Hi, Im struggling to try and segment nuclei as my cells tend to clump in many places in the hydrogel, I need advice on the best solution as Im new to image J.Is there a macro which could help?Im attaching a few images to clarify.B3.tif (935.4 KB) B2.tif (995.3 KB) B7.tif (836.3 KB) B7.tif (836.3 KB)
I had a look at your images. What do you want to do for your analysis?
If you just want to do a detection to count the nuclei you will have an easier time.
You could just apply a Gaussian Filter:
Process > Filters > Gaussian Blur…
Then go for a maximum detection:
Process > Find Maxima…
Segmentation for getting the area of each nucleus might be tricky.
Also the images you provided have problems such as saturation: https://imagej.net/Detect_Information_Loss
Make sure that the data that goes into analysis does not have these problems.
A maxima detection would be in this examples rather hard to do.
If possible I would also go for a microscope that has better optical sectioning.
There is quite a bit of out of focus light in my impression.