I have a set of images, each containing three channels: a red and green channel of cytoplasmic CTb stain, and a blue channel labeling Fos nuclei. I am having a bit of a problem with being able to consistently identify and effectively segment cells within this image set. I thought my struggle might originate from background variation, so I applied both illumination function and enhance speckles operations in an attempt to remedy this but I don’t feel it has been sufficient. I can get a good count if I tweak a bunch of settings between each image, but this is time consuming and I was hoping I could streamline the process by having a consistent set of parameters that work for the entire image set.
Here are some sample images:
BO FOS.zip (4.5 MB)
And here is a sample pipeline I have been working on:
TestPipeline.cppipe (32.8 KB)
Does anyone have any advice for me? I have been working on this for a while and am a bit stumped. In case this is relevant, eventually I hope to determine colocalization between CTb and Fos channels.