I wanted to know how I could count the number of nerves in cryosections of the cornea after staining with Beta III tubulin. What software is available for automatic or manual counting?
Hi Baffour
What type of microscopy are you using to image your sample?
how thick is your section? Is Beta III tubulin identifying only your cell type of interest?
You should be able to stain with a nuclear marker as well.
You can then segment the image for cell nuclei and subsequently you can analyse those areas - or if your marker is in the cytosol a ring around those objects - in an image of a marker which identifies your cell type of interest. This way you get all the objects, which are poritive for your cell identification marker.
For a few images you can use FiJi (FiJi.sc) for large number of images use CellProfiler (cellprofiler.org).
Best
Heiko
I agree with the previous answer and would add to the list Qupath software (https://qupath.github.io/) - there is a tool for cell counting as well.
Heiko Dussmann Erdem Yildiz Thank you so much for your suggestions. I am counting the number of nerve fibers in the cornea on cryosections. The nuclei of the nerve fibers are located outside the eye, so I cannot count the nuclei but the cut ends of the nerves on cryosections. The problem is that most of the cut ends of the fibers appear with varying sizes and intensity which makes it tough to count with IMAGE J.
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