Morphological segmentation to ROI

Hello,
I need to segment cells with membrane stain , that are touching. i got some nice results with morphological segmentation plugin, which generated a nice colored image of the cells( image is attached). Is there a way to generate the ROI of each of the cell to the ROI table?


thank you!
Irit

Hello,
yes there is.

  • make sure to use 8-connectivity in the options of the plugin.
  • press “create” to create the image
  • use the threshold adjuster to set a threshold, so that only the dams are not selected.
  • use the Analyze Particles with the option Add to manager
    Best regards,
    Volker

thank you! got it!! it helped a lot!

This is quite a common request.

The suggestion by @volker is straigh-forward – but might be computationally inefficient on very large images, because it is running an unnecessary connected-component analysis (i.e. Analyze Particles) where the pixels already contain unique labels (i.e. intensity values) for each separate object.

Instead of the above suggestion, you can also try this script by @NicoKiaru on your label images:


Because converting between ImageJ 1.x ROIs and label images of various sources is such a common and recurrent task, I suggested a while ago to centrally implement converters taking care of this:

So everyone, feel free to comment on this issue and/or file pull requests as appropriate :slightly_smiling_face:

1 Like

Thank you Jan, this looks great!
but I’m quite new at this more complicated stuff, can you explain how I incorporate this code in my macro?
and i do i call my image to the function? i apologize for my inexperienced questions…