Metadata-Version: 2.4
Name: napari-phasors
Version: 0.6.4
Summary: A simple plugin to use phasor analysis
Author-email: Bruno Pannunzio <bpannunzio@pasteur.edu.uy>, Marcelo Leomil Zoccoler <marzoccoler@gmail.com>, Joaquín Rivero <jrivero94@outlook.com>, Bruno Schuty <schutyb@schutyb.com>, Leonel Malacrida <lmalacrida@pasteur.edu.uy>
License: 
        Copyright (c) 2026, Marcelo L. Zoccoler, Bruno Pannunzio, Joaquín Rivero, Bruno Schuty
        and Leonel Malacrida. All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
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Project-URL: Homepage, https://github.com/napari-phasors/napari-phasors
Project-URL: Bug Tracker, https://github.com/napari-phasors/napari-phasors/issues
Project-URL: Documentation, https://github.com/napari-phasors/napari-phasors#README.md
Project-URL: Source Code, https://github.com/napari-phasors/napari-phasors
Project-URL: User Support, https://github.com/napari-phasors/napari-phasors/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: phasorpy>=0.10
Requires-Dist: qtpy
Requires-Dist: biaplotter>=0.4.2
Requires-Dist: fbdfile
Requires-Dist: sdtfile
Requires-Dist: ptufile
Requires-Dist: tifffile
Requires-Dist: pandas
Requires-Dist: pyqt6
Requires-Dist: pawflim
Requires-Dist: scipy
Requires-Dist: czifile
Requires-Dist: lfdfiles
Provides-Extra: testing
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Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari; extra == "testing"
Requires-Dist: qtpy; extra == "testing"
Requires-Dist: scikit-image; extra == "testing"
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Requires-Dist: pyqt6; extra == "testing"
Requires-Dist: pandas; extra == "testing"
Requires-Dist: black; extra == "testing"
Requires-Dist: isort; extra == "testing"
Requires-Dist: ruff; extra == "testing"
Requires-Dist: pre-commit; extra == "testing"
Requires-Dist: phasorpy>=0.10; extra == "testing"
Requires-Dist: tifffile; extra == "testing"
Requires-Dist: fbdfile; extra == "testing"
Requires-Dist: sdtfile; extra == "testing"
Requires-Dist: ptufile; extra == "testing"
Requires-Dist: pawflim; extra == "testing"
Requires-Dist: scipy; extra == "testing"
Requires-Dist: czifile; extra == "testing"
Requires-Dist: lfdfiles; extra == "testing"
Dynamic: license-file

# napari-phasors

[![License BSD-3](https://img.shields.io/pypi/l/napari-phasors.svg?color=green)](https://github.com/napari-phasors/napari-phasors/raw/main/LICENSE)
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[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.14647626-blue.svg)](https://doi.org/10.5281/zenodo.14647626)

A comprehensive plugin for phasor analysis in napari. Based on the
[phasorpy](https://www.phasorpy.org/) library.

----------------------------------

## Documentation

Full documentation, including step-by-step guides and the API reference, is
available at **[https://napari-phasors.readthedocs.io](https://napari-phasors.readthedocs.io)**.

## Features

- **Reading** a wide range of FLIM and hyperspectral file formats:
    - **Raw data formats:**
        - `.ptu`, `.fbd`, `.sdt`, `.lsm`, `.tif`, `.tiff`, `.czi`, `.flif`, `.bh`, `.b&h`, `.bhz`, `.lif`, `.bin`, `.json`
    - **Processed data formats:**
        - `.ome.tif`, `.ome.tiff`, `.r64`, `.ref`, `.ifli`, `.lif`, `.json`
- **Phasor analysis** on multiple layers simultaneously, including support for stacking multiple raw data files
- **Calibration** using reference images with known lifetimes
- **Filtering** with median, wavelet, and automatic thresholding (Otsu, Li, Yen)
- **Component analysis** for multi-component systems
- **Phasor Mapping** — colormap apparent/normal lifetime, phasor phase, and phasor modulation per pixel, with interactive 1D histograms, statistics tables, and arc overlay tools
- **FRET analysis** with donor trajectory visualization and multi-layer donor/background source selection
- **Selections** via manual drawing, circular/polar/elliptical cursors, and automatic clustering
- **Exporting** results as OME-TIF or CSV (multiple layers simultaneously)

## Installation

There are several ways to install napari-phasors:

### Easiest: napari's plugin manager

If you already have [napari](https://napari.org) installed, go to
**Plugins → Install/Uninstall Plugins...**, search for **napari-phasors**,
and click **Install**.

### Standalone installer (no Python required)

Pre-built installers for Windows (`.exe`), macOS
(`.dmg`), and Linux (`.sh`) are available on the
[latest release](https://github.com/napari-phasors/napari-phasors/releases/latest)
page. Download and run — no Python installation
needed. Installers are ~350–470 MB and bundle
everything required.

### Using conda + pip

We recommend using [miniforge](https://conda-forge.org/download/). If you
use Anaconda or Miniconda, replace `mamba` with `conda`.

    mamba create -y -n napari-phasors-env napari pyqt6 python=3.14 # or 3.12, 3.13

Activate the environment :

    conda activate napari-phasors-env
    pip install napari-phasors

### Development version

    pip install git+https://github.com/napari-phasors/napari-phasors.git

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

### Pre-commit Hooks

This project uses [pre-commit](https://pre-commit.com/) to run **black**,
**isort**, and **ruff** automatically on every commit. To set it up:

```bash
pip install pre-commit
pre-commit install
```

From now on, every `git commit` will auto-format and lint your code before
the commit goes through. You can also run the hooks manually on all files:

```bash
pre-commit run --all-files
```

## License

Distributed under the terms of the [BSD-3] license,
"napari-phasors" is free and open source software.

Please cite doi: [https://doi.org/10.5281/zenodo.14647626](https://doi.org/10.5281/zenodo.14647626)
if napari-phasors contributes to a project that leads to a publication.

## Issues

If you encounter any problems, please [file an issue] along with a detailed
description.

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/napari-phasors/napari-phasors/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
