| Name | napari-copick JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | A plugin for collaborative annotation in cryoET using copick |
| upload_time | 2025-07-27 04:05:56 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | The MIT License (MIT)
Copyright (c) 2024 Kyle Harrington
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE. |
| keywords |
annotation
copick
cryo-et
cryoet
napari
plugin
tomography
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# napari-copick
[](https://github.com/kephale/napari-copick/raw/main/LICENSE)
[](https://pypi.org/project/napari-copick)
[](https://python.org)
[](https://github.com/kephale/napari-copick/actions)
[](https://codecov.io/gh/kephale/napari-copick)
[](https://napari-hub.org/plugins/napari-copick)
A plugin for collaborative annotation in cryoET using copick
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->
## Installation
You can install `napari-copick` via [pip]:
pip install napari-copick
To install latest development version:
pip install git+https://github.com/copick/napari-copick.git
## Usage
### Using a copick config file
```bash
napari-copick run --config path/to/copick_config.json
```
### Using dataset IDs from CZ cryoET Data Portal
```bash
napari-copick run --dataset-ids 10440 10441 --overlay-root /path/to/overlay_root
```
You can specify multiple dataset IDs separated by spaces.
### GUI Usage
The plugin provides an intuitive interface with two loading options:
1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file
2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path
After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.
### Tomogram Handling
napari-copick now handles multiscale zarr arrays directly:
- Automatically detects and loads all available resolution levels
- Creates a proper multiscale image stack using napari's native multiscale API
- Uses dask for efficient lazy loading of large tomogram data
- Applies appropriate scaling factors based on the voxel size metadata
This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.
## Contributing
Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [MIT] license,
"napari-copick" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/kephale/napari-copick/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
## Code of Conduct
This 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).
## Reporting Security Issues
If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
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"description": "# napari-copick\n\n[](https://github.com/kephale/napari-copick/raw/main/LICENSE)\n[](https://pypi.org/project/napari-copick)\n[](https://python.org)\n[](https://github.com/kephale/napari-copick/actions)\n[](https://codecov.io/gh/kephale/napari-copick)\n[](https://napari-hub.org/plugins/napari-copick)\n\nA plugin for collaborative annotation in cryoET using copick\n\n\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",
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