I hope someone super expert can help me!
I’ve to do 3D segmentation of DAPI channel in order to count number of all nuclei in 10 um ( z stacks) of mouse colon tissue.
I would like to do that because my plan is to measure the fluorescent intensity of tight junctions expressed in villi and crypts and because in each picture the area and morphology changes I’m planning to measure the fluo intensity in the area corresponding on epithelial cells ( villi) and then divide this value for the number of cells ( ROI) corresponding at that area.
Is this possible?
If no which approach do you suggest?
I’ve tried making maximum intensity projection with dapi channel but nuclei overlapped and I cannot get exactly the number of all 10 um tissue.
CAN you help me please???
Here attached and example of maximum intensity projection and the segmentation ( with all filters but as you can see it doesn’t work …)