Just added to 3D Slicer 5.5 is the new Colorize Volume module! I tried it on a fully segmented rattlesnake skull with really nice results comparable to the expensive proprietary software VGStudio Max. I played around with the Volume Rendering settings, as well as Lights module (from the SandBox extension), and cropping to an ROI in the Volume Rendering module to bisect and view the inside of the skull. I am still exploring the various functions of this module but I am excited to see what else I can do with it.
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@jaimigray these are gorgeous. Hope biologists trying to migrate away from proprietary software will find these inspirational.
This is a very new feature not completely test, with other extension. perhaps you can find the time to try with the Animator module of SlicerMorph, and see if the cropping other features within the animator works well to make mp4s of these.
Thanks for sharing.
To continue this thread, I would like to show you more rattlesnake images, this time I used to Colorize volume module to render the skull inside the transparent skin
Then I tried without the skull segment, using the whole volume to render the skull instead. This gave me control over the skull colormap.
Then a density colormap for fun!
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Thanks for sharing, really nice!
(and kind of scary, too)
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Perfect for Halloween!
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It looks astonishing. Could you please tell me how you did? Do you first run the Total segmentator module and then the Colorize volume?
You need a segmentation to work with Colorize Volume. You can run TotalSegmentator on one of the sample CT datasets from Slicer to obtain a segmentaiton and play with the module.
There is also a very short tutorial with self-contained data, if you want to give it a try:
Thank you very much, Sir.
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Hit CTRL+F (Module Finder shortcut) and search for , or from Module selector navigate to SlicerMorph->Input and Output->ImportFromURL .
Now in the current latest version,
3D Slicer Version: 5.8.1
SlicerMorph Version: c944db9 (2025-06-26)
it has become:
Hit CTRL+F (Module Finder shortcut) and search for , or from Module selector navigate to SlicerMorph->SlicerMorph hUtilities->ImportFromURL .
The effect is excellent.
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The Colorize Volume module is still available in the Sandbox extension as described at:
Yeah, scary! haha
Maybe this Module solve the dithering problem we had a few years ago with the SlicerFab results for Voxel Printing…¿?
Yes, the Colorize Volume module solves the problem of artifacts at segment boundaries caused by the difference in level of details between the original CT and the segmentation.
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Those volume rendering settings are really nice! Looking forward to using it.
Happy to hear that!
now we need a Voxel Printing or Pixel Fabrication license for PolyJet that still works for general users hahaha.
Do you think we should close the issue on Github - https://github.com/SlicerFab/SlicerFab/issues/14 ?
Hi Jaimi,
Could you have some details on steps of how you set up this density-colormap? Thanks a lot.
Slicer can help with preparing input data in any format a printer software needs it.
What is the current preferred data structure? RGBA volume? What are the supported file formats? NRRD, Nifti, …?
We can probably resolve the issue in 1-2 hours with the help of Claude.
Do you mean that we don’t need to resolve it because commercial software includes the dithering already and there is no other way of getting your volumetric data to a printer?
Hi Andras
The preferred data structure is RGBA, but there are little chances around the world to use at least the Voxel Printing license from Stratasys, for eample, they already deleted the chance in Grab CAD.
Anyway, is pretty interesting to have the SlicerFab extension working. I made a volume with Colorize Volumen, and then export the slices in png format using SlicerFab and the dithering works fine, so I consider it done for experimental and research purpouses.
Thanks for your patience.
Hi Aiden, the density colormaps were made using the Volume Rendering module, giving me full control over the colormap for the skull and the ability to make the rest of the datasets invisible using the opacity controls. Then I used the Colorize Volume module to create another rendering layer for the skin. I made both the volume rendering and colorize volume layers visible at the same time to create this effect.