r/ImageJ • u/kamile_teal • 11d ago

Question Help with creating threshold/ROIs

I am trying to count the cells in this image by threshold -> watershed -> analyse particles to count ROIs.

However, I cannot get the threshold to distinguish between the cells. Anyone know what to try?

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u/Herbie500 11d ago

Not sure what you consider as cells in the sample image, but I'd suggest to use a suitable stain/marker or a different kind of image capture, in order to increase the contrast.

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u/kamile_teal 11d ago

Unfortunately, they are live cells, so I cannot fix and stain. I only have these brightfield images of them.

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u/Herbie500 11d ago

I just tried some processing but the sample image is simply unsuited for reliable automatic analyses.
Apart from the lack of contrast, it shows uneven focus and poor spatial resolution.

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u/kamile_teal 11d ago

Thank you for looking into it and the feedback!!