Along with Federico Claudi and Luigi Petrucco, we have developed: BrainGlobe: Open python tools for morphological analyses in systems neuroscience.

BrainGlobe tools rely on the BrainGlobe Atlas API which is a Python API for interfacing with varied neuroanatomical atlases in a standardised way. The software can be found here, and the paper was published at The Journal of Open Source Software.

The list of BrainGlobe software can be found here and the documentation is here.