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PyPI version Website Twitter

brainglobe

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).

Funding Information

The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information can be found on this website.

BrainGlobe tools

This package provides all BrainGlobe tools in one place, requested through a single command.

You can read more about the individual tools on the documentation website. Currently included packages, and whether they come with the pip and conda-forge installs are listed below:

Package pip conda from brainglobe import Documentation
BrainGlobe Atlas API ☑ ☑ bg_atlasapi Site
bg-space ☑ ☑ bg-space Site
brainreg ☑ ☑ brainreg Site
brainglobe-segmentation ☑ ☑ brainglobe_segmentation Site
brainrender Site
cellfinder ☑ Pending cellfinder_core Site
morphapi ☑ Pending morphapi Site

Installation

We recommend users install into a fresh virtual environment using pip; since this will resolve all complex dependencies (like tensorflow) automatically, across all operating systems and (compatible) Python versions.

Recommended: via pip

The brainglobe package can be installed from PyPI into a Python environment by running

pip install brainglobe

This will fetch and install all brainglobe packages and tools into your current environment. Alternatively, you can download the source from PyPI here.

Alternatives: via conda

We are currently in the process of making BrainGlobe's tools available from conda-forge as an alternative to PyPI. However certain tools are currently not available on conda-forge, specifically:

  • brainrender (in progress)
  • morphapi (in progress)
  • cellfinder (see below)

In your desired virtual environment, run

conda install -c conda-forge brainglobe

to install the compatible BrainGlobe tools. This will install all BrainGlobe tools that are compatible with your platform and which are currently available via conda-forge.

cellfinder and conda-forge

Choosing to install via conda will provide the (source code for the) cellfinder tool. However due to an ongoing issue with tensorflow's availability on conda-forge, the install will not provide tensorflow itself. This is because tensorflow versions newer than 1.14.0 are not provided via conda channels, and cellfinder-core (one of the brainglobe tools) requires a version between 2.5.0 and 2.11.1. See this issue on GitHub for more details. Users that want to run cellfinder will need to manually install a compatible version of tensorflow into their environment, before running the conda install command above.

  • Windows users will have to manually install their own version of tensorflow if they want to use the conda-forge install and the cellfinder tools.
  • conda-forge may be able to resolve the dependencies automatically for Linux and MacOS users, however we do not guarantee this. In such a case, a manual install of tensorflow will be required first.

If using the conda-forge install; attempting to import any of cellfinder, cellfinder-napari, or cellfinder-core in your Python scripts may throw an error if the issues above cannot be resolved on your platform. Similarly, attempting to use cellfinder's CLI functionality will also raise an error.

Contributing

Contributors to BrainGlobe are absolutely encouraged, whether to fix a bug, develop a new feature, or add a new atlas. If you would like to contribute, please take a look at our developer documentation.