I’m trying to do particle analysis with stained droplets. Since the preparation only allows multiple layers to be created (otherwise the larger droplets would be destroyed), I wonder how I can substract the slightly colored background from the image.
So far I tried Substract background (rolling Ball) commadn, combined with Enhance Local Contrast (CLAHE) and tried to replace red with magenta afterwards to simplify the color thresholding (did it in HSB color space with Default thresholding). It should be as automated as possible for a stack of images.
It allready worked out for a reduced amount of layers, though I’m still struggeling to seperate the particles from one another.
Any suggestions on how I might proceed; which functions of Image J might come in handy?
Thanks in advance.