Table 1.
Journal-defined custom variables
| AcquireSettingFile | used in Load Autofocus Acquire Settings to define the file to be loaded |
| AcquireSettings | binary (Y/N) variable used in TMA Scanning Master to confirm that focus acquire settings have been set and saved correctly |
| ActiveImage | binary (Y/N) variable used in TMA Scanning Master to confirm that Stage list array.tif is open and active when using an existing stage list array file |
| AugmentRegionNumber | defined in AddToAllROINumbers and used in IncreaseROINumbers to indicate the constant value to be added when renumbering a set of ROIs |
| BottomRightX | used in Region label to array (or Region label to array (existing stage list array)) and used in SlideZ focus to define location of ROI designated for use in determining the central focal plane of each slide |
| BottomRightY | used in Region label to array (or Region label to array (existing stage list array)) and used in SlideZ focus to define location of ROI designated for use in determining the central focal plane of each slide |
| column | used in Segment TMA to define the grid |
| CurrentDpZ | used in scan slide adjust to track the most recent deep focus result within an ROI |
| CurrentSlide | used in SlideZ focus, scan tissue, and ROI focus and determined based on FirstROI variable |
| CurrentX, CurrentY | used in SlideZ focus and ROIZ focus to track stage position |
| Difference | used in Threshold finder to report the calculated threshold for the current image |
| Directory | defined by the Scan Slide variable ScanSlide.Directory and used in scan tissue |
| DpFocCh | defined in TMA Scanning Master and used in scan slide adjust to encode the channel, i.e. illumination settings, used for deep focusing |
| DpFocChk | used in scan slide adjust as counter to determine when a deep focus should be performed within an ROI |
| DpFocExp | defined in scan slide adjust to record value for entry into the summary log |
| DpFocInt | defined in TMA Scanning Master and used in scan tissue and scan slide adjust to indicate number of tiles imaged before deep focusing within an ROI |
| DpFocRange | defined in TMA Scanning Master and used in scan slide adjust to indicate the range, in microns, to be scanned when deep focusing within an ROI |
| DpStepSz | defined in TMA Scanning Master and used in scan slide adjust to indicate the size, in microns, of steps used when deep focusing within an ROI |
| DpFocVar | defined in TMA Scanning Master and used in scan slide adjust to indicate the size, in microns, of the acceptable difference in z between a newly identified focal point and the previous deep focal point when deep focusing |
| DpThreshold | defined in TMA Scanning Master and used in scan slide adjust to indicate the threshold used to determine if tissue is present when deep focusing |
| EndTime | defined in TMA Scanning Master and used in Record variables. |
| ErrorCode | Used in ROI focus and ROITissueNotFound. |
| FirstROINumber | used in Segment TMA to define the grid |
| FirstROIPos1 | binary (Y/N) variable used in TMA Scanning Master to ask if the first ROI on slide 1 is numbered 1 |
| FirstROISlide1, FirstROISlide2, FirstROISlide3, FirstROISlide4 | defined in TMA Scanning Master and used in SlideZ focus, scan tissue, and ROI focus to indicate the number of the first ROI on each slide. |
| FirstSubZ | numerical variable defined in ROI focus and used in scan slide adjust to tag the first tile within an ROI and to track the degree of discordance between previous and new focus positions |
| FnFocCh | defined in TMA Scanning Master and used in scan slide adjust to record the channel, i.e. illumination settings, used for fine focusing within an ROI |
| FnFocChk | introduced in scan tissue and used in scan slide adjust as a counter to determine when a fine focus should be performed within an ROI |
| FnFocExp | defined in scan slide adjust for entry into the summary log |
| FnFocInt | introduced in TMA Scanning Master and used in scan tissue and scan slide adjust to indicate the number of tiles imaged before fine focusing is performed within an ROI |
| FnFocRange | introduced in TMA Scanning Master and used in scan slide adjust to indicate the range, in microns, to be scanned when fine focusing within an ROI |
| FnFocStepSz | introduced in TMA Scanning Master and used in scan slide adjust to indicate the size, in microns, of steps used when fine focusing within an ROI. |
| FnFocVar | introduced in TMA Scanning Master and used in scan slide adjust; the size, in microns, of the acceptable difference in z between a newly identified focal point and the previous fine focal point when fine focusing within an ROI |
| FnThreshold | introduced in TMA Scanning Master and used in scan slide adjust to indicate the threshold used to determine if tissue is present in scan slide adjust |
| Focus | binary (Y/N) variable used in TMA Scanning Master to ask if z-origin is set and correct objective is in place |
| FocusChannel | defined by user in TMA Scanning Master and FocusAcquireSettings, used in Load Autofocus Acquire Settings, SlideZ Focus, ROI focus, and scan slide adjust to pass current focus channel information between journals |
