Use Local Atlas with Cellfinder


I was wondering if there was a way to use an atlas stored on my computer for cellfinder’s registration step. The only issue I’m finding is that the atlas information I have is formatted differently compared to brainglobe’s formatting, e.g. I have .nii files. Any advice @adamltyson ?

Hi Kailyn,

This would be possible, but you would have to reformat your atlas to create a BrainGlobe Atlas API compatible version. At the moment, we don’t have this process well documented. You would need to create a script such as this one to create, and package the atlas.

If you’re willing to make this atlas publicly available, we’d be happy to help you (there are a few other users doing the same at the moment).


Hey Adam,

I will take a look at the script, thank you! And my research mentor is waiting on some peer reviews on the atlas before making it publicly available, but I think that is definitely on the radar when he chooses to do so. :slight_smile:

Great! If he’s willing to add the atlas to BrainGlobe, we can provide an API for others to use in in their software, and immediate compatibility with other BG software (brainreg, cellfinder, brainrender etc). Hopefully this will help the atlas be used, cited etc …

Feel free to get in touch with any questions, this stuff needs much better documentation.