Metadata-Version: 2.4
Name: napari-phasors
Version: 0.5.0
Summary: A simple plugin to use phasor analysis
Author-email: Bruno Pannunzio <bpannunzio@pasteur.edu.uy>, Marcelo Leomil Zoccoler <marzoccoler@gmail.com>, Bruno Schuty <schutyb@schutyb.com>, Leonel Malacrida <lmalacrida@pasteur.edu.uy>
License: 
        Copyright (c) 2024, Marcelo L. Zoccoler, Bruno Pannunzio, 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,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
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        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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: 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>=0.8
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: pyqt5
Requires-Dist: pawflim
Requires-Dist: scipy
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: pytest; extra == "testing"
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"
Requires-Dist: biaplotter>=0.4.2; extra == "testing"
Requires-Dist: PyQt5; 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>=0.8; 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"
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)
[![PyPI](https://img.shields.io/pypi/v/napari-phasors.svg?color=green)](https://pypi.org/project/napari-phasors)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-phasors.svg?color=green)](https://python.org)
[![tests](https://github.com/napari-phasors/napari-phasors/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/napari-phasors/napari-phasors/actions/workflows/run-tests.yml)
[![codecov](https://codecov.io/gh/napari-phasors/napari-phasors/branch/main/graph/badge.svg)](https://codecov.io/gh/napari-phasors/napari-phasors)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-phasors)](https://napari-hub.org/plugins/napari-phasors)
[![Documentation Status](https://readthedocs.org/projects/napari-phasors/badge/?version=latest)](https://napari-phasors.readthedocs.io/en/latest/?badge=latest)
[![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

- Read FLIM and hyperspectral files (`.fbd`, `.sdt`, `.ptu`, `.lsm`, `.ome.tif`)
- Simultaneous multi-layer phasor analysis with primary-layer selection
- Calibration, filtering (median / wavelet), and automatic thresholding
- Phasor selections: circular cursors, automatic clustering, and manual drawing
- Phasor Mapping: colormap apparent/normal lifetime, phasor phase, and modulation per pixel, with an interactive 1D histogram and statistics table
- Component analysis and FRET trajectory analysis
- Export as OME-TIF or CSV (multiple layers simultaneously)

## Installation

You can install `napari-phasors` via [pip]. Follow these steps from a
terminal.

We recommend using `miniforge` whenever possible. Click
[here](https://conda-forge.org/download/) to choose the right download option for your OS.
**If you do not use `miniforge`, but rather Anaconda or Miniconda, replace
the `mamba` term whenever you see it below with `conda`.**

Create a conda environment with napari by typing :

    mamba create -y -n napari-phasors-env napari pyqt python=3.12

Activate the environment :

    mamba activate napari-phasors-env

Install `napari-phasors` via [pip] :

    pip install napari-phasors

Alternatively, install latest development version with :

    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/
