{"name":"napari-track-edit","display_name":"Napari Track Edit","visibility":"public","icon":null,"categories":["Utilities"],"schema_version":"0.3.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-track-edit.main_app","title":"Open all menus and the lineage view","python_name":"napari_track_edit.application_menus.main_app:MainAppWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.tracking_group","title":"Open tracking widgets","python_name":"napari_track_edit.application_menus.main_app:TrackingGroupWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.editing_group","title":"Open editing widgets","python_name":"napari_track_edit.application_menus.main_app:EditingGroupWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.getting_started","title":"Open Getting started menu","python_name":"napari_track_edit.application_menus.main_app:GettingStarted_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.tracking","title":"Open Tracking menu","python_name":"napari_track_edit.application_menus.main_app:Tracking_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.tracks_list","title":"Open Tracks List menu","python_name":"napari_track_edit.application_menus.main_app:TrackList_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.editing_selection","title":"Open Editing && Selection menu","python_name":"napari_track_edit.application_menus.main_app:EditingSelection_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.visualization","title":"Open Visualization menu","python_name":"napari_track_edit.application_menus.main_app:Visualization_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.features","title":"Open Feature menu","python_name":"napari_track_edit.application_menus.main_app:Feature_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.groups","title":"Open Groups menu","python_name":"napari_track_edit.application_menus.main_app:Groups_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.table","title":"Open Table menu","python_name":"napari_track_edit.application_menus.main_app:Table_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.lineage_view","title":"Open Lineage View menu","python_name":"napari_track_edit.application_menus.main_app:LineageView_LauncherWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.solve","title":"Run motile tracking (backend only)","python_name":"napari_track_edit.motile.backend.solve:solve","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.Fluo_N2DL_HeLa","title":"Load Fluo-N2DL-HeLa tracking dataset","python_name":"napari_track_edit.example_data:Fluo_N2DL_HeLa","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.Fluo_N2DL_HeLa_crop","title":"Load Fluo-N2DL-HeLa tracking dataset (crop)","python_name":"napari_track_edit.example_data:Fluo_N2DL_HeLa_crop","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-track-edit.Mouse_Embryo_Membrane","title":"Load Mouse Embryo_Membrane tracking dataset","python_name":"napari_track_edit.example_data:Mouse_Embryo_Membrane","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-track-edit.main_app","display_name":"Open all widgets","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.tracking_group","display_name":"Open tracking widgets","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.editing_group","display_name":"Open editing widgets","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.getting_started","display_name":"Widget - Getting started","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.tracking","display_name":"Widget - Tracking","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.tracks_list","display_name":"Widget - Tracks List","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.editing_selection","display_name":"Widget - Editing & Selection","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.visualization","display_name":"Widget - Visualization","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.features","display_name":"Widget - Features","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.groups","display_name":"Widget - Groups","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.table","display_name":"Widget - Table","autogenerate":false,"default_dock_area":"right"},{"command":"napari-track-edit.lineage_view","display_name":"Widget - Lineage View","autogenerate":false,"default_dock_area":"right"}],"sample_data":[{"command":"napari-track-edit.Fluo_N2DL_HeLa","key":"Fluo-N2DL-HeLa","display_name":"Fluo-N2DL-HeLa (2D)"},{"command":"napari-track-edit.Fluo_N2DL_HeLa_crop","key":"Fluo-N2DL-HeLa-crop","display_name":"Fluo-N2DL-HeLa crop (2D)"},{"command":"napari-track-edit.Mouse_Embryo_Membrane","key":"Mouse_Embryo_Membrane","display_name":"Mouse Embryo Membranes (3D)"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configurations":{}},"package_metadata":{"metadata_version":"2.4","name":"napari-track-edit","version":"1.1.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Napari plugin for interactive tracks and segmentation annotation","description":"\n\n# Napari Track Edit\n\n[](https://github.com/live-image-tracking-tools/napari-track-edit/actions)\n[](https://codecov.io/gh/live-image-tracking-tools/napari-track-edit)\n\n![\"Napari](\"docs/source/images/logo_transparent.png\")
