Metadata-Version: 2.1
Name: napari-moltrack
Version: 0.0.22
Summary: Single molecule tracking package for Napari
Author: Piers Turner
Author-email: piers.turner@physics.ox.ac.uk
License: 
        Copyright (c) 2024, Piers Turner
        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
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Bug Tracker, https://github.com/piedrro/napari-moltrack/issues
Project-URL: Documentation, https://github.com/piedrro/napari-moltrack#README.md
Project-URL: Source Code, https://github.com/piedrro/napari-moltrack
Project-URL: User Support, https://github.com/piedrro/napari-moltrack/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 :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: napari[all]
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scipy
Requires-Dist: pyqtgraph
Requires-Dist: picassosr
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: scipy
Requires-Dist: opencv-python
Requires-Dist: tqdm
Requires-Dist: originpro
Requires-Dist: pyqt5-tools
Requires-Dist: torch
Requires-Dist: cellpose>=3.0.1
Requires-Dist: omnipose
Requires-Dist: trackpy
Requires-Dist: shapely
Requires-Dist: astropy
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: pyqt5; extra == "testing"

# napari-moltrack

[![License BSD-3](https://img.shields.io/pypi/l/napari-moltrack.svg?color=green)](https://github.com/piedrro/napari-moltrack/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-moltrack.svg?color=green)](https://pypi.org/project/napari-moltrack)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-moltrack.svg?color=green)](https://python.org)
[![tests](https://github.com/piedrro/napari-moltrack/workflows/tests/badge.svg)](https://github.com/piedrro/napari-moltrack/actions)
[![codecov](https://codecov.io/gh/piedrro/napari-moltrack/branch/main/graph/badge.svg)](https://codecov.io/gh/piedrro/napari-moltrack)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-moltrack)](https://napari-hub.org/plugins/napari-moltrack)

A Napari plugin for single molecule localisation *and* tracking based on **Picasso**, **GPUfit** and **Trackpy**.
This plugin was designed to detect/track single molecules inside cells, but can be used for any other SMLM/tracking application.

All functions are parallelised/GPU accelerated where possible to increase performance.
Multiple datasets can be loaded and processed in parallel.

Single molecule localisations can be filtered by their properties (e.g. photons, width, etc.) and can be rendered as a super resolution image.

Segmentations can be used to exclude regions froHm single molecule localisation and tracking.
Segmentations can be added automatically using Cellpose or can be added manually. Includes tools for editing/modifying segmentations at a sub-pixel resolution.

Compatible with both single and multi channel .tif and .fits files.

napari-moltrack was written by Piers Turner, Kapanidis Group, University of Oxford....

https://www.physics.ox.ac.uk/research/group/gene-machines

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

This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

## Installation

You can install `napari-moltrack` via [pip]:

    pip install napari-moltrack


To install latest development version :

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

## License

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

## 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/piedrro/napari-moltrack/issues

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