I am trying to create an analysis pipeline to segment islets in fluorescence images (input: image1, manual_ROI: image2) either of FIJI or Cellprofiler 3. The common segmentation methods in FIJI does not lead to accurate segmentation as it requires high sigma values for Gaussian filer. Using cellprofiler with specific configuration, it is manageable to segment the islets, yet there are false positives that requires several steps to exclude them.
I have TWO questions:
1- regarding common segmentation with FIJI/cellprofiler, are there any specific plug-ins you suggest to use for such segmentation?
2- in case of using machine-learning methods, what would you suggest?
Thanks in advance