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brainglobe-registration.json
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{
"name": "brainglobe-registration",
"display_name": "BrainGlobe Registration",
"visibility": "public",
"icon": "",
"categories": [],
"schema_version": "0.2.1",
"on_activate": null,
"on_deactivate": null,
"contributions": {
"commands": [
{
"id": "brainglobe-registration.make_registration_widget",
"title": "BrainGlobe Registration",
"python_name": "brainglobe_registration.registration_widget:RegistrationWidget",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
},
{
"id": "brainglobe-registration.load_sample",
"title": "Sample Data",
"python_name": "brainglobe_registration.sample_data:load_sample_data",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
}
],
"readers": null,
"writers": null,
"widgets": [
{
"command": "brainglobe-registration.make_registration_widget",
"display_name": "BrainGlobe Registration",
"autogenerate": false
}
],
"sample_data": [
{
"command": "brainglobe-registration.load_sample",
"key": "example",
"display_name": "2D coronal mouse brain section"
}
],
"themes": null,
"menus": {},
"submenus": null,
"keybindings": null,
"configuration": []
},
"package_metadata": {
"metadata_version": "2.2",
"name": "brainglobe-registration",
"version": "0.0.2",
"dynamic": null,
"platform": null,
"supported_platform": null,
"summary": "A napari plugin for registration to a BrainGlobe atlas.",
"description": "# brainglobe-registration\n\n[](https://github.com/brainglobe/brainglobe-registration/raw/main/LICENSE)\n[](https://pypi.org/project/brainglobe-registration)\n[](https://python.org)\n[](https://github.com/brainglobe/brainglobe-registration/actions)\n[](https://codecov.io/gh/brainglobe/brainglobe-registration)\n[](https://napari-hub.org/plugins/brainglobe-registration)\n\nRegistration to a BrainGlobe atlas using Elastix\n\n----------------------------------\n\n> [!WARNING]\n> This tool is in very early development. The interface may change and some features are not yet available.\n\nA [napari] plugin for registering images to a BrainGlobe atlas.\n\n\n\n## Usage\n\n1. Open `napari`.\n2. [Install the plugin](#Installation).\n3. Open the widget by selecting `Plugins > BrainGlobe Registration` in the napari menu bar near the\ntop left of the window.\n\nThe `BrainGlobe Registration` plugin will appear on the right hand side of the napari window.\n4. Open the image you want to register in napari (a sample 2D image can be found by selecting `File > Open Sample > Sample Brain Slice`).\n5. Select the atlas you want to register to from the dropdown menu.\n\nThe atlas will appear in the napari viewer. Select the approximate `Z` slice of the atlas that you want to register to,\nusing the slider at the bottom of the napari viewer.\n\n6. Adjust the sample image to roughly match the atlas image.\nYou can do this by adjusting X and Y translation as well as rotating around the centre of the image.\nYou can overlay the two images by toggling `Grid` mode in the napari viewer (Ctrl+G).\nYou can then adjust the color map and opacity of the atlas image to make manual alignment easier.\n\nThe sample image can be reset to its original position and orientation by clicking `Reset Image` in the `BrainGlobe Registration` plugin window.\n7. Select the transformations you want to use from the dropdown menu. Set the transformation type to empty to remove a step.\nSelect from one of the three provided default parameter sets (elastix, ARA, or IBL). Customise the parameters further in the\n`Parameters` tab.\n8. Click `Run` to register the image. The registered image will appear in the napari viewer.\n\n\n\n## Installation\n\nWe strongly recommend to use a virtual environment manager (like `conda` or `venv`). The installation instructions below\nwill not specify the Qt backend for napari, and you will therefore need to install that separately. Please see the\n[`napari` installation instructions](https://napari.org/stable/tutorials/fundamentals/installation.html) for further advice on this.\n\nYou can install `brainglobe-registration` via [pip]:\n\n pip install brainglobe-registration\n\nor [via napari](https://napari.org/stable/plugins/start_using_plugins/finding_and_installing_plugins.html).\n\nTo install the latest development version :\n\n pip install git+https://github.com/brainglobe/brainglobe-registration.git\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"brainglobe-registration\" is free and open source software\n\n## Seeking help or contributing\nWe are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).\n\n\n## Acknowledgements\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[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[file an issue]: https://github.com/brainglobe/brainglobe-registration/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",
"description_content_type": "text/markdown",
"keywords": null,
"home_page": null,
"download_url": null,
"author": null,
"author_email": "Brainglobe Developers <hello@brainglobe.info>",
"maintainer": null,
"maintainer_email": null,
"license": "BSD-3-Clause",
"classifier": [
"Development Status :: 2 - Pre-Alpha",
"Framework :: napari",
"Intended Audience :: Science/Research",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Operating System :: OS Independent",
"License :: OSI Approved :: BSD License",
"Topic :: Scientific/Engineering :: Image Processing"
],
"requires_dist": [
"napari>=0.4.18",
"brainglobe-atlasapi",
"brainglobe-utils>=0.4.3",
"dask",
"dask-image",
"itk-elastix",
"lxml_html_clean",
"numpy",
"pandas",
"pytransform3d",
"qtpy",
"pytest; extra == \"dev\"",
"pytest-cov; extra == \"dev\"",
"pytest-mock; extra == \"dev\"",
"pytest-qt; extra == \"dev\"",
"coverage; extra == \"dev\"",
"tox; extra == \"dev\"",
"black; extra == \"dev\"",
"mypy; extra == \"dev\"",
"pre-commit; extra == \"dev\"",
"ruff; extra == \"dev\"",
"setuptools_scm; extra == \"dev\"",
"pyqt5; extra == \"dev\""
],
"requires_python": ">=3.10",
"requires_external": null,
"project_url": [
"Homepage, https://brainglobe.info",
"Bug Tracker, https://github.com/brainglobe/brainglobe-registration/issues",
"Documentation, https://github.com/brainglobe/brainglobe-registration#README.md",
"Source Code, https://github.com/brainglobe/brainglobe-registration",
"User Support, https://forum.image.sc/tag/brainglobe"
],
"provides_extra": [
"dev"
],
"provides_dist": null,
"obsoletes_dist": null
},
"npe1_shim": false
}