Cell candidate detection

To change how the cell candidates are detected, you can change the following options:

• --save-planes Whether to save the individual planes after processing and thresholding. Useful for debugging.

• --outlier-keep Don’t remove putative cells that fall outside initial clusters

• --artifact-keep Save artifacts into the initial xml file

• --max-cluster-size Largest putative cell cluster (in cubic um) where splitting should be attempted. Default: 100000

• --soma-diameter The expected soma size in um in the x/y dimensions. Default: 16

• --ball-xy-size The size in um of the ball used for the morphological filter in the x/y dimensions. Default: 6

• --ball-z-size The size in um of the ball used for the morphological filter in the z dimension. Default: 15

• --ball-overlap-fraction The fraction of the ball that has to cover thresholded pixels for the centre pixel to be considered a nucleus pixel. Default: 0.6

• --log-sigma-size The filter size used in the Laplacian of Gaussian filter to enhance the cell intensities. Given as a fraction of the soma-diameter. Default: 0.2

• --threshold The cell threshold, in multiples of the standard deviation above the mean. Default: 10

• --soma-spread-factor Soma size spread factor (for splitting up cell clusters). Default: 1.4