mindscope_utilities is now a deprecated repo that will no longer be supported. It's functionality and many of it's individual functions have, and will continue to be moved over to the brain_observatory_utilities repo: https://github.com/AllenInstitute/brain_observatory_utilities
Utilities for loading, manipulating and visualizing data from the Allen Institute Mindscope program.
Functions in this repository depend on the AllenSDK https://github.com/AllenInstitute/AllenSDK
Set up a dedicated conda environment:
conda create -n mindscope_utilities python=3.8
Activate the new environment:
conda activate mindscope_utilities
Make the new environment visible in the Jupyter
pip install ipykernel
python -m ipykernel install --user --name mindscope_utilities
Install mindscope_utilities
pip install mindscope_utilities
Or if you intend to edit the source code, install in developer mode:
git clone https://github.com/AllenInstitute/mindscope_utilities.git
cd mindscope_utilities
pip install -e .
Tests are run on CircleCI on every github commit.
Tests can be run locally by running the following at the command line:
flake8 mindscope_utilities
pytest
We are no longer supporting this repo. We are supporting the brain_observatory_utilities repo which provides much of the same functionality as this repo