I have a question regarding the analysis of a distinct shape within a complex image. I am currently analyzing fluorescent macro images (only 10x) of in vivo models, whereby I determine the surface area of two different structures via freehand tracing. This is time consuming, which is why i would like to automate it via a macro for example to allow for batch processing.
The problem is that it is hard to ‘isolate’ the shape via thresholding since there are numerous other structures present in my images which contain the same level of fluorescence. Do you have any tips on how to deal with a challenge like this? I am trying the weka segmentation algorithm, but this is not suitable for shape recognition i guess, since it also sees other structures as the one I am looking for
I could upload a picture if requested!