I would like to segment yeast cells by first segmenting the nuclei and then propagating to the overall cell. I applied RescaleIntensity module but still the nuclei intensities are so much higher than the cytosolic intensities. For IdentifySecondaryObject module I am using Global Otsu with 3 classes, assigning middle intensity to foreground. Sometimes, the segmentation results include background. I also applied a FilterObjects module but that caused downstream error because of the 1:1 relationship. I would appreciate if you can take a look at our images and pipeline attached.
CP_Otsu3Classes.cppipe (17.6 KB)