Measure MEAN shape parameters for cells or nuclei

Parameters:

Name	#	Type	Description
Morphological parameter	1	string	Plots and saves time course of selected morphological data
Place positions into columns	2	boolean	Data from multiple stage positions will appear in new columns instead of being appended below the existing data. This option requires the MD output to be turned on.
Approximate cell diameter	3	integer	Diameter of the nucleus in pixels
Debris cutoff (percentile)	4	real	Brighter details of the image than this will be ignored
Minimum cell fluorescence (%)	5	real	Cells dimmer than this will be rejected. Increase this value if debris dimmer than the cells is detected.
Cell boundaries (% of max fluorescence)	6	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	7	boolean	Weld touching segments if they form a rounder object together. Use this to avoid objects fragmenting into multiple segments.
Minimum shape factor	8	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. The exports shape parameters to Excel Data Window.
*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.

Keywords: apoptosis, necrosis, cell cycle, cell division, cell growth, cell counting

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 parameter has been added.