It looks like the blurs are out of focus cells deep in the gel. A
pinhole confocal might yield the best data (or maybe SPIM).
Cleaning up what you have might be a partial work around. A rolling ball
subtraction (paraboloid 6) or a bandpassFFT (8,0,autoscale) can lessen
the scattered background. The uneven label will pose the next problem
for threshold-- skeletonizing the membrane vs picking up the entire
cell. Using a gamma 0.6 to make the scatter more uniform, ditto the
label, before the rolling ball, seems to pick up most cells with Li
threshold.
Better data = better results.
regards
On 2/5/2021 2:54 AM, OBEID Patricia 154904 wrote:
> Hello
> I try to improve my images before doing an Auto Threshold for the rest of the quantifications.
> I have a significant background noise related to the Fibrin gel in which the cells develop.
> In the attached images, the arrows point to areas I would like to "erase" and the cells are circled in green.
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> Patricia
> _______________________________________
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