CIPipeline (imported as ci_pipe) is a Python library for building and running calcium-imaging processing pipelines used by the CGK Laboratory. It provides core pipeline primitives, optional adapters for Inscopix (isx) and CaImAn (caiman), utilities, plotters and example Jupyter notebooks.
The project was developed as a final project by students from Facultad de Ingeniería, Universidad de Buenos Aires, under the supervision of a tutor, in collaboration with the CGK Laboratory.
Contributors:
- Gonzalez Agustín
- Loyarte Iván
- Rueda Nazarena
- Singer Joaquín
- Fernando Chaure (Tutor)
- Install the library from PyPI
pip install cipipeline- Optional: Install Inscopix
isx(required for theisxmodule)
- Repository: https://github.com/Inscopix/isx
- Inscopix: https://www.inscopix.com
Follow the isx repository documentation for installation details (some Inscopix packages may require credentials or vendor-specific installers).
- Optional: Install CaImAn (required for the
caimanmodule)
CaImAn strongly recommends installing via conda for full functionality; follow the CaImAn docs.
- Jupyter (recommended for opening example notebooks)
pip install jupyterlab
# or
pip install notebook- PyPI package: https://pypi.org/project/cipipeline
- Inscopix / isx: https://github.com/Inscopix/isx and https://www.inscopix.com
- CaImAn: https://github.com/flatironinstitute/CaImAn and https://caiman.readthedocs.io
- Jupyter starter guide: https://jupyter.org/install
- CGK Lab: https://cgk-lab.example # replace with the real lab page URL
Example Jupyter notebooks live in docs/examples. To run them locally:
git clone <repo>
cd <repo>
pip install -e .
# install optional dependencies if needed (isx, caiman)
jupyter lab
# open notebooks in docs/examplesRead the Spanish translation in README.es.md (or view both sections in the repository).