I am brand new to image analysis. I am attempting to analyze confocal images of a 3D gel of human cancer cells that have been treated with a fluorescent live/dead assay. I’ve tried the 3D Objects Counter in Fiji on the dead (left window below) and live (right window below) but with poor accuracy based on what I can see on the light/grayscale image (center window below) - effectively undercounting cells.
Here is the appearance of the images when I open the czi in Fiji with Bio-Formats using hyperstack view with autoscale and split channels:
I’m wondering what tools you might recommend using to do this analysis with more accurate results? I’m willing to learn any software package that might help. I have 54 gels each with 33 images that need to be analyzed. I’ve been doing one-by-one with the aforementioned methodology but have put that on hold for now due to the questionable accuracy.
EDIT: I should probably add that these cells have been treated with an intervention which, at high doses, can impact the morphology of the cell (some break). Example: