I am fairly new to using Fiji and segmentation and I am trying to find a way to get a mask for my cells from my brightfield image. So far I had been adding a cytosolic fluorescent marker to my cells that made this step way easier but for my current set up it is not possible to do this and I was wondering if I could get any tips on the segmentation of images like this (see attached images).
I usually try filters like Gaussian Blur or mean to even out the cell’s inside but still I didn’t manage to find a “protocol” that would be useful for all my images
Moreover, I have a theoretical question about thresholding. Within an experiment where all the images have been taken with the same settings in the microscope, what is the best way to threshold said images? Pick one algorithm and “Auto” threshold each image with the same algorithm? Or is it better to set a manual threshold and apply it to all the images? Does this make a difference? I got this question from my boss and unfortunately my knowledge is quite limited to be able to answer to this properly so any help would be much appreciated!
Thanks a lot in advance!