Hello! My name is Vladimir, I am pathology trainee in pathology department of National Cancer Research Center, St.Petersburg, Russia. I can not figure out which algorithm to use for analysis. Can someone explain how to analyze the number of cells in this photo? Is it possible?
That is quite a tricky image you’ve got there… What you have to do is segment those cells - so here are a few helpful links on segmenting in Fiji:
- ImageJ wiki - the best place to learn everything about ImageJ/Fiji!!
- “Introduction to Fiji” workshop and corresponding slides- worth the time to get a solid intro (more recently updated slides are here)
- Principles page - collection of principles for the entire image analysis process, from acquisition to processing to analysis
- Segmentation page
- **“Segmentation in Fiji” workshop and corresponding slides (more recently updated slides are here)
- Trainable Weka Segmentation (TWS) plugin and it is scriptable via macro code - a great tool for segmentation that comes directly with Fiji. NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. If you are just getting started, we recommend downloading/using Fiji.
- MorphoLibJ plugin - another great tool for segmentation that comes with Fiji, providing more options/techniques… comes with Morphological Segmentation tool
In your case… you have to first deal with the uneven illumination issue you have in this image. Only then can you move forward in putting together a workflow to better segment your cells. Perhaps taking a look at TWS (linked above) is a good step after background correction?
Is there any other way to image these cells - for example - using a fluorescent marker to count them? This would make things much easier in the end…