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I am new to the forum, but was wondering if someone could offer me some help. I have pictures of ovarian cells and am trying to measure the nucleus to cytoplasm ratios of each cell (see picture attached). I am trying to find a way to automate it since I have thousands of cells to measure from multiple pictures. For my initial step I am trying to differentiate the cells from the background and the noise within the image (which is mostly just broken cells that I can’t measure). I have tried to do this with the Weka segmentation tool in Fiji as well as pixel differentiation in ilastik. However, both of these methods have proven difficult, and the AIs are having a hard time identifying my cells in their entirety and separating them from the objects I don’t want to measure (broken cells). I have tried distinguishing my eccentricity, shape, etc., but nothing has seemed to work.
Once I figure out how to distinguish my cells from background and noise, my goal is to have the program measure the nucleus-to-cytoplasm ratio of each cell in an image. I know with Analyze Particles in Fiji you can measure the area of an object, but is there a way to measure the nucleus-to-cytoplasm ratio? I have played with CellProfiler a bit as well as it seems to be able to distinguish between nuclei, cytoplasms and cells, however I’m not very confident it’s measuring the right boundaries as I got some pretty off results when I did a test run.
Any help or advice I can get on this process would be appreciated, thanks!