cytracker settings

CyTracker Settings

List of settings

Common properties

Property	Type	Description
FrameRange	numeric	List of frames to process. Set to infinity (Inf) to process all frames.
SeriesRange	numeric	List of series to process. Set to infinity (Inf) to process all series in the movie.
OutputMovie	logical	If true, movies showing the segmentation and tracking will be saved. Set to false otherwise.
UseMasks	logical	If false, the algorithm will segment the cells. Set to true if you want to code to use existing masks (must be multi-page TIFF files). The mask files must be named using the following pattern: <filename>_<seriesNum>_masks.tif.
InputMaskDir	char	If this property is blank (''), the program will prompt you to select the folder containing the cell masks. You can also specify the path to the directory. Note: this property is only used if UseMasks = true.
RegisterImages	logical	If true, images wil be registerd to the previous frame. This helps handle microscope drift.
ChannelToRegister	char or numeric	Specify the channel to register on. The channel can be specified either by position (e.g. 2) or by name (e.g. Cy5). It is highly recommended to use a fluorescent channel as brightfield images are likely to register incorrectly.
SaveMasks	logical	If true, masks will be exported during processing.
ImageReader	char	Which reader to use. Current choices are bioformats or nd2sdk.
EnableParallel	logical	If true, the processing will be run in parallel. Note: The MATLAB Parallel Processing toolbox must be installed.
MaxWorkers	numeric	Specifies the maximum number of workers MATLAB should spawn for the parallel processing. Set to infinite (Inf) to use the maximum your computer can handle.
SwapZandT	logical	If true, swaps the z and t coordinates. Mainly as a workaround for issues with BioformatsImage

Cell Segmentation

Property	Type	Description
ChannelToSegment	char or numeric	Specifies the channel containing cells to segment. The channel can be specified either by position (e.g. 1) or by name (e.g. BF offset)
SegMode	char	Specifies the cell segmentation algorithm to use. Current choices are: brightfield, fluorescence, or experimental. See Cell Segmentation Algorithms.
ThresholdLevel	numeric	Specifies the sensitivity for the cell segmentation algorithm. See Cell Segmentation Algorithms.
MaxCellMinDepth	numeric	Sets the minimum cell depth for the segmentation modes which use the watershed algorithm to distinguish cell clumps (currently brightfield and fluorescence). See Cell Segmentation Algorithms.
CellAreaLim	[1x2] numeric	Specify the [min max] cell area (in pixels).

Spot detection

Property	Type	Description
SpotChannel	char or numeric	Specifies the channel containing spots to segment (if available). The channel can be specified either by position (e.g. 2) or by name (e.g. GFP). If this property is left blank (''), then spot detection will not be carried out.
SpotSegMode	char	Specifies the spot segmentation algorithm. Current choices are localmax,diffgaussian andDoG. DoG and diffgaussian are the same. See Spot Detection Algorithms.
SpotThreshold	numeric	Specifies the sensitivity for spot detection. See Spot Detection Algorithms.
SpotBgSubtract	logical	Specifies whether the spot background
should be subtracted (only for localmax algorithm).
MinSpotArea	numeric	Minimum spot area
UseSpotMask	logical	If true, spot mask should be used
SpotMaskDir	char	Location of spot masks
DoGSpotDiameter	numeric	Expected spot diameter (in pixels) for
difference of Gaussians filter
SpotErodePx	numeric	Number of pixels to erode spot mask
(to remove spots near the edge)

Tracking

For more details on these options, consult the Linear Assignment Toolbox wiki

Property	Type	Description
LinkedBy	char	Specifies the property used to link cells.
LinkCalculation	char	Specifies the calculation algorithm to calculate the linking score.
LinkingScoreRange	[1x 2] numeric	Specifies the [min max] score to link cells.
MaxTrackAge	numeric	The number of frames a track can miss before it is stopped.
TrackDivision	logical	If true, the code will look for division events.
MinAgeSinceDivision	numeric	The minimum number of frames after a division event before a new division event can occur.
DivisionParameter	char	Specifies the parameter used to determine if division occurred.
DivisionCalculation	char	Specifies the calculation algorithm to calculate the division score.
DivisionScoreRange	[1x2] numeric	Specifies the [min max] score to be considered a division event.
DivisionLinkToFrame	numeric	Specifies the number of frames to check if a division event occured.
LAPSolver	char	Specifies the algorithm used to solve the linear assignment problem. The current available options are munkres and lapjv.

Importing/Exporting settings

The functions importOptions and exportOptions can be used to load/save the tracker options. For example, the load an existing settings file:

>> importOptions(CT)

will cause a dialog box to pop up, prompting the user to select a file to load.

Similarly, to save the current options (a settings file is saved automatically after processing):

>> exportOptions(CT)

will produce a dialog box to select the location to save the file.

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