A super-repository for managing a set of packages used for processing the BraiDyn-BC data files.

First, clone the repository, and initialize it with submodules:

git clone https://github.com/BraiDyn-BC/bdbc-data-pipeline.git
cd bdbc-data-pipeline
git submodule init && git submodule update  # clones the submodules

# within an appropriate (virtual) python environment
python install.py --help

# running `install.py` with particular
# installation targets will install
# the required libraries

If you intend to perform DeepLabCut-based atlas registration, we recommend installing DeepLabCut/Tensorflow first, before installation of the libraries in this repository.

In case you encounter issues building up a CUDA-aware environment, please refer to this document.

For a brief overview of the packages, please refer to the docs directory.

Before installing, please make sure you prepare an environment with Python 3.10+, by running e.g.

# in case you have (Ana)conda; for venv etc., the shell command must be different
conda create -n bdbc "python==3.10"

First, clone the repository along with its submodules:

git clone --recurse-submodules https://github.com/BraiDyn-BC/bdbc-data-pipeline.git
cd bdbc-data-pipeline

Then you can run install.py, e.g. as follows:

python install.py

By running the above command, the script attempts to install everything in this repository (along with all the external dependencies).

For more detailed instructions about install.py, please refer to the documentation.

The resulting package versions (in a python 3.10 environment) may be found under the requirements-python3.10 directory.

When using the code from this repository (and any of the sub-repositories), please cite:

Kondo, Sehara, Harukuni, Aoki et al. (2025) A multimodal dataset linking wide-field calcium imaging to behavior changes in mice during an operant lever-pull task. BioRxiv 2025.02.03.631599