\n\nA napari plugin for interactive visualization, navigation, and editing of object tracking results. You can open and edit existing tracking data, manually create new tracking results, or run automatic tracking with [motile](https://github.com/funkelab/motile).\nThe full documentation of the plugin can be found [here](https://liveimagetrackingtools.org/napari-track-edit/).\n\nMotile is a library that makes it easy to solve tracking problems using optimization\nby framing the task as an Integer Linear Program (ILP).\nSee the motile [documentation](https://funkelab.github.io/motile)\nfor more details on the concepts and method.\n\n----------------------------------\n\n## Installation\n\nUsers can download and install an executable application from the github release, or\ninstall from `pypi` in the environment of their choice (e.g. `venv`, `conda`) with the command\n`pip install napari-track-edit`.\nCurrently, napari-track-edit requires python >=3.11.\n\n### Recommended extras\n\nFor better performance, you can install optional extras:\n\n- **numba**: Speeds up candidate graph construction significantly.\n ```bash\n pip install napari-track-edit[numba]\n ```\n\n- **gurobi**: Uses the Gurobi solver instead of the default open-source solver. Gurobi is\n much faster but requires a license (free for academics).\n ```bash\n pip install napari-track-edit[gurobi]\n ```\n\nYou can install multiple extras at once: `pip install napari-track-edit[numba,gurobi]`.\n\n### Gurobi license version mismatch\n\nIf you have a Gurobi license and encounter an error about license version mismatch,\nyou may need to install a specific version of `gurobipy` that matches your license.\nUse one of the version-specific extras:\n\n```bash\npip install napari-track-edit[gurobi12] # For Gurobi 12.x licenses\npip install napari-track-edit[gurobi13] # For Gurobi 13.x licenses\n```\n\n### For developers\n\nDevelopers can clone the GitHub repository and then use `uv` to install and run the code.\nSee the developer guide in [`DEVELOPER.md`](DEVELOPER.md) for more information.\n\n## Usage\nStart napari and open all widgets via `Plugins` > `Napari Track Edit` > `Open all widgets`.\n\nFrom here you can:\n- load your own Labels or Points data to [track with motile](https://liveimagetrackingtools.org/napari-track-edit/tracking.html#tracking-with-motile),\n- load an image to [manually track objects](https://liveimagetrackingtools.org/napari-track-edit/tracking.html#tracking-from-scratch),\n- or [load existing tracking data](https://liveimagetrackingtools.org/napari-track-edit/saving_loading.html#loading-tracks) to explore or edit.\n\nIf you would like to see an example first, go to `Plugins` > `Napari Track Edit` > `Widget - Getting started`, and click on one of the two examples, `Hela cells (2D)` or `Mouse embryo (3D)`, to download and view them:\n\n- Fluo-N2DL-HeLa is a 2D dataset of images and segmentations of HeLa cells from the [`cell tracking challenge`](https://celltrackingchallenge.net/2d-datasets/).\n- Mouse Embryo Membrane is a 3D dataset of images and segmentations of a membrane labeled developing early mouse embryo (4-26 cells)\nfrom [`Fabrèges et al (2024)`](https://www.science.org/doi/10.1126/science.adh1145) available [`here`](https://zenodo.org/records/13903500).\n\nFor details, please read the [documentation](https://liveimagetrackingtools.org/napari-track-edit/).\nIf you are new to napari-track-edit, you can follow this [tutorial](https://liveimagetrackingtools.org/napari-track-edit/napari-track-edit_tutorial.html) to learn the basics.\n\nhttps://github.com/user-attachments/assets/cd23271d-bbe6-40c2-80cb-8404136a564a\n\n## Issues\n\nIf you encounter any problems, please\n[file an issue](https://github.com/live-image-tracking-tools/napari-track-edit/issues)\nalong with a detailed description.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Caroline Malin-Mayor ","maintainer":null,"maintainer_email":null,"license":"BSD 3-Clause License","classifier":["Development Status :: 5 - Production/Stable","Framework :: napari","Intended Audience :: Developers","Intended Audience :: End Users/Desktop","Intended Audience :: Science/Research","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["napari<0.10.0,>=0.7.1","funtracks<3,>=2.2.0","platformdirs<5,>=4","numpy<3,>=2","magicgui>=0.10.1","qtpy<3,>=2.4","scikit-image>=0.25","motile<1,>=0.4","pydantic<3,>=2","tifffile[all]>=2025.1.10","tqdm<5,>=4","dask[array]>=2021.10.0","fonticon-fontawesome6<7,>=6","pyqtgraph<1,>=0.13","fastplotlib<0.7,>=0.6.1","pygfx==0.15.3","wgpu<0.30,>=0.29","napari-orthogonal-views>=0.5.0","lxml_html_clean<1,>=0.4","zarr<4,>=2.18.7","blosc2<4.12,>=4.11","psygnal<0.16,>=0.15.1","numba>=0.62.1; extra == \"numba\"","gurobipy; extra == \"gurobi\"","gurobipy<13,>=12; extra == \"gurobi12\"","gurobipy<14,>=13; extra == \"gurobi13\"","pyqt6<7,>=6.7; extra == \"all\""],"requires_python":">=3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/live-image-tracking-tools/napari-track-edit/issues","Documentation, https://liveimagetrackingtools.org/napari-track-edit/"],"provides_extra":["numba","gurobi","gurobi12","gurobi13","all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}