I hope you can help me with a difficult image analysis task. I have microscopic images of a filamentously growing bacterium and want to analyze what proportion of the projected area is caused by dense biomass (clumps/pellets) and what proportion is occupied by freely dispersed mycelia.
I tried to apply different grey value thresholds and ridge detection, but this unfortunately leads to a lot of false-postive detection. With sharpened images the result is a little bit better, but I could not manage to trace all of the filaments, because some of them are not perfectly in focus.
Do you see a possibility to perform a good trancing of the mycelia and maybe also segment the image in parts according to the degree “clumpiness” as I sketched in the attached image?
I’m looking forward to your ideas. Many thanks for your help!