I’m working on a pipeline to count the number of primordial follicles in mice ovaries. I’m used to count fluorescent granulosa cells with for example DAPI/PCNA or DAPI/BrdU. The main difference here is that I did whole mount immunofluorescence so as it’s the entire ovary I can’t use DAPI that only results in a very blurry signal due to the very high density of cells.
Moreover, several oocytes are overlapping and as there are different stages of development I would like to be able to differentiate the oocytes based on their size but it might not be essential. If I can get it working for the primordial follicles it would already be great.
I attached a picture and the (very simple) pipeline I’m using for now and that I’m sure can be improved.
Thanks for your help !
Oocytes_Counting.cpproj (113.4 KB)
Stitch_Zstack.tif (3.4 MB)