Parameters to set

Mandatory

• Signal image - set this to the image layer containing the labelled cells

• Background image - set this to the image layer without cells

• Voxel size (z) - in microns, the plane-spacing (from one 2D section to the next)

• Voxel size (y) - in microns, the voxel size in the vertical (top to bottom) dimension

• Voxel size (x) - in microns, the voxel size in the horizontal (left to right) dimension

Optional

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

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

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

• Filter width - 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 intensity threshold, in multiples of the standard deviation above the mean. Default: 10

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

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

• Trained model - To use your own network (not the one supplied with cellfinder) specify the model file.

Misc options

• To only analyse a limited number of planes (e.g. for speed during optimisation) you can:

  • Tick the Analyse local box. This will only process the planes around the currently selected plane

  • Set the Start plane and End plane, to e.g. 1000 and 1100, to only process the 100 planes between 1000 and 1100.

• To ensure that cellfinder doesn't use all the CPU cores on a machine, the Number of free cpus can be set. Default: 2

• To increase the logging (e.g. for troubleshooting), tick the Debug box.