Questions for Identifying primary objects

Hello, I want to extract the cell outline and identify each cell in the embryonic epithelium. The cells are outlined with a membrane marker. I cleaned the image and converted the orginal image to binary file. I wonder how to identify each cell in a binary image like this. Also the cell outline isn’t quite perfect with breaks and distortions (likely caused by noise). I wonder if there is a better way to segment the image. I am attaching here also the pipeline I used to clean the image. Thanks
test.cp (6.33 KB)


Your pipeline appears to do quite well at cleaning up the image! I would probably add the following:

  • Another Morph to get the convex hull of the ax3_morph2 image (the convex hull is the smallest polygon that encloses the foreground pixels)

  • Invert the intensity of ax3_morph2 with ImageMath

  • Use MaskImage to mask the inverted image with the convex hull image, to restrict the region of interest.

  • Use IdentifyPrimaryObjects to find objects in the masked image.

I also attach another pipeline which takes an alternate approach and may be helpful as well.

2011_08_02.cp (4.37 KB)

Thanks a lot, Mark. That’s really helpful. The cells are segmented very well with the pipeline you gave.