How to calculate the cluster number in this image

Sample image and/or codeUCSC54 (3) 5x.czi (16.3 MB)

  • Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
  • Share a minimal working example of your macro code.


  • What is the image about? Provide some background and/or a description of the image. Try to avoid field-specific “jargon”.

Hi all, I have one image taken with polychrome camera at 5x magnifications.
There are many clusters in this image.

Analysis goals

  • What information are you interested in getting from this image?
    I would like the software to pick up the clusters for me automatically and calculate the area for each cluster. Are there any plug-in or features within Qupath to do that?



  • What stops you from proceeding?
  • What have you tried already?
  • Have you found any related forum topics? If so, cross-link them.
  • What software packages and/or plugins have you tried?