are detected and their expected values is also set.
Recognise Bands by Tops In this mode bands are recognised by the expected positions of the peak tops. Fixed fraction mode In this mode bands will be labelled if the number of bands detected matches that in the bands list. If there are more or less bands detected then the bands will only be labelled with the band index. Forced Fraction Mode In this mode bands are only labelled with the set names if there is the correct number of bands and they are in the correct position according to the Target Co-ordinate. Band This is the band index and will be used to number all peaks in a scan trace from left to right. Component The component column is where the name of the expected peak is entered. Target Co-ordinate This is the expected distance in mm of a peak from the origin and does not refer to the migration distance from the point of application of the sample. Low Limit This is where the lower limit of the expected clinical range for a particular band is entered. Upper Limit This is where the upper limit of the expected clinical range for a particular band is entered. Include in total area
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This check box is used to include or exclude a band form the total calculated area i.e. Albumin can be excluded from the total area and only the other globulin values are used. Calibrator This check box is used to indicate whether a band is to be used as the calibrator when using an internal calibrant i.e. the internal calibrator used to spike urine protein samples. Low control This is where the lower limit of the expected control range for a particular band in a normal control is entered. Upper control This is where the upper limit of the expected control range for a particular band in a normal control is entered. Low abnormal control This is where the lower limit of the expected control range for a particular band in an abnormal control is entered. Upper abnormal control This is where the upper limit of the expected control range for a particular band in an abnormal control is entered. Mean Normal This is where the target mean for each band in the normal control is added SD Normal This is where the SD for each band in the normal control is added. Mean Abnormal This is where the target mean for each band in the abnormal control is added SD Abnormal This is where the SD for each band in the abnormal control is added. Ratio Set up This is, were ratios are defined and stored for each gel type.
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2.7.1.5 Smoothing and Filtering This is where the degree of smoothing or filtering to be used on each gel type is set.
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2.7.1.6 Gain Settings Auto gain Auto gain sets the y-axis at 100% and this is the highest point on the trace, therefore regardless of the actual value the maximum point will always be 100% of the scale. Manual gain In manual gain the scale is displayed as a percentage but the scale is fixed by setting the maximum O.D. value. The scan trace is displayed relative to this scale. Constant gain In constant gain the maximum O.D. value of the y-axis is set and the scale displays this. The trace is displayed relative to this value.
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2.7.1.7 Lot ID. This is where the Lot numbers for the controls currently in use for an individual gel type are entered. This lot number is stored in the database and can be retrieved against any results used in a Levey-Jennings plot.
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2.8 Creating and Editing a Report 2.8.1 Creating a new report Select New Report in the Report submenu. This will open a new report window that will display the report template layout with all of the functions that are required to create new template designations. 2.8.2 Editing an existing report Select Edit Report in the Report submenu. This will open a report window that will display the report template layout with all of the functions that are required to edit the template designations. Standard Pt Icons and Menus Sample Indices Specific Information designations Standard formatting icons Block information designation icons Page layout
2.8.3 Template layout icons and menus 2.8.3.1 Standard Pt Icons and Menus These are the standard icons and menus used throughout Platinum and their function should be sort elsewhere in the manual. 2.8.3.2 Page Layout This is where the report template layout will be displayed showing the relationship between different blocks of information. Block Information designation icons These icons allow the designation of blocks of information or images to an area of the report template. This allows the operator to insert an external image final such as a hospital logo. This allows the operator to insert and display free hand text or use one of the specific information designations to be displayed.
