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cberri / Quanty-cFOS

An unbiased tool to count Fos/c-fos positive cells
MIT License
6 stars 3 forks source link

Empty files #1

Open AlexPek opened 4 months ago

AlexPek commented 4 months ago

Hi! While running the plugin on Fiji, some images give empty files with NAN-NAN counts. Can you advise on how to fix it? I know for a fact the images have positive cells, but I'd like to have them be counted with the rest of the images. Thanks! -Alex

cberri commented 4 months ago

Hey Alex, You could try to play with the threshold and the size filter. However If the images are very different I think is very difficult to find a global setting.

The manual optimization is somthing I would use to test different setting until you are happy with the counts.

I hope it helps.

Carlo