My master’s project revolves around getting a 3d image of the trigeminal ganglion that’s stained with NeuN. Currently I’m struggling to find good software to analyse my images. All the examples I see online are using perfect Z-stacks so when I try to replicate it on my data it doesn’t work. I’m just wondering if this can even be counted with automated methods?
This is a maximum projection of one of my samples.
I tried ImageJ 3D object counter but the thresholding is too simplistic and excludes a lot of my cells while the algorithm will extend and mark whole areas as a cell because there is one pixel connecting it.
The best thing that kind of worked so far is QuPath but it isn’t really equipped to deal with Z stacks well. I’ve also tried CellProfiler.
No one in the lab has done such analysis before so I’m looking for help here…