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This allows the operator to insert a free hand straight line on the template. This allows the operator to insert a free hand box on the template. This allows the scan image for the selected sample to be displayed. This allows the scan trace for the selected sample to be displayed. This allows the band list information such as band names and values to be displayed for the selected sample. This allows the patient demograhic information for the selected sample to be displayed This allows a image of an attached IFE to be displayed for the selected sample. This allows the display of the whole gel image or search results. This allows all of the band information for all selected samples to be displayed. This allows the statistics for all selected samples to be displayed
This allows data from the validation table to be displayed. Standard Formatting icons These icons allow the standard formatting of any information that will be displayed through the template.
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Specific Information designations. These designations are used to label areas on the template to display specific information for the selected sample. Choosing any designation from page# to disk file date will display gel specific information regardless of the sample or samples selected. The remaining designations refer to the specific sample selected. For example demographics name 1 will display the title of demographics field 1 whilst demographics 1 will display the contents of that field. Sample indices This allows the operator to define for which sample information will be displayed.
2.8.4 How to create a template layout. In the new report window select either a block information designation icon or the text icon. Move the cursor over the page layout and click and drag a box of the correct size. This will then be the area where that information is displayed. The designation of the information that will be displayed can be changed by selecting the box and then selecting a new specific information designation. The sample the information refers to can be set by changing the sample index which is also displayed in the box along with the designation whilst in the report template window. This information is not displayed in the actual report. The information box can be further formatted using the standard formatting icons and menus to alter lines and fonts etc.
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2.8.5 Producing a report In Platinum it is possible to produce reports that display any combination of results in any format that is required. These formats are set up as templates in the report configuration menu that is only available through the supervisor level however all templates are available to the operator at the user level. 2.8.6 Selection of a report To select a report format select Load report in the Report submenu. This will open a menu where it is possible to browse for the required report. Once the report is selected the template will be displayed in a window. To return to the analysis window the report template window should be closed.
2.8.7 Previewing a report Once a report template has been selected it is possible to preview how results will appear in the final report. To see the preview either select Preview Report in the Report submenu or select the report preview icon . To return to the analysis window use the same icon as a toggle.
2.8.8 Printing a report To print a report it is possible to do so by either selecting Print in the File submenu or by selecting the print icon . Only those samples that are active on the whole gel image will be printed in the report. It is possible to either print each sample in a single report or to collate all the scan traces in one overlay image. This is done in the print preview window by selecting Single Graph in the Report submenu. The preview will display the over-laid traces before printing.
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2.9 Performing statistics Within Platinum it is possible to perform some basic statistical analysis on the scan data and display or print this information. To compare data from several or many scan results it is necessary to have all of the results in the same analysis window either on a single gel image or as the results of a database search. Once all of the samples are displayed together it is necessary to select all samples or those that are required for the analysis. This can be done either by selecting Select All in the Edit submenu or by holding down the Ctrl key while selecting the desired samples. When all of the required samples are selected then select Statistics in the Gel submenu and the statistics window will be displayed. In the Index column the index of each band is displayed and the number of samples n is in brackets. The name of each band is indicated in the band column. The remaining column or columns can be determined in the supervisor mode. These columns are used to display the mean plus or minus the standard deviation and the c.v. for the area, area % or concentration.
