I have been working on co-culture of two different cell types and trying to find a consistent way to quantify the percentage of each cell type in the co-culture. Nuclei staining usually turns out very nice so there is no issue quantifying them. However, both cell types exhibit quite similar-looking nuclei so it’s not possible to distinguish them based solely on the nuclei (green image). One cell type can be specially stained with collagen-I as shown in the red image. Mainly, I’m just looking for a reliable way to count these red cells, from which I could determine its percentage in the co-culture.
I’m completely new to Cell Profiler so I’m still playing around with all the settings and features of the software. However, if anyone can point me to some general direction on what I could try that would be very well appreciated. Is this achievable using solely CellProfiler or would ilastik also help?