Hi. I have brightfield images of stem cells. I need to count the total number of cells/image. Some cells are individual and some cells are in colonies. Using average cross-sectional area of individual cells, how can I calculate the number of individual cells in a colony. And then also calculate the total number of cells on the image?
I have tried the watershed feature but it does not provide accurate results unfortunately.
Thank you in advance!
If you include a representative image, this might be an easier question to answer. Based on your description, I would hazard to guess that your cells are too dense and possibly overlapping for thresholding and watershedding to work well. There are a couple of other things that you can try.
Cell Counter plug-in: https://imagej.net/ij/plugins/cell-counter.html
https://doi.org/10.3791%2F54719
If you are using multiple colors, you can try isolating the channels and then trying to threshold and watershed. If your cells are dense then you should take overlap into account. You can look for this by using the Image Calculator “AND” function.
Depending on their morphology, the Binary Feature Extractor may also work.
https://imagej.net/plugins/biovoxxel-toolbox#binary-feature-extractor
There are more options out there if these don't work, but these may get you started.
Hope it works!
- Melissa
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