{"name":"napari-trackastra","display_name":"trackastra","visibility":"public","icon":"resources/icon.png","categories":["Image Processing"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-trackastra.example_data_bacteria","title":"Sample bacteria images and masks","python_name":"napari_trackastra._sample_data:example_data_bacteria","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-trackastra.example_data_hela","title":"Sample bacteria images and masks","python_name":"napari_trackastra._sample_data:example_data_hela","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-trackastra.track","title":"Create Plugin","python_name":"napari_trackastra:Tracker","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-trackastra.track","display_name":"Trackastra tracking","autogenerate":false}],"sample_data":[{"command":"napari-trackastra.example_data_bacteria","key":"unique_id.1","display_name":"bacteria"},{"command":"napari-trackastra.example_data_hela","key":"unique_id.2","display_name":"hela"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-trackastra","version":"0.2.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Napari plugin for cell tracking with trackastra.","description":"# napari-trackastra\n\n[![PyPI](https://img.shields.io/pypi/v/napari-trackastra.svg?color=green)](https://pypi.org/project/napari-trackastra)\n[![tests](https://github.com/weigertlab/napari-trackastra/workflows/tests/badge.svg)](https://github.com/weigertlab/napari-trackastra/actions)\n[![codecov](https://codecov.io/gh/weigertlab/napari-trackastra/branch/main/graph/badge.svg)](https://codecov.io/gh/weigertlab/napari-trackastra)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-trackastra)](https://napari-hub.org/plugins/napari-trackastra)\n\nA napari plugin for cell tracking with [`trackastra`](https://github.com/weigertlab/trackastra).\n\n![demo](https://github.com/weigertlab/napari-trackastra/assets/8866751/097eb82d-0fef-423e-9275-3fb528c20f7d)\n\n\n## Installation\n1. Please install napari as outlined [here](https://napari.org/stable/tutorials/fundamentals/installation.html).\n\n2. After that, install the latest version of this plugin from PyPI with:\n    ```\n    pip install napari-trackastra\n    ```\n\nNotes:\n- 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).\n- On Windows currently only supported for Python 3.10.\n\n## Usage\n\n- `trackastra` expects a timeseries of raw images and corresponding segmentations masks as input.\n- We provide some demo data at `File > Open Sample > trackastra`.\n- Tracked cells can be directly saved in\n    - [Cell Tracking Challenge format (CTC)](https://celltrackingchallenge.net/datasets/)\n    - [Graph Exchange File Format (GEFF)](https://liveimagetrackingtools.org/geff/)\n- Results can be drag-and-dropped back into napari for inspection.\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Benjamin Gallusser, Martin Weigert","author_email":"bgallusser@gmail.com, marweigert@gmail.com","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2024, Martin Weigert\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","scikit-image","trackastra>=0.4.1","napari-ctc-io","napari-geff>=0.0.3","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/weigertlab/napari-trackastra/issues","Documentation, https://github.com/weigertlab/napari-trackastra#README.md","Source Code, https://github.com/weigertlab/napari-trackastra","User Support, https://github.com/weigertlab/napari-trackastra/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}