As I’ve mentioned before, I’ve been on the hunt for tools that allow me to efficiently analyze microscopy images, perhaps even automate that process. ImageJ leaves me wanting and Photoshop doesn’t have the power to do analysis.
[CellProfiler[() is promising, but its made mostly for automation. Interacting with the images is challenging.
I found this tool called QuPath that is made precisely for tissue sections.
You can define regions easily, draw cell borders, and then measure the internal features of an ROI, like intensity or if your signal is punctate, such as for ISH, you can count puncta.
I think this is going to be very useful and I recommend that you try it out.
If you want to try it out, check out the page. But also look at this discussion I started. It doesn’t work right out of the box for some purposes, like DRG counting. But with a little fiddling, it will get the job done.