| FocusROISlide1, FocusROISlide2, FocusROISlide3, FocusROISlide4 | introduced in TMA Scanning Master and used in Region label to array (or Region label to array (existing stage list array)) to indicate the number of the ROI to be used in determining the central focal plane of each slide |
| Height | used in SlideZ focus and ROI focus to direct stage y movements within the ROI |
| Homed | binary (Y/N) variable used in TMA Scanning Master to ask if stage is calibrated. |
| HowFarToMoveX | used in SlideZ focus and ROI focus to direct stage x movements within the ROI |
| HowFarToMoveY | used in SlideZ focus and ROI focus to direct stage y movements within the ROI |
| InitialZ | defined in TMA Scanning Master and used in SlideZ focus to record stage z position at start of TMA Scanning Master |
| Label | used in Region label to array and Region label to array (existing stage list array) to record the numerical value of the region label |
| LoadSave | used in LoadSaveRescanSettings to indicate whether settings are being loaded or saved |
| Mag | used in TMA Scanning Master, Review Scans, and Stich, Stack and Save Images to record the magnification setting used during TMA scanning |
| message | used in TMA Scanning Master, SlideZ focus, ROI focus, and Record variables to create text for entry into the summary log |
| moveXY | used in SlideZ focus and ROI focus to control how far in x and y directions the stage moves when focusing; the default value of 4 moves the stage 1/4 of the total width or height of the ROI |
| Name | used in scan tissue as string variable defined by Image.StageLabel for creating scan file name |
| NewArray | binary (Y/N) variable used in TMA Scanning Master to ask if a stage list array file needs to be created |
| NewDirectory | used in Stitch Stack and Save Images to define \stitched_stacks directory |
| NumberofScans | used in Review Scans and Stitch Stack and Save Images to calculate file names |
| Path | used in Review Scans and Stitch Stack and Save Images to calculate file names |
| Pattern | integer string used in SlideZ focus and ROI focus to move the xy stage within the ROI when determining focus points |
| Position | integer variable that increments for each plane in the stage list array file in add top left or bottom right position to array and Region label to array (or Region label to array (existing stage list array)) after being set to 1 in TMA Scanning Master |
| ReducedDpThreshold | defined in DpFnFocusSettings or in response to prompts and used as lower threshold in scan slide adjust |
| ReducedFnThreshold | defined in DpFnFocusSettings or in response to prompts and used as lower threshold in scan slide adjust |
| ReducedROIZCount | defined and used in ROITissueNotFound to track the number of times a focal point has been determined |
| ReducedROIZThreshold | defined in SlideROIFocusSettings or in response to prompts and used as lower threshold in ROITissueNotFound |
| RegionColumn | used in transfer shrink transfer TMA to number ROIs |
| RegionRow | used in transfer shrink transfer TMA to number ROIs |
| RepeatSlideROIZCount | defined and used in SlideZ-TissueNotFound to track the number of times a focal point has been determined |
| RepeatTotalZThreshold | defined in SlideROIFocusSettings or in response to prompts and used as lower threshold in SlideZ-TissueNotFound |
| ReviseThreshold | defined in ROITissueNotFound and used scan slide adjust to indicate that reduced deep and fine focus thresholds should be used when identifying tissue |
| ROI | used in Review Scans and Stitch Stack and Save Images to calculate file names |
| ROIDirectory | used in OpenPrelimAndROIs and LoadAdjustedRegions to track the directory where the preliminary scan and ROIs are stored. |
| ROIgroup | used in Save all slide ROIs to determine which ROI group is being saved |
| ROISetCount | used in Reload ROIs to count the sets being loaded |
| ROISetLoad | used in Reload One ROI Set to determine which ROI set should be loaded |
| ROISetNumber | used in Save and clear ROIs to determine which ROI set is being saved |
| ROISetsTotal | used in Reload ROIst o determine how many ROI sets will be loaded |
| ROIZ | used in ROI focus to record z origin of each ROI |
| ROIZ1, ROIZ2, ROIZ3 | temporary variables used in ROI focus to record focal points |
| ROIZcount | used in ROI focus to track the number of times a focal point has been determined |
| ROIZFocCh | defined in TMA Scanning Master and used in ROI focus to indicate the channel, i.e. illumination settings, used to determine the origin focal plane for each ROI |
| ROIZFocExp | defined in ROI focus to retains value for entry into the summary log |
| ROIZFocRange | defined in TMA Scanning Master and used in ROI focus to indicate the range, in microns, to be scanned in determining the origin focal plane for each ROI |
| ROIFocSettings | binary (Y/N) variable used in TMA Scanning Master to ask if the default (hard coded) settings will be used for ROI focus |
| ROIZFocStepSz | defined in TMA Scanning Master and used in ROI focus to indicate the size, in microns, of steps used when determining the origin focal plane for each ROI |