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2.10 Performing Levey-Jennings analysis This function allows the user to ensure that results obtained for patient samples are correct through the use of a corresponding control on the gel. In addition it allows the user to see developing trends in performance before a control actually falls out of range. To begin information on the control ranges must be entered into the bands list tab in the gel configuration table. This is activated from the Gel sub menu. In the Bands tab enter the mean and SD values for both the normal and abnormal control currently in use. In the Lot ID tab enter the Lot number for the current controls in use. When the gel is scanned, the control lanes must be indicated by marking them as either normal or abnormal. At any point a LeveyJennings analysis may be performed. This is begun either through use of the icon or through the Validation sub menu. In the initial LJ window select the gel type, control type and date range for the analysis then select OK. The LJ plot and table will be displayed. To alter the bands which are used in the analysis check or uncheck the selection in the View sub menu. The LJ report can be preview and edited like a standard report.
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2.11 Configuration for ESH connection. To allow Platinum to communicate with an ESH unit there are certain configurations that must be set. 2.11.1 Customise menu configuration. Configuration is set up in the File/ Customise submenu. There are several parameters that must be set in Platinum to match those in the ESH unit configuration. In addition there are two tick boxes that are selectable. Ensure Positive patient ID. This should be ticked, as this will ensure that the gel number is entered before a scan is performed. It is this number that is matched with the tray number sent from the ESH that ensures the correct gel is matched to the correct set of samples. Display inspector window. Ticking this box will display a window during communication with the ESH and indicate the status of the data transfer.
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2.12 Configuration for LIMS connection. To allow Platinum to communicate with a LIMS there are certain configurations that must be set. 2.12.1 Customise menu configuration. Configuration is set up in the File/ Customise submenu. There are three configuration menus that need to be completed for the LIMS communication. Configure Demographics. In the demographics configuration one of the fields is marked as the LIS Identifier. This is the identifier that is sent to the LIMS to identify the patient record required.
Receiving from LIMS. In this menu the communication parameters should be set to match those of the LIMS system.
Sending to LIMS. In this menu the communication parameters should be set to match those of the LIMS system. In addition those items being sent to the LIMS should be checked.
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2.12.2 Gel Configuration. In the Gel/Configure gels submenu in the gel type tab it is required that the LIMS name for the chemistry values are entered. When patient results are returned from the LIMS Platinum identifies the correct values using these tags.
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2.14 Specification of Communication between Platinum and LIMS Systems Any communication between two devices is defined on several levels. Physical Layer The lowest level is known as the physical layer. In order for Platinum to send results to a LIMS system the computer that runs Platinum must be connected to the LIMS system with a serial interface cable. Since the computer that runs Platinum is a DTE device, a null modem cable may be required to make the connection. Data Link Layer This level has procedures for link establishment and release, synchronisation, sequential control, error detection and error recovery. Platinum supports two data link implementations that lack any of the above. These are called no protocol and Xon / Xoff. The Xon / Xoff protocol provides only the most basic of synchronisation. It is strongly suggested that the third protocol, ASTM 1381, be used. This protocol provides for synchronisation as well as error checking. Please refer to the official ASTM 1381 release documents for details on this protocol. Network Layer, Transport Layer, Session Layer These layers are of no consequence for communications over serial cables. Presentation Layer: Sending Data to the LIMS This level deals with the formatting of the data being sent. Platinum has a number of data items that can be sent to the LIMS. These will be described below. The protocol used is based on ASTM standard 1394. Please refer to the official ASTM 1394 release documents for details on this protocol. Under the ASTM 1394 protocol, communication takes place by sending a number of records. Each message sent to the LIMS contains at least the following records: Header record Patient record Order record Result record(s) Terminating record
1
There may be multiple patient records, each with one or more order records , each with one or more result records. 2 Following either patient, order, or result records, Comment records may be included . Most data items that are sent are sent in the form of Result records. Header and terminating records follow the ASTM1394 standard precisely.
