Nuclei geometry analysis

Dear forum members, can someone suggest an optimal tool for quantitative volumetric analysis of nuclei shape&structure for hdf5 image? This is an Arabidopsis lateral root staining with DAPI and scanned with 3D.
I am attaching an example.
I appreciate any help you can provide. ### Sample image and/or code

  • 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 β€œjargon”.

Analysis goals

  • What information are you interested in getting from this image?


  • 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?

I think you need to tag your question with e.g. #segmentation or other analysis-related tags or possible analysis tool names. Bio-formats is not an analysis tool.

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