Help to automate cell counting in brain section stained with cresyl violet

Sample image and/or code

Sample 20x.tif (14.3 MB)


Hi I am a newbie at image processing. I have to perform some cell counts for different areas of the hippocampus, CA1, CA2 CA3 and Dentate Gyrus. As I have over 200 pictures to analyse, I need an automated method to do it efficiently.

  • What is the image about? Provide some background and/or a description of the image. Try to avoid field-specific “jargon”.

This image is a 20X image of a mouse brain section stained with cresyl violet showing the dentate gyrus and the CA1.

Analysis goals

Automated cell counts across different regions of the brain


I have previously tried to use methods such as thresholding and/or making the images binary+outline+fill holes+watershed. However, the problem with cresyl violet staining is that the nuclei is not uniform and ImageJ/Fiji cannot seem to process watershed correctly - it keeps splitting one cell into many because of the tiny puncta in the centre of the nucleus. Is there a way to help me automate that properly?