1 2
IN Platinum, there is always a single order record. Platinum only includes comment records at the Order record level.
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Patient Record A patient record takes this form: P|index||demofield1|demofield2|demofield3|\r Index gets consecutive values when multiple patient records are sent in a single message. The order of the demographic fields is identical to the order in which demographic fields are set up in Platinum. Note that Platinum does not follow the strict ASTM1394 standard here. \r indicates a carriage return character (13). NB Demographic data are sent as part of the patient record only. Order Record An order record takes the following form: O|index|||^^ânalysistype\r Index gets consecutive values when multiple order records are sent for a single patient. NB Gel analysis type is sent as part of the order record, and is repeated in all result records. \r indicates a carriage return character (13). Comment Record The comment record takes this form: C|index|I|comments\r Where: index gets consecutive values for each comment record \r indicates a carriage return character (13). Gel Name The gel name, if selected to be sent, is sent as a comment record: C|index|I|gelname\r Where: index gets consecutive values for each comment record \r indicates a carriage return character (13).
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Gel Lot The gel lot number, if selected to be sent, is sent as a comment record: C|index|I|gellotnumber\r Where: index gets consecutive values for each comment record \r indicates a carriage return character (13). Total Chemistry Value The total chemistry value is sent as a result record, as follows: R|index|^^ânalysistype^Total Chemistry Value|3.00|(mg/l)||||F|||20010730175834\r Where: index gets consecutive values for each result record 3.00 is the total chemistry value (mg/l) is the concentration unit as entered in the gel setup F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13). External Albumin The external albumin value is sent as a result record, as follows: R|index|^^Âpplicator SP24Êxternal Albumin|0.00|(mg/l)||||F|||20010730175834\r Where: index gets consecutive values for each result record 0.00 is the external albumin value (mg/l) is the concentration unit as entered in the gel setup F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13). Band Lists The user may choose to send band list items as percentage area, concentration, and/or area of each band. These items are sent as follows: R|index|^^Âpplicator SP24âlbumin^%|58.19|%||N||F|||20010730175834\r R|index|^^Âpplicator SP24âlbuminÛ|1.75|(mg/l)|1.00-2.00|N||F|||20010730175834\r R|index|^^Âpplicator SP24âlbuminÎ|1162|||||F|||20010730175834\r Where:
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index gets consecutive values for each result record % indicates the area percentage U indicates concentration I indicates band area 58.19, 1.75, 1162 are the bands relative area, concentration, area %, (mg/l) are the units 1.00-2.00 is the result normal range N, H, L are result range flags (only N is shown here) F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13).
At the end of the band list result records additional records for total values are included: R|index|^^Âpplicator SP24^TotalÛ|3.00|(mg/l)||||F|||20010730175834\r R|index|^^Âpplicator SP24^TotalÎ|1997|||||F|||20010730175834\r No record for total relative area is included. Ratio Values If ratios are calculated for the bands, they are sent as follows: R|index|^^Âpplicator SP24^Ratio|0.94|||||F|||20010730175834\r index gets consecutive values for each result record Ratio is the name that was given the ratio 0.94 is the calculated ratio F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13).
Trace Values If the user elects to send trace values to the LIMS, they are sent as follows: R|index|^^Âpplicator SP24^TraceValues|0.0424^0.0420^0.0424^^0.0391|||||F|||20010730175834\r Where: index gets consecutive values for each result record \r indicates a carriage return character (13). The trace values are separated by the component delimiter character, in this case the caret (^).
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Scan Image If the user elects to send the scan image to the LIMS, it is sent as follows: R|index|^^Âpplicator SP24^ScanImage|RGBvaluesLine1^RGBvaluesLine2^^|||||F|||20010730175834\r Where: index gets consecutive values for each result record RGBvaluesLine1 hexadecimally coded R, G, B values for each pixel on the first line of the image. For instance: f2eae8f0e8e6f1e9e7 defines three pixels F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13). IFE images If the user elects to send the IFE images to the LIMS, it is sent as follows: R|index|^^Âpplicator SP24ÎFE1|RGBvaluesLine1^RGBvaluesLine2^^|||||F|||20010730175834\r If applicable, a second IFE image is sent: R|index|^^Âpplicator SP24ÎFE2|RGBvaluesLine1^RGBvaluesLine2^^|||||F|||20010730175834\r Where: index gets consecutive values for each result record RGBvaluesLine1 hexadecimally coded R, G, B values for each pixel on the first line of the image. For instance: f2eae8f0e8e6f1e9e7 defines three pixels F indicates this is a final result 20010730175834 is YYYYMMDDHHMMSS where YYYY is the measurement year, MM is the month, DD is the date, HH is the hour, MM is the minutes, and SS is the seconds. \r indicates a carriage return character (13). Example message A complete message with selected results for two patients is shown below.
