Let’s start with a full disclosure, I am not a computer guy, but I started playing around with CellProfiler recently, the 3.0 version. However most of available pipelines for different purposes on adipose tissue biology are made for older versions and hence not compatible.
Question: Has anyone adapted the H&E staining cell size quantification pipeline to the 3.0v? It is available in an old thread. (Adipocyte H&E Cell Profiler Pipeline)
Second thing is that I am currently struggling with another issue, I want to do lineage tracing on adipocytes based on fluo intensity, but also based on morphology (i.e. are they stained AND multilocular instead of unilocular…). So for that I figured that the autofluorescence in a random channel would be enough if I consider that unilocular cells (big empty ones) would lack significant signal compared to multilocular cells(where autofluorescent cytoplasm is more important).
Here comes the question: When you manage to segment your cells into objects, how do you extrapolate those objects in other channels (images) to measure intensity of signals? which are the best modules to do so without too many complications, should I identify the staining of my channels as objects and relate them to the cell object or can I just ask CP to give me the measurements of different images (channels) where the cell objects are?
Thanks for any help about these two things!
here some examples, extracellular matrix staining for segmentation and autofluo channel