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Open python tools for morphological analyses in systems neuroscience

The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.

We have three aims:

  • Develop specialist software for specific analysis and visualisation needs, such as cellfinder and brainrender.

  • Develop core tools to facilitate others to build interoperable tools in Python, e.g. the BrainGlobe Atlas API.

  • Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).

The BrainGlobe project is generously supported by the Sainsbury Wellcome Centre and the Institute of Neuroscience, Technical University of Munich, with funding from the Chan Zuckerberg Initiative, Wellcome, the Gatsby Charitable Foundation and the Munich Cluster for Systems Neurology - Synergy.


  1. brainrender Public

    a python based software for visualization of neuroanatomical and morphological data.

    Python 399 60

  2. cellfinder Public

    Automated 3D cell detection and registration of whole-brain images

    Python 136 37

  3. bg-atlasapi Public

    A lightweight python module to interact with atlases for systems neuroscience

    Jupyter Notebook 67 18

  4. brainreg Public

    Automated 3D brain registration with support for multiple species and atlases.

    Python 74 22

  5. Segmentation of 3D shapes in a common anatomical space

    Python 17 6

  6. morphapi Public

    Apis to download neuronal morphologies from publicly available datasets

    Python 9 5


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