Automatic ROI drawing with 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. |
Mean shape factor |
6 |
real |
1 for disc, smaller for irregular shapes. 0 for not checking |
Description:
Segments the maximum intensity projection of the time lapse, creates ROIs from the segments and copies ROIs back to the original image. The original image is not changed.
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.