Create 3D images?

Is there software to convert the coronal sections of the human brain atlas to 3D versions? I am interested in smaller areas of a few (5 - 10) successive sections. If not, is there a recommended CAD program to do this?

Hi sabrawer,

Please refer to this earlier post in the Community Forum:
Allen Human Reference Atlas - 3D, 2020 (new!) - General - Allen Brain Map Community Forum (

Thank you

Thanks. Looks good. I will try that.

In case it’s useful, both brainrender and brainrender-napari, can be used to view arbitrary regions of the Allen human brain atlas.

Thank you.

Right now my interest is strictly in anatomy,. As a retired physicist (but not a professional neuroscientist, and with no affiliation) interested in brain function (not POP-brain function), I need a detailed understanding of neuroanatomy so I can read the literature intelligently (or as intelligently as I could get). The literature does not seem to be all THAT complicated, it is usually well written, and I find it to be extremely interesting. My difficulty is envisioning what brain areas publications are referring to, where these areas are, and how they are relatively situated. I believe this is important for understanding on my level of non-professionalism.

The very wonderful brain atlas I think would be most useful (to me at least) IF I can make some 3D sketches (these don’t have to be publication-quality). What data set would have ALL the information (and ONLY the information) used for what is visible in the interactive brain atlas? How could I access that data? What is the data format? Would it work with, for example, itksnap, with brain render, with some CAD program, or with Adobe’s new 3D software?

Allen brain atlas is a wonderful find for a very interested and very technical person such as myself. The interactive web application is great. But I cannot for the life of me figure out how to take it any further. If people like myself are not an an intended audience of (and I assume everyone there is very very busy), well then, I can only beg for scraps-of-help. But for very broad accessibility, to an audience a bit like (or much better than) myself, documentation (or some kind of ready help) would be essential.

I have a friend who is an expert on (and consults on) drug development, and very concerned about brain degeneration, who would love to see some 3D sketches of brain anatomy. They are hard to come by.

As another example, I did email one author of a non-freely-acessible publication to ask for a pdf. Not only didn’t I get the pdf, I got no response whatsoever. So the problem is, for me, non-trivial.

I am doing some things with images screen-copied from the interactive viewer, in photoshop and sketchup, but it is slow going and, in the end, not satisfactory.

I am a very good Python programmer, but I do require documentation (I don’t to have access to knowledgeable humans with the required info). Life is short.

Anyway, thanks again.