cipipeline 0.2.1

CIPipeline is a tool to analyze and process Calcium Imaging data.

CIPipeline / CI_Pipe

English

Short description

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.

Development team

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)

Installation tutorial

1. Install the library from PyPI

pip install cipipeline

2. Optional: Install Inscopix isx (required for the isx module)

• 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).

3. Optional: Install CaImAn (required for the caiman module)

• Project: https://github.com/flatironinstitute/CaImAn
• Docs: https://caiman.readthedocs.io

CaImAn strongly recommends installing via conda for full functionality; follow the CaImAn docs.

4. Jupyter (recommended for opening example notebooks)

pip install jupyterlab
# or
pip install notebook

Useful links

• 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 Laboratory page

• CGK Lab: https://cgk-lab.example # replace with the real lab page URL

Example guide

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/examples

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Read the Spanish translation in README.es.md (or view both sections in the repository).