Metadata-Version: 2.4
Name: napari-trackastra
Version: 0.2.1
Summary: Napari plugin for cell tracking with trackastra.
Author: Benjamin Gallusser, Martin Weigert
Author-email: bgallusser@gmail.com, marweigert@gmail.com
License: 
        Copyright (c) 2024, Martin Weigert
        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
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Project-URL: Bug Tracker, https://github.com/weigertlab/napari-trackastra/issues
Project-URL: Documentation, https://github.com/weigertlab/napari-trackastra#README.md
Project-URL: Source Code, https://github.com/weigertlab/napari-trackastra
Project-URL: User Support, https://github.com/weigertlab/napari-trackastra/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
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: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scikit-image
Requires-Dist: trackastra>=0.4.1
Requires-Dist: napari-ctc-io
Requires-Dist: napari-geff>=0.0.3
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"
Dynamic: license-file

# napari-trackastra

[![PyPI](https://img.shields.io/pypi/v/napari-trackastra.svg?color=green)](https://pypi.org/project/napari-trackastra)
[![tests](https://github.com/weigertlab/napari-trackastra/workflows/tests/badge.svg)](https://github.com/weigertlab/napari-trackastra/actions)
[![codecov](https://codecov.io/gh/weigertlab/napari-trackastra/branch/main/graph/badge.svg)](https://codecov.io/gh/weigertlab/napari-trackastra)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-trackastra)](https://napari-hub.org/plugins/napari-trackastra)

A napari plugin for cell tracking with [`trackastra`](https://github.com/weigertlab/trackastra).

![demo](https://github.com/weigertlab/napari-trackastra/assets/8866751/097eb82d-0fef-423e-9275-3fb528c20f7d)


## Installation
1. Please install napari as outlined [here](https://napari.org/stable/tutorials/fundamentals/installation.html).

2. After that, install the latest version of this plugin from PyPI with:
    ```
    pip install napari-trackastra
    ```

Notes:
- For tracking with an integer linear program (ILP, which is optional), follow the [installation instructions of the main `trackastra` package](https://github.com/weigertlab/trackastra/blob/main/README.md#installation).
- On Windows currently only supported for Python 3.10.

## Usage

- `trackastra` expects a timeseries of raw images and corresponding segmentations masks as input.
- We provide some demo data at `File > Open Sample > trackastra`.
- Tracked cells can be directly saved in
    - [Cell Tracking Challenge format (CTC)](https://celltrackingchallenge.net/datasets/)
    - [Graph Exchange File Format (GEFF)](https://liveimagetrackingtools.org/geff/)
- Results can be drag-and-dropped back into napari for inspection.

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