Read VTK files from the Allen Brain Atlas in Blender



The Allen Brain Atlas provides most of their tracked brain data as 3d-files in the VTK-format. I found it difficult to find a converter for this format that would give me e.g. an obj-file. I came across the Graph Toolbox for Matlab which can read vtk-files and write obj-files. However, their importer did not work for that particular version of the vtk-format. Here is read_Allen_vtk.m, an m-file that I derived from read_vtk.m, which is able to extract all vertices and face-data from the vtk-files. You can then save them using write_obj() and open them in the 3d-tool of your choice. In the  upper image you see the hippocampus and entorhinal cortex of the mouse in Blender.

One thought on “Read VTK files from the Allen Brain Atlas in Blender

  1. Hi Martin,

    I am currently attempting to download VTK files of the whole and specific brain areas from the Allen Brain Atlas Brain Explorer program. I have been having a lot of difficulty finding where the actual VTK files are stored. From your blog, it appears as though you have had success doing this. I was curious if you would be able to share the procedure with me so I can download the files and eventually convert them into a Blender friendly format.

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