Metadata-Version: 2.4
Name: camap
Version: 0.1.3
Summary: CaMAP — Calcium imaging mapping and analysis pipeline
Project-URL: Homepage, https://miniscope.github.io/CaMAP/
Project-URL: Documentation, https://miniscope.github.io/CaMAP/
Project-URL: Repository, https://github.com/miniscope/CaMAP
Project-URL: Issues, https://github.com/miniscope/CaMAP/issues
Author-email: t-sasatani <sasatani.dev@gmail.com>
License: AGPL-3.0
License-File: LICENSE
Keywords: calcium-imaging,deconvolution,hippocampus,miniscope,neuroscience,place-cells,rate-maps,spatial-coding
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Affero General Public License v3
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: <3.14,>=3.11
Requires-Dist: click>=8.3.1
Requires-Dist: ipympl>=0.10.0
Requires-Dist: numpy>=1.24.0
Requires-Dist: opencv-python>=4.13.0.92
Requires-Dist: pandas>=2.0.0
Requires-Dist: plotly>=5.0.0
Requires-Dist: pyarrow>=23.0.0
Requires-Dist: pydantic>=2.7.0
Requires-Dist: pyyaml>=6.0.0
Requires-Dist: rich>=13.0.0
Requires-Dist: scipy>=1.10.0
Requires-Dist: tqdm>=4.65.0
Requires-Dist: xarray>=2025.10.1
Requires-Dist: zarr>=2.17.0
Provides-Extra: all
Requires-Dist: autodoc-pydantic>=2.0.1; extra == 'all'
Requires-Dist: black>=24.1.1; extra == 'all'
Requires-Dist: ipykernel>=7.1.0; extra == 'all'
Requires-Dist: ipympl>=0.10.0; extra == 'all'
Requires-Dist: ipython>=9.9.0; extra == 'all'
Requires-Dist: ipywidgets>=8.1.8; extra == 'all'
Requires-Dist: jupyterlab>=4.5.3; extra == 'all'
Requires-Dist: myst-parser>=3.0.0; extra == 'all'
Requires-Dist: nbmake>=1.5.5; extra == 'all'
Requires-Dist: pre-commit>=3.7.1; extra == 'all'
Requires-Dist: pytest-cov>=7.0.0; extra == 'all'
Requires-Dist: pytest-timeout>=2.3.1; extra == 'all'
Requires-Dist: pytest>=9.0.2; extra == 'all'
Requires-Dist: ruff>=0.2.0; extra == 'all'
Requires-Dist: setuptools-scm>=8.0; extra == 'all'
Requires-Dist: sphinx-book-theme>=1.1.0; extra == 'all'
Requires-Dist: sphinx-click>=6.2.0; extra == 'all'
Requires-Dist: sphinx-design>=0.6.1; extra == 'all'
Requires-Dist: sphinx>=7.0.0; extra == 'all'
Requires-Dist: sphinxcontrib-mermaid>=2.0.0; extra == 'all'
Provides-Extra: dev
Requires-Dist: black>=24.1.1; extra == 'dev'
Requires-Dist: pre-commit>=3.7.1; extra == 'dev'
Requires-Dist: ruff>=0.2.0; extra == 'dev'
Requires-Dist: setuptools-scm>=8.0; extra == 'dev'
Provides-Extra: docs
Requires-Dist: autodoc-pydantic>=2.0.1; extra == 'docs'
Requires-Dist: myst-parser>=3.0.0; extra == 'docs'
Requires-Dist: sphinx-book-theme>=1.1.0; extra == 'docs'
Requires-Dist: sphinx-click>=6.2.0; extra == 'docs'
Requires-Dist: sphinx-design>=0.6.1; extra == 'docs'
Requires-Dist: sphinx>=7.0.0; extra == 'docs'
Requires-Dist: sphinxcontrib-mermaid>=2.0.0; extra == 'docs'
Provides-Extra: notebook
Requires-Dist: ipykernel>=7.1.0; extra == 'notebook'
Requires-Dist: ipympl>=0.10.0; extra == 'notebook'
Requires-Dist: ipython>=9.9.0; extra == 'notebook'
Requires-Dist: ipywidgets>=8.1.8; extra == 'notebook'
Requires-Dist: jupyterlab>=4.5.3; extra == 'notebook'
Provides-Extra: tests
Requires-Dist: nbmake>=1.5.5; extra == 'tests'
Requires-Dist: pytest-cov>=7.0.0; extra == 'tests'
Requires-Dist: pytest-timeout>=2.3.1; extra == 'tests'
Requires-Dist: pytest>=9.0.2; extra == 'tests'
Provides-Extra: zones
Requires-Dist: opencv-python>=4.5.0; extra == 'zones'
Description-Content-Type: text/markdown

# CaMAP

[![Tests](https://github.com/miniscope/CaMAP/actions/workflows/test.yml/badge.svg)](https://github.com/miniscope/CaMAP/actions/workflows/test.yml)
[![PyPI](https://img.shields.io/pypi/v/camap)](https://pypi.org/project/camap/)
[![License: AGPL-3.0](https://img.shields.io/badge/License-AGPL--3.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)

Calcium imaging mapping and analysis pipeline. Extracts neural events from
calcium traces, aligns them with animal behavior, and computes spatial
tuning metrics including rate maps, spatial information, stability, and
place-cell classification.

> **Alpha-stage** in `0.x` — APIs may change between minor releases.

## Install

```bash
pip install camap
```

`oasis-deconv` is required for the deconvolution step; see
[Installation](https://miniscope.github.io/CaMAP/installation.html) for the
recommended install path.

## Minimum example

```python
from camap.dataset import BaseCaMAPDataset

ds = BaseCaMAPDataset.from_yaml("config.yaml", "data_paths.yaml")
ds.load()
ds.preprocess_behavior()
ds.deconvolve()
ds.match_events()
ds.compute_occupancy()
ds.analyze_units()
ds.save_bundle("output/session_name")
```

## Documentation

- [Installation](https://miniscope.github.io/CaMAP/installation.html)
- [Quickstart](https://miniscope.github.io/CaMAP/quickstart.html)
- [Pipeline Details](https://miniscope.github.io/CaMAP/pipeline.html)

## License

AGPL-3.0. See [LICENSE](LICENSE).
