Cells or Nuclei segmentation

Parameters:

Name	#	Type	Description
Approximate cell diameter	1	integer	Diameter of the nucleus in pixels
Debris cutoff (percentile)	2	real	This percentile of the image histogram sets the intensity value where the maximum of the Look Up Table (LUT) is scaled. Use -1 to override this with fixed value set below ant "Max value".
Minimum cell fluorescence (%)	3	real	Cells dimmer than this in filtered and 1-1000 rescaled images will be rejected. Increase this value if debris dimmer than the cells is detected.
Cell boundaries (% of max fluorescence)	4	real	Cells dimmer than this in filtered rescaled TMRM+FLIPR projection images will be rejected. Increase this value if debris dimmer than the cells is detected.
Weld segments into round objects	5	boolean	Weld touching segments if they form a rounder object together. Use this to avoid objects fragmenting into multiple segments.
Minimum shape factor	6	real	1 for disc, smaller for irregular shapes. 0 for not checking

Description:

Segments an image of cytosolic or nuclear stain into single cells or nuclei.

*If single nuclei are detected as multiple segments, increase the approximate cell diameter. In addition, you may turn segment welding on.
*If multiple nuclei are detected as single segments, decrease the approximate cell diameter. In addition, you may turn segment welding off.
*If debris is detected a nuclei, increase minimum cell fluorescence.
*If dimmer cells are missed, decrease minimum cell fluorescence.
*If bright debris outshines cells, decrease debris cutoff percentile.

V2
Segment welding has been enabled and separation of segments has been disabled.
No clipping during intensity scaling for seed calculation.
Intensity classifiers are applied to the seeds, as well as to the secondary segmentation.
V3
Fixed association of Minimum cell fluorescence (%) with intensity classifiers and Cell boundaries (% of max fluorescence) with Watershed "Determine boundaries at" function parameters.
Minimum shape factor pipeline parameter was added.