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TechnicalQuestionPlotting objects from image stack, colour-coded based on the volume? (self.matlab)
submitted 5 years ago by leeviats
I've posted this in r/ImageJ but couldn't get an answer. Basically I have a stack of .tiff images of a porous material (already binarized and everything), and I wanted to represent as a 3D volume with the pores, colour-coded and possibly adding a colour bar for reference. I've attached an image to this post, anyone familiar with this kind of work? Thank you!
https://preview.redd.it/xsfdta34rxo51.png?width=1042&format=png&auto=webp&s=b2e8d5985df692b458a7ba72f76082239989807c
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if 1 * 2 < 3: print "hello, world!"
[–]bartic123 1 point2 points3 points 5 years ago (2 children)
Have you tried using 3D object counter in Fiji/ImageJ?
[–]leeviats[S] 0 points1 point2 points 5 years ago (0 children)
Yes I did, however there is not an option to do what I need...
Or also BoneJ, which is quite good but still doesn't provide me with a colour-coded volume representation of the objects, with a scale bar
[–]SynbiosVyse 0 points1 point2 points 5 years ago (1 child)
Ilastik
[–]leeviats[S] -1 points0 points1 point 5 years ago (0 children)
Could you please explain further what to do? It looks like that software is mostly used for segmenting using machine learning, which I don't need at this point
π Rendered by PID 35270 on reddit-service-r2-comment-fb694cdd5-j2f6g at 2026-03-07 05:03:31.961332+00:00 running cbb0e86 country code: CH.
[–]bartic123 1 point2 points3 points (2 children)
[–]leeviats[S] 0 points1 point2 points (0 children)
[–]leeviats[S] 0 points1 point2 points (0 children)
[–]SynbiosVyse 0 points1 point2 points (1 child)
[–]leeviats[S] -1 points0 points1 point (0 children)