Details on all the cellfinder cell detection parameters.
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