I am trying to get cell segmentation on a 20 um tissue slice mounted on glass slide. The tissue is placenta which has a lot of connective tissue and non-uniform nuclei (variations in size and shape). Images taken with a spinning disk confocal.
I’ve been unsuccessful using a standard cell segmentation protocol in Fiji (Find maxima: segmented particles). Thresholding or max. filtering makes the nuclei large and bleed into each other which makes it even more difficult for the software to segment properly. Does anyone have experience with dealing with these kinds of samples?
Attached is a snip of what my tissue looks like in Fiji and the TIF file. Thank you!example of DAPI.tif (8.2 MB)