I am currently working with zebrafish in vivo and trying to use CellProfiler to make an analysis of epithelial tissue. So far we have had a problem with over-segmentation, particularly in the region of the notochord. It seems that CellProfiler does a wonderful job of finding cells towards the outer edges, but as it moves inward it sees objects which are not there at all.
We have had decent success with analyzing GFP, but we are unable to get good segmentation with E-cadherin stains. Oddly, the cadherin stains are visually easier to see, but CellProfiler does a better job with the GFP. Does anyone have any experience with membrane based segmentation and analysis that would be willing to provide some advice? I’ve spent many hours playing with the software, as has a rotating grad student in the lab, and neither of us has had much success with membrane analysis in CellProfiler. We have had good results from other software, but we would like to utilize the robustness and the stability of CellProfiler to achieve these analyses if possible.
Also, is there a way to quantify the area, height, and width of each identified cell in CellProfiler? Looking at the outputs from the standard modules seems to suggest that the software takes a measurement of the entire object (in our case, a section of in vivo zebrafish) then figures out the quantification of that, not the individual cells. Am I missing something? Is this capability built into CellProfiler?
Thank you for your time!