3D segmentation & volume rendering

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I have some issues with segmenting & volume rendering of areas in my image stack. I have tried several ways:

  • the Interactive 3D Segmentation plug-in: it only imports a few images of the stack if I ask to import the complete stack (20 images), so I can’t create a nice 3D segmentation this way.
  • segmentation with Segmentation Editor, followed by Create surfaces: the output of the segmentation editor is a 8-bit color file, but the Create Surfaces plug-in does not recognize it as such. I’ve also tried to create binary images and then use the Create Surfaces plug-in, but that leaves my pc running out of memory, so I guess this is not the way to go…

Should these plug-ins still be working properly, do you think I’m doing
something wrong or is there already an alternative I am missing? Perhaps @bene.schmid knows more about it?

Thanks a lot for your help!



You can either convert the image first to RGB and then use the 3D Viewer, or use this script I created to render label images (8-bit color) with their original colors in the viewer.


Thank you for the advise! I tried to use your script but I am still getting errors as output. The 3D Viewer is loaded, but no image is viewed. I tried with label files created with the segmentation editor and also with output from the MorphoLibJ Label Edition plugin. The latter output has several labels in one figure though, is that perhaps a problem for the 3D Viewer?


@EmmaRV, can you post here (or upload it somewhere) an example of the label image you are trying to render in 3D?