| ROIZFocVar | defined in TMA Scanning Master and used in ROI focus to indicate the size, in microns, of the acceptable difference in z between two identified focal points when determining the origin focal plane for each ROI |
| ROIZThreshold | defined in TMA Scanning Master and used in ROI focus to indicate the threshold used to determine if tissue is present in ROI focus. |
| row | used in Segment TMA to define the grid |
| ScanName | used in Review Scans and Stitch Stack and Save Images to store temporary file names |
| ScanslideCheck | used in TMA Scanning Master to query user about Scan Slide settings |
| ScanslideFocSettings | used in TMA Scanning Master to query user about Scan Slide settings |
| ScanSlideSettingFile | used in SaveCurrentAndUsedSettings to record the Scan Slide save directory |
| ScanSettings | binary (Y/N) variable used in TMA Scanning Master to confirm that settings have been entered correctly |
| SkipConfigurationQuestions | used in TMA Scanning Master to bypass configuration questions |
| slide | used in segment TMA to record the number of the slide for which ROIs are being defined |
| Slide1Z, Slide2Z, Slide3Z, Slide4Z | introduced in TMA Scanning Master and used in SlideZ focus and ROI focus to record of central focal plane for each slide. |
| SlideFocSettings | binary (Y/N) variable used in TMA Scanning Master to ask if the default (hard coded) slide and ROI focus settings will be used |
| SlideLayout | binary (Y/N) variable used in TMA Scanning Master to ask if the default (hard coded) slide layout will be used |
| SlideROIZ1 | introduced in TMA Scanning Master and used in SlideZ focus to record focal points determined within SlideZ focus |
| SlideROIZ2, SlideROIZ3 | used in SlideZ focus to record focal points determined within SlideZ focus |
| SlideROIZcount | used in SlideZ focus to track the number of times a focal point has been determined |
| SlideZ | introduced in TMA Scanning Master and used in SlideZ focus as temporary variable to record central focal plane determined for slide (based on designated ROI) |
| SlideZFocExp | defined in SlideZ Focus for entry into the summary log |
| SSfocus | binary (Y/N) variable used in TMA Scanning Master to ask if focusing journals are used within Scan Slide |
| Stage position | used in add top left or bottom right position to array |
| StartImage | defined in segment TMA and used in transfer shrink transfer TMA journals |
| StartingScan | used in Review Scans and Stitch Stack and Save Images to calculate file names |
| StartTime | defined in TMA Scanning Master and used in Record variables |
| SubZ | used in scan slide adjust and before each image set the Z to track the most recent fine focus result within an ROI |
| SuitePath | used in Load Autofocus Acquire Settings to detrermine where the journals and acquire settings are stored |
| tempdir | used in TMA Scanning Master and Review Scan Summary to hold the path and file name for the Edge List Log file |
| TissuePresent | used in SlideZ focus and ROI focus to indicate that, based on scaling and threshold variables, tissue is present in the field imaged |
| TissuePresentDp | used in scan slide adjust to determine if tissue is present, based on scaling and threshold variables, before deep focusing. |
| TissuePresentFn | used in scan slide adjust to determine if tissue is present, based on scaling and threshold variables, before fine focusing |
| TopLeftX | used in Region label to array (or Region label to array (existing stage list array)) and SlideZ focus to define location of ROI designated for use in determining the central focal plane of each slide |
| TopLeftY | used in Region label to array (or Region label to array (existing stage list array)) and SlideZ focus to define location of ROI designated for use in determining the central focal plane of each slide |
| TotalPlanes | introduced in TMA Scanning Master and used in Region label to array existing stage list array) to indicate number of planes in existing stage list array file |
| TotalSlideNumber | used in TMA Scanning Master to indicate number of slides on stage |
| TotalZFocCh | introduced in TMA Scanning Master and used in SlideZ focus to indicate the channel, i.e. illumination settings, used to determine the central focal plane of each slide |
| TotalZFocStepSz | introduced in TMA Scanning Master and used in SlideZ focus to indicate the size, in microns, of steps used when determining the central focal plane of each slide |
| TotalZFocVar | introduced in TMA Scanning Master and used in SlideZ focus to indicate the size, in microns, of the acceptable difference in z between two identified focal points when determining the central focal plane of each slide |
| TotalZRange | introduced in TMA Scanning Master and used in SlideZ focus to indicate the range, in microns, to be scanned in determining the central focal plane of each slide |
| TotalZThreshold | introduced in TMA Scanning Master and used in SlideZ focus to indicate the threshold used to determine if tissue is present in SlideZ focus |
| Width | used in SlideZ focus and ROI focus to direct stage x movements within the ROI |
| Xrange | used in SlideZ focus and ROI focus to direct stage x movements within the ROI |
| Yrange | used in SlideZ focus and ROI focus to direct stage y movements within the ROI |