The Allen Brain Cell Atlas (ABC Atlas) aims to empower researchers worldwide to explore and analyze multiple whole-brain datasets simultaneously. As the Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas, this groundbreaking platform will keep growing, opening up endless possibilities for groundbreaking discoveries and breakthroughs in neuroscience. With the ABC Atlas, researchers everywhere can gain new insights into the brain’s complex workings, advancing our understanding of this amazing organ in ways we never thought possible.
https://AllenInstitute.github.io/abc_atlas_access
JupyterBook Contribution Guide
Note: for scientific questions regarding the data this repository is accessing, please use the Allen Institute's community forum. If you are having an issue with the code or notebooks not running properly please open an issue on this Github repository. However, please see below.
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
To install base package with the cache object in your python environment, use pip with the following command:
pip install git+https://github.com/alleninstitute/abc_atlas_access.gitTo install the package with all optional dependencies, specifically those needed to re-run the notebooks, you can use the following command:
pip install "abc_atlas_access[notebooks] @ git+https://github.com/alleninstitute/abc_atlas_access.git"We assume that you already have Jupyter installed if you are re-running the notebooks. Running the getting_started notebook will also help you install the package.