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H|\^&||PT|M$^Platinum^1.0|1 Microsoft Way||5555555\r P|1|bb||\r O|1|||^^Âpplicator SP24\r C|1|I|Scan is okay\r C|2|I|Applicator SP24\r R|1|^^Âpplicator SP24^Total Chemistry Value|3.00|(mg/l)||||F|||20010730175834\r R|2|^^Âpplicator SP24Êxternal Albumin|1.00|(mg/l)||||F|||20010730175834\r R|3|^^Âpplicator SP24âlbumin^%|57.86|%||N||F|||20010730175834\r R|4|^^Âpplicator SP24âlbuminÛ|1.74|(mg/l)|1.00-2.00|N||F|||20010730175834\r R|5|^^Âpplicator SP24âlbuminÎ|1185|||||F|||20010730175834\r R|6|^^Âpplicator SP24âlpha 1^%|4.54|%||N||F|||20010730175834\r R|7|^^Âpplicator SP24âlpha 1Û|0.14|(mg/l)|1.00-2.00|L||F|||20010730175834\r R|8|^^Âpplicator SP24âlpha 1Î|93|||||F|||20010730175834\r R|9|^^Âpplicator SP24âlpha2^%|10.75|%||N||F|||20010730175834\r R|10|^^Âpplicator SP24âlpha2Û|0.32|(mg/l)|1.00-2.00|L||F|||20010730175834\r R|11|^^Âpplicator SP24âlpha2Î|220|||||F|||20010730175834\r R|12|^^Âpplicator SP24^beta^%|14.04|%||N||F|||20010730175834\r R|13|^^Âpplicator SP24^betaÛ|0.42|(mg/l)|1.00-2.00|L||F|||20010730175834\r R|14|^^Âpplicator SP24^betaÎ|288|||||F|||20010730175834\r R|15|^^Âpplicator SP24^gamma^%|12.79|%||N||F|||20010730175834\r R|16|^^Âpplicator SP24^gammaÛ|0.38|(mg/l)|1.00-2.00|L||F|||20010730175834\r R|17|^^Âpplicator SP24^gammaÎ|262|||||F|||20010730175834\r R|18|^^Âpplicator SP24^TotalÛ|3.00|(mg/l)||||F|||20010730175834\r R|19|^^Âpplicator SP24^TotalÎ|2048|||||F|||20010730175834\r R|20|^^Âpplicator SP24^Ratio|0.93|||||F|||20010730175834\r P|2|cc||\r O|1|||^^Âpplicator SP24\r C|1|I|Scan looks fine\r C|2|I|Applicator SP24\r R|1|^^Âpplicator SP24^Total Chemistry Value|0.00|(mg/l)||||F|||20010730175835\r R|2|^^Âpplicator SP24Êxternal Albumin|0.00|(mg/l)||||F|||20010730175835\r R|3|^^Âpplicator SP24âlbumin^%|58.82|%||N||F|||20010730175835\r R|4|^^Âpplicator SP24âlbuminÛ|0.00|(mg/l)|1.00-2.00|L||F|||20010730175835\r R|5|^^Âpplicator SP24âlbuminÎ|1174|||||F|||20010730175835\r <alpha1 through beta peaks omitted> R|15|^^Âpplicator SP24^gamma^%|12.30|%||N||F|||20010730175835\r R|16|^^Âpplicator SP24^gammaÛ|0.00|(mg/l)|1.00-2.00|L||F|||20010730175835\r R|17|^^Âpplicator SP24^gammaÎ|245|||||F|||20010730175835\r R|18|^^Âpplicator SP24^TotalÛ|0.00|(mg/l)||||F|||20010730175835\r R|19|^^Âpplicator SP24^TotalÎ|1996|||||F|||20010730175835\r R|20|^^Âpplicator SP24^Ratio|0.93|||||F|||20010730175835\r L|1 Presentation Layer: Asking the LIMS for Demographics and Chemistry Values This level deals with the formatting of requests to the LIMS to send demographic information,. And with the format that the LIMS should use to reply to these requests.
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Format of Information Request Platinum can ask the LIMS fro information in two different ways: using a LIS identifier or using a gel identifier and a lane index (not implemented yet). The LIS identifier is one of the demographics that were set up using the File | Customise menu option. The demographic field to be used to query the LIMS is indicated by setting its Field Type to LIS identifier or LIS Identifier/Unique String (indicating a field that is used both to query the LIMS and to ensure uniqueness of values in the Platinum database). Typically, this field will be a tube number. Platinum can ask the LIMS for demographic information using one message per worklist line, or one message for all worklist lines. The second method reduces overhead considerably and is preferred. Indicate which format to use by means of the File | Customise | Receiving from LIMS menu option. The information request has the following format: header record request record [[request record]] terminator record The request record specifies the LIS identifier as follows: Q|1|5000^^||GelScan||||||||\r where 5000 is the LIS identifier. If Gel ID and lane index are used the format is: Q|1|^12345^4||GelScan||||||||\r where 12345 is the Gel ID, and 4 is the lane index. Example Requests This example asks for demographics and chemistry values for tubes with identifiers 5000 and 5001: H|\^&||PT|VMSC^Platinum^1.0|Liesbergstraat 9||2927704\r Q|1|5000^^||GelScan||||||||\r Q|2|5001^^||GelScan||||||||\r L|1\r If separate messages were used for each tube, there would have been two messages: H|\^&||PT|VMSC^Platinum^1.0|Liesbergstraat 9||2927704\r Q|1|5000^^||GelScan||||||||\r L|1\r and H|\^&||PT|VMSC^Platinum^1.0|Liesbergstraat 9||2927704\r Q|1|5001^^||GelScan||||||||\r
