{"name":"napari-copick","display_name":"copick","visibility":"public","icon":"","categories":["Annotation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-copick.make_qwidget","title":"napari copick","python_name":"napari_copick:CopickPlugin","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-copick.make_qwidget","display_name":"napari copick","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-copick","version":"1.8.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plugin for collaborative annotation in cryoET using copick","description":"# napari-copick\n\n[![License MIT](https://img.shields.io/pypi/l/napari-copick.svg?color=green)](https://github.com/kephale/napari-copick/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-copick.svg?color=green)](https://pypi.org/project/napari-copick)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-copick.svg?color=green)](https://python.org)\n[![tests](https://github.com/kephale/napari-copick/workflows/tests/badge.svg)](https://github.com/kephale/napari-copick/actions)\n[![codecov](https://codecov.io/gh/kephale/napari-copick/branch/main/graph/badge.svg)](https://codecov.io/gh/kephale/napari-copick)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-copick)](https://napari-hub.org/plugins/napari-copick)\n\nA plugin for collaborative annotation in cryoET using copick\n\n![interface.png](https://github.com/copick/napari-copick/raw/main/docs/assets/interface.png)\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-copick` via [pip]:\n\n    pip install napari-copick\n\nTo install latest development version:\n\n    pip install git+https://github.com/copick/napari-copick.git\n\n## Usage\n\n### Using a copick config file\n\n```bash\nnapari-copick run --config path/to/copick_config.json\n```\n\n### Using dataset IDs from CZ cryoET Data Portal\n\n```bash\nnapari-copick run --dataset-ids 10440 10441 --overlay-root /path/to/overlay_root\n```\n\nYou can specify multiple dataset IDs separated by spaces.\n\n### GUI Usage\n\nThe plugin provides an intuitive interface with two loading options:\n\n1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file\n2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path\n\nAfter loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.\n\n### Tomogram Handling\n\nnapari-copick now handles multiscale zarr arrays directly:\n\n- Automatically detects and loads all available resolution levels\n- Creates a proper multiscale image stack using napari's native multiscale API\n- Uses dask for efficient lazy loading of large tomogram data\n- Applies appropriate scaling factors based on the voxel size metadata\n\nThis direct zarr handling provides better performance and more flexibility compared to relying on external plugins.\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-copick\" 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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/kephale/napari-copick/issues\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\n## Code of Conduct\n\nThis project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto:opensource@chanzuckerberg.com).\n\n## Reporting Security Issues\n\nIf you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).\n","description_content_type":"text/markdown","keywords":"annotation,copick,cryo-et,cryoet,napari,plugin,tomography","home_page":null,"download_url":null,"author":null,"author_email":"Kyle Harrington <czi@kyleharrington.com>, \"Utz H. Ermel\" <utz.ermel@czii.org>","maintainer":null,"maintainer_email":null,"license":"The MIT License (MIT)\n\nCopyright (c) 2024 Kyle Harrington\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.","classifier":["Development Status :: 2 - Pre-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 :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Programming Language :: Python :: Implementation :: CPython","Programming Language :: Python :: Implementation :: PyPy","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["click","copick-shared-ui>=0.5.0","copick>=1.23.1","fsspec","magicgui","napari","napari-ome-zarr","numpy","pydantic>=2","qtpy","scikit-image","trimesh","zarr","black>=25.1.0; extra == 'dev'","hatch-vcs>=0.4.0; extra == 'dev'","hatchling>=1.25.0; extra == 'dev'","pre-commit>=4.2.0; extra == 'dev'","ruff>=0.12.0; extra == 'dev'","napari; extra == 'testing'","pyqt6; extra == 'testing'","pytest; extra == 'testing'","pytest-cov; extra == 'testing'","pytest-qt; extra == 'testing'","tox; extra == 'testing'","tox-gh-actions; extra == 'testing'","tox-uv; extra == 'testing'"],"requires_python":">=3.10","requires_external":null,"project_url":["Repository, https://github.com/kephale/napari-copick","Issues, https://github.com/kephale/napari-copick/issues","Documentation, https://github.com/kephale/napari-copick#README.md","Bug Tracker, https://github.com/kephale/napari-copick/issues","Source Code, https://github.com/kephale/napari-copick","User Support, https://github.com/kephale/napari-copick/issues"],"provides_extra":["dev","testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}