Cellpose reloaded

Volker B├Ącker Montpellier Ressources Imagerie 04.03.2021


  • Remember cellpose?
  • New batch button
  • New features
  • Example result
  • Download

Remember cellpose?


New batch button

New features

  • runs the segmentation on all images in the folder of the current image
  • you can run cytoplasm-segmentation followed by nuclei-segmentation
  • new macro to batch-convert the segmentation results to rois
  • cytoplasm and nuclei segmentation can be run on the same input data
    • results are added (not overwritten)

Example Result

  • rois in overlay
  • nuclei rois in group 1
  • cytoplasm rois in group 2
  • macro to create membrane rois from cytoplasm rois


  • https://github.com/MontpellierRessourcesImagerie/cellpose