| Name | napari-trackastra JSON |
| Version |
0.1.6
JSON |
| download |
| home_page | None |
| Summary | Napari plugin for cell tracking with trackastra. |
| upload_time | 2024-10-22 12:21:27 |
| maintainer | None |
| docs_url | None |
| author | Benjamin Gallusser, Martin Weigert |
| requires_python | >=3.10 |
| 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 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. |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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# napari-trackastra
[](https://pypi.org/project/napari-trackastra)
[](https://github.com/weigertlab/napari-trackastra/actions)
[](https://codecov.io/gh/weigertlab/napari-trackastra)
[](https://napari-hub.org/plugins/napari-trackastra)
A napari plugin for cell tracking with [`trackastra`](https://github.com/weigertlab/trackastra).
## 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 to [Cell Tracking Challenge format](https://celltrackingchallenge.net/datasets/).
- 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/
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