Metadata-Version: 2.4
Name: cipipeline
Version: 0.2.1
Summary: CIPipeline is a tool to analyze and process Calcium Imaging data.
Author-email: Gonzalez Agustín <agngonzalez@fi.uba.ar>, Loyarte Iván <iloyarte@fi.uba.ar>, Rueda Nazarena <nrueda@fi.uba.ar>, Singer Joaquín <josinger@fi.uba.ar>
License: MIT License
        
        Copyright (c) 2025 CGKlab
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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Project-URL: Homepage, https://github.com/CGK-Laboratory/ci_pipe
Project-URL: Repository, https://github.com/CGK-Laboratory/ci_pipe
Requires-Python: <3.11,>=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: rich>=13.7.0
Requires-Dist: PyYAML>=6.0
Dynamic: license-file

# 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

```bash
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)

```bash
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:

```bash
git clone <repo>
cd <repo>
pip install -e .
# install optional dependencies if needed (isx, caiman)
jupyter lab
# open notebooks in docs/examples
```

---

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