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parameters-to-set.md

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Details on all the cellfinder cell detection parameters.

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.

{% hint style="info" %} The parameter values will be saved between sessions. The values can be reset by clicking the Reset defaults button. {% endhint %}