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L|1\r Format of Demographic and Chemistry Value Information The LIMS should reply to a request for information by sending a message that is formatted as follows: header record patient record (for each requested LIS identifier; if the patient is found) order record (if TCV or Albumin records are found) result record for Total Chemistry value (if applicable) result record for External Albumin (if applicable) [[patient record, order record, results records]] terminator record For each request, the LIMS should send exactly one response. If requests are combined into a single message, a single response message is expected. If requests are sent separately for each demographic, the LIMS should immediately respond to each request. Platinum will not send further requests before it has received a response. Patient Record The patient record should be formatted as follows: P|index||demofield1|demofield2|demofield3|\r Index gets consecutive values when multiple patient records are sent in a single message. The order of the demographic fields is identical to the order in which demographic fields are set up in Platinum. Note that Platinum does not follow the strict ASTM1394 standard here. \r indicates a carriage return character (13). If no demographics are known, do not send a patient record. A header and terminator record should still be sent. Order Record The order record should only be sent if at least one of Total Chemistry Value and External Albumin is available. It should be formatted as follows: O|index|||^^^MeasTypeName\r Index gets consecutive numbers when multiple order records are sent. However, for each patient the index starts at 1. MeasTypeName is the type of measurement, it is ignored here. \r indicates a carriage return character (13). Result Record The result records for Total Chemistry Value and External Albumin ( external chemistry) should only be sent if they are available. They take the following form: R|index|^^^MeasType^TCV|value|unit||||flag|||datestamp\r
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R|index|^^^MeasTypeÂlbumin|value|unit||||flag|||datestamp\r Index gets consecutive numbers when multiple result records are sent. However, for each patient the index starts at 1. MeasType is the type of measurement, it is ignored here. TCV is the name the LIMS uses for the total chemistry value. This name should be entered in the gel definition in Platinum, using the Gel | Configure Gels menu option. NB If the LIMS sends a result that does not match this name, the result will be ignored and a warning will be displayed. Albumin is the name the LIMS uses for the external albumin value. This name should be entered in the gel definition in Platinum, using the Gel | Configure Gels menu option. NB If the LIMS sends a result that does not match this name, the result will be ignored and a warning will be displayed. Value is the value of the item. Unit is the concentration unit. NB If it does not match the concentration unit that was entered in the gel definition in Platinum a warning will be displayed, but the value will be accepted. No unit conversion is attempted. Flag is ignored. Datestamp is ignored. \r indicates a carriage return character (13). Example LIMS Response This example contains (in order) a result with known TCV and Albumin values, a result with only a TCV value, and a result with no chemistry values. H|\^&||PT|VMSC^Platinum^1.0|Liesbergstraat 9||2927704\r P|1|Smith|5001|\r O|1|||^^^Serum Protein\r R|1|^^^Serum Protein^Chemistry Value|0.71|g/l||||F|||20010517142352\r R|2|^^^Serum ProteinÂlbumin|0.16|g/l||||F|||20010517142352\r P|2|Johnson|5005|\r O|1|||^^^Serum Protein\r R|1|^^^Serum Protein^Chemistry Value|0.22|g/l||||F|||20010517142352\r P|3|Mordichai|5007|\r L|1\r Logging The most recently received message from the LIMS is always stored in the current Directory for Gel Files (set using the File | Customise option), under the name FROMLIMS.log. This file may be inspected for debugging purposes.
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HL-2-1532P DOI 2006/06 (2) English

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3

gel analysis interpretation sample process management

v3.0 user manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.0 Understanding the main Platinum functions.

1.3 Active analysis window

Platinum Software version 3.0 Manual

1.3.1 Menu Bar

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.2 Edit Submenu

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.3 View submenu

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.4 Validation submenu

Platinum Software version 3.0 Manual

1.3.1.5 Worklist submenu

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.7 Scan Sub menu

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.8 Comment Submenu

Platinum Software version 3.0 Manual

1.3.1.9 Report Submenu

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

1.3.1.10 Database Submenu

Platinum Software version 3.0 Manual

1.3.1.11 LIMS Sub Menu

Platinum Software version 3.0 Manual

1.3.1.12 Window Submenu

Platinum Software version 3.0 Manual

Function Keys Default search terms

Demographic configured search terms

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual

Platinum Software version 3.0 Manual