Table 2.

Commonly configurable parameters in tgmm_config.txt

Parameter	Value range	Description/instructions
anisotropyZ	positive real number, usually greater than 1	Ratio of Z pixel scaling to X,Y scale. Refer to step 46.
backgroundThreshold	non-negative integer	Examine a typical image in Fiji to assess the mean intensity level (pixel values) in several background regions. Err on low side to minimize false negative detections.
persistanceSegmentationTau	positive real number	Nominal TGMM segmentation will use this parameter. With a typical image open in Fiji, draw a straight segment across several adjacent nuclei. Use Plot Profile (Analyze menu) to see the peaks and valleys. τ should be just lower than the intensity difference between the peaks and valleys. Examine several regions of several images for best results.
minTau	non-negative real number	Least possible difference between peaks and valleys as above. Will be used by TGMM to recursively break up large supervoxels using higher (but not lower) τ‘s than this value. Default = 0 to 2 for 8-bit images, 2 to 12 for 16-bit.
radiusMedianFilter	non-negative integer	Use to pre-process images prior to segmentation. We recommend values between 0 and 3 depending on size of nuclei and image noise. Default = 2.
sigmaGaussianBlurBackground	non-negative integer	Use to pre-process images prior to segmentation. We recommend setting to 10 times radiusMedianFilter.
useBlurredImageForBackgroundDetection	0 or 1	Use to pre-process images prior to segmentation. Will call background where pixel values in the blurred image are below backgroundThreshold. Default = 0.
weightBlurredImageSubtract	real number between 0 and 1	Use to pre-process images prior to segmentation. The blurred image is multiplied by this number then subtracted from median filtered image prior to segmentation. Default = 0.25.
temporalWindowForLogicalRules	positive integer	Tracking solution at each time point is subjected to rules governing splits, deaths, and new births – considering time points + or - this number away. Default = 4 to 6.
SLD_lengthTMthr	positive integer	Temporal window to declare short-lived division daughters viable or nonviable in the tracking solution. We recommend a value equal to (or less than) temporalWindowForLogicalRules.