You could use ImageJ software.

Thank you for your comment Ershad.

I am working a lot with ImageJ but unfortunately, I was not able to do it there.

Of course, it is possible just to visualize my core in 3D but it is not possible to highlight different constituents. I used 3D Viewer and downloaded several plugins. Do you know how can I do it?

Thank you

Damir Gadylyaev did you try trainable weka segmentation plugins in imageJ?

Have you looked at the program Dragonfly (https://www.theobjects.com/dragonfly/index.html) from Objects Research Systems? You can define your ROI's based on threshold ranges or multiple different ways.

Looks like you need volume rendering software. Many are available for free but some of the limitations is memory size and dependent on the type of graphics card on your computer. An alternative option would be to create a surface of 3 densities (ice, organic, & mineral) by setting thresholds to make an isosurface. To do this you can use Isosurf or Stradview from Cambridge. VTK can also create surfaces using marching cubes or marching tetrahedrons. Paraview will also do the same. Once you have created isosurfaces you can visualize and convert to other formats using MeshLab. All softwares mentioned are free. Hope this helps you on your project.

Dear Robert Goulet, thank you for your suggestion. Dragonfly looks very promising. It may sound silly but I couldn't launch it. Since it works only within Nvidia and AMD graphics. So both Windows and Linux versions didn't work for me. Also, Dragonfly doesn't support remote desktop so wasn't able to use it on my remote computer.

Dear Reuben Reyes thank you for your comment, I must say that even the first sentence was already super helpful. I started to look for available volume rendering software.

I especially liked 3D Slicer. Using it I was able to visualize my core.

Dear Damir Gadylyaev, yes Dragonfly does require a PC with a little more memory and a nicer graphic's card (and an NVIDIA card if you want to use their Deep Learning tools), but one nice feature (similar to 3D Slicer, which I'm glad you were able to use and is a good tool) is there is a Non-Commercial license that makes the software free for academics. We have several HP Z-workstations in our lab that we installed HP's remote access program (for Z-workstations) on and are able to use Dragonfly remotely (at home) using that software, but yes we ran into trouble getting Dragonfly to run remotely via Microsoft's Remote Desktop app. Best, Rob

I second 3D Slicer as well! You can get nice images and animations of Volume Renderings, and if you want 3D models to export, you can use the Segment Editor to create different segments for the materials you want to separate. Check the Slicer discourse (https://discourse.slicer.org/) and YouTube for tutorials.