Hi everyone,
I have been working recently on 3D models of snake scales from Gelsight and scanning electronic microscopy and I need to have elevation profiles of these 3D models to conduct shape analyses. I was supposed to use QuSlicer from Python's package QuSTo but I encountered some problems to lunch QuSlicer correctly (always the same error message). So, I'm searching for an alternative with another Software (maybe 3D Slicer ?) to obtain these elevation profiles.
If you have any suggestions I'll be happy to read them.
Ps: I put you an elevation profile file in the expected format.
Thanks.
3D Slicer is a free, open-source software platform that can be used for a variety of medical image analysis tasks, including the creation of elevation profiles from 3D models. 3D Slicer can import a variety of file formats, including common 3D model formats such as STL and PLY, which are the formats that are commonly used for 3D models generated from Gelsight and scanning electron microscopy.
Once you have imported your 3D model into 3D Slicer, you can use the built-in segmentation tools to create a surface model of the object of interest (in your case the snake scales). Then, you can use the "Models" module to create a representation of the surface as a mesh. This mesh can then be exported as an STL file and then be loaded in a meshing software (e.g. the open-source package MeshLab) where you can use the appropriate function to generate cross-sections or elevation profiles of the surface.
Another alternative is to use ImageJ. There are several plugins available, such as 3D Object Counter and 3D Viewer, that can import 3D models, create surface models, and generate elevation profiles.
It's also worth noting that if you are looking for a specific type of representation of the elevation profile, like height maps, you can use other softwares like Blender or Rhino. They allow to project the surface of the 3D model onto a plane and export the resulting image in 2D format (e.g. PNG, TIFF, etc.).
Keep in mind that not all the softwares are compatible with all file formats and also not all may have the same functionalities, it's worth to check the software documentation and tutorials before to proceed.
Adrien Mathou There are numerous approaches for obtaining elevation profiles from 3D models, and the optimum strategy will depend on the software and resources you have available.
One approach is to employ an open-source software platform for medical image processing and visualization, such as 3D Slicer. The "Models to Label Map" module in 3D Slicer allows you to convert a 3D model into a 2D label map, which can subsequently be used to build an elevation profile.
Another approach would be to employ image processing techniques to extract 3D information from Gelsight and SEM pictures, which may be accomplished by utilizing libraries like OpenCV, ITK, and scikit-image, all of which are commonly used in the medical imaging sector, In this scenario, you may use point cloud libraries like as PCL (Point Cloud Library) or CloudCompare to extract the elevation profile by extracting the color or intensity of each pixel in the picture and assuming them as the z values for the point cloud that you wish to generate.
Matlab, Rhino, and ImageJ are other strong alternatives for processing and analyzing 3D models; for example, with Rhino, you may use the "section plane" command to generate an elevation profile. I hope this provides you some ideas to think about as you attempt to extract elevation profiles from your 3D models.
Example of blender 3DSlicer & other interesting Addons used in project Malagueira UÉvora ~ ~ ~
https://8d2.es/mod/page/view.php?id=3131
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