I have images of ganglia with the following staining:
2 Tubb3 (af488)
3 TH (af568)
4 CHaT (af647)
I have a macro in imageJ in which I set the threshold for each channel, per image and export the data (for example area and %area).
Lately I have noticed that the cell sizes may play a role in the ganglia, so I want to count the cells in a ganglia so that I can learn more about the amount of cells and the size of the cells.
I am not very experienced in image analysis and I have tried to do this in imageJ and Cellprofiler. The biggest issues I ran into are that my cells are irregular in shape, and intensity. This makes segregating the cells a problem for me. Also my dapi staining is not usable in most of my sections, so I will have to use one of the other stainings (probably tubb3, since this is the most prominently present in the ganglia)
Can anyone advice me on how to handle and proceed with this problem? Ideally I would like to use imageJ, since I can then include the script into the one I already have.
E11219A_gl16-01_s03_AF488.zip (8.5 MB)