I am measuring autophagic body cross-sections in TEM images of yeast. The outlines of the bodies are sometimes clear and sometimes indistinct. Right now I manually outline the bodies (see examples below), and would like a way to automate this, although I suspect it will be hard.
I’ve spent some time trying out the different plugins in the “segmentation” menu of FIJI, as well as the "MorphoLibJ” library, and haven’t found anything that will do the trick. The WEKA trainable segmentation tool seemed the most promising, but didn’t seem good enough on its own. (I actually had better luck with Ilastik, but even that wasn’t accurate enough to really be useful). Are there any other ImageJ plugins that I should be trying out?