{"name":"napari-amdtrk","display_name":"Amend segmentation and track","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-amdtrk.get_reader","title":"Open data with Amend segmentation and track","python_name":"napari_amdtrk._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-amdtrk.make_sample_data","title":"Load sample data from Amend segmentation and track","python_name":"napari_amdtrk._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-amdtrk.make_amdtrkwidget","title":"Make amend track widget","python_name":"napari_amdtrk._widget:AmdTrkWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-amdtrk.get_reader","filename_patterns":["*"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"napari-amdtrk.make_amdtrkwidget","display_name":"Amend track widget","autogenerate":true}],"sample_data":[{"key":"napari-amdtrk - simple","display_name":"basic tracks","uri":"simple","reader_plugin":null},{"key":"napari-amdtrk - full","display_name":"complete cell cycle tracks","uri":"full","reader_plugin":null}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-amdtrk","version":"1.1.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"Manually amend segmentation and track within napari","description":"# napari-amdtrk\n\n[](https://github.com/Jeff-Gui/napari-amdtrk/raw/main/LICENSE)\n[](https://pypi.org/project/napari-amdtrk)\n[](https://python.org)\n[](https://github.com/Jeff-Gui/napari-amdtrk/actions)\n[](https://codecov.io/gh/Jeff-Gui/napari-amdtrk)\n[](https://napari-hub.org/plugins/napari-amdtrk)\n\nAmend segmentation and track within napari manually.\n\n![\"overview\"](\"preview.png\")
\n\n\n### [:eyes: watch a demo video](https://drive.google.com/file/d/1oHPdYcKv-QgOWylm21DnOF1NlVNsRIcL/view)\n\n----------------------------------\n\n### Input data structure\n\nNapari-amdtrk reads an input directory which includes:\n- An intensity image (`tif`) in txyc (or txy) format\n- An object mask (`tif`) in txy format\n- An object table (`csv`) with following essential columns:\n - frame: time frame\n - trackId: ID of the track, starting from 1\n - Center_of_the_object_0: x coordinate\n - Center_of_the_object_1: y coordinate\n - continuous_label: the corresponding label (intensity value) of the object in the object mask (You may use `skimage.measure.label` to get it from a binary mask).\n\n- A config file named `config.yaml` (_other names are not allowed_)\n\n Within the config file, there should be:\n - intensity_suffix: suffix of the intensity image (e.g., for `foo_GFP.tif`, use `GFP` in the config). For multiple intensity images, separate them with commas (e.g., `GFP, mCherry`)\n - mask_suffix: suffix of the mask image\n - track_suffix: suffix of the tracked object table\n - frame_base: index of the first frame (either `0` or `1`)\n - stateCol: __optional__ column name for the cell state (e.g., cell cycle phase) in the object table. Leave blank if the object table does not contain it\n\n__Napari-amdtrk will modify mask and track files in place.__ Other files are not affected.\n\n---\n### Quick start\n\n1. Open `napari` GUI.\n2. `File` > `Open folder` > choose `Amend segmentation and track`\n3. `Plugins` > `napari-amdtrk: Amend track widget` > `Run`\n4. In `layer list`, select the `segm` layer to start editing.\n\nPlease check out the demo video [here](https://drive.google.com/file/d/1oHPdYcKv-QgOWylm21DnOF1NlVNsRIcL/view) and the sample data (see below).\n\n----------------------------------\n\n### Sample data\n\nTo load sample data, `File` > `Open Sample` > `napari-amdtrk` > `basic tracks` or `complete cell cycle tracks`.\n\n- basic tracks: simple cell tracks as essential input data.\n- complete cell cycle tracks: cell tracks with additional cell cycle features.\n\nThe above operations will download data to `~/.amd_trk/_sample_data/` (__~230MB__). After downloading is finished, sample data will be loaded.\n\n_Notes_\n- Please cite this repository if using the plugin in your work (try `About` > `Cite this repository` upper right of this homepage).\n \n- Sample data (cell track videos) have been published with [_pcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling_](10.1093/bioinformatics/btac602). We acknowledge Dr Kuan Yoow Chan and members of his lab for generating the data. \n\n----------------------------------\n\n### Keyboard shortcuts\n\n- ↑ and ↓: toggle different operations\n- enter: run the operation\n\n- Available to a selected object:\n - control + 9: shrink the object mask\n - control + 0: expand the object mask\n\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n## Installation\n\nPlease install `napari` GUI first:\n\n python -m pip install \"napari[all]\"\n\nYou can install `napari-amdtrk` via [pip]:\n\n pip install napari-amdtrk\n\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-amdtrk\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\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":"https://github.com/Jeff-Gui/napari-amdtrk-plugin","download_url":null,"author":"Yifan Gui","author_email":"jeffgui9912@gmail.com","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy (<1.24)","magicgui","qtpy","trackpy","pandas","scikit-image","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/Jeff-Gui/napari-amdtrk-plugin/issues","Documentation, https://github.com/Jeff-Gui/napari-amdtrk-plugin/blob/master/README.md","Source Code, https://github.com/Jeff-Gui/napari-amdtrk-plugin"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}