{"name":"napari-ome-zarr-navigator","display_name":"napari OME-Zarr Navigator","visibility":"public","icon":"","categories":["Dataset","Visualization"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-ome-zarr-navigator.make_img_browser","title":"Image Browser","python_name":"napari_ome_zarr_navigator:ImgBrowser","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ome-zarr-navigator.make_roi_loader","title":"ROI Loader","python_name":"napari_ome_zarr_navigator.roi_loader:ROILoaderImage","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ome-zarr-navigator.hiPSC_zarr","title":"Load hiPSC sample data from Zenodo","python_name":"napari_ome_zarr_navigator._sample_data:hiPSC_zarr","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ome-zarr-navigator.leukemia_zarr","title":"Load leukemia PDX sample data from Zenodo","python_name":"napari_ome_zarr_navigator._sample_data:leukemia_zarr","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-ome-zarr-navigator.make_img_browser","display_name":"Image Browser","autogenerate":false},{"command":"napari-ome-zarr-navigator.make_roi_loader","display_name":"ROI Loader","autogenerate":false}],"sample_data":[{"command":"napari-ome-zarr-navigator.hiPSC_zarr","key":"unique_id.1","display_name":"hiPSC"},{"command":"napari-ome-zarr-navigator.leukemia_zarr","key":"unique_id.2","display_name":"leukemia"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-ome-zarr-navigator","version":"0.2.6","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to browse OME-Zarr plates by conditions and load images, labels and features from ROIs","description":"# napari-ome-zarr-navigator ![](\"https://raw.githubusercontent.com/fractal-napari-plugins-collection/napari-ome-zarr-navigator/master/docs/images/navigator_logo.png\")
\n\n[](https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator/raw/main/LICENSE)\n[](https://pypi.org/project/napari-ome-zarr-navigator)\n[](https://python.org)\n[](https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator/actions)\n[](https://codecov.io/gh/fractal-analytics-platform/napari-ome-zarr-navigator)\n\nA plugin to browse OME-Zarr plates by conditions and load images, labels and features from ROIs\n\n\n## Usage\n\nThe ImageBrowser recognizes OME-Zarr plates that were loaded via [napari-ome-zarr](https://github.com/ome/napari-ome-zarr) and allows the selection of wells in the multiwell plate.\n\n![\"navigator_1\"](\"https://github.com/user-attachments/assets/86c0c0d5-df4c-4579-8719-c36efe67485c\")
\n\nThe ImageBrowser allows to zoom to a given well (\"Go to well\") & puts a white bounding box around the selected well.\n\n![\"navigator_2\"](\"https://github.com/user-attachments/assets/13ead72a-de0e-4b03-8051-b9759af4a131\")
\n\nUsing prototype `condition tables` (to be defined better, see sample data provided by the plugin orthe example in the test data below), the ImageBrowser allows for selecting subsets of the well list based on conditions defined in the `condition table`. The [operetta-compose Fractal task package](https://github.com/leukemia-kispi/operetta-compose) provides a task to create such condition tables.\n\n\n![\"navigator_3\"](\"https://github.com/user-attachments/assets/f8cb9311-49ef-43fd-9358-4193ffb58877\")
\n\nThe ROI loader (formerly [available separately as a napari plugin](https://github.com/jluethi/napari-ome-zarr-roi-loader)) can be used standalone or integrated with the ImageBrowser. If a well is selected from the ImageBrowser, all the images in that well can be loaded via the ROI loader.\nThis supports:\n- Loading images from different multiplexing acquisitions\n- Loading any ROI based on [Fractal ROI tables](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/#roi-tables)\n- Loading label images\n- Loading feature measurements (based on [Fractal feature tables](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/#feature-tables) in the AnnData format)\n\nThis approach of loading label images and feature data has been optimized for and tested with the [napari feature classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier).\n\n![\"navigator_4\"](\"https://github.com/user-attachments/assets/0548c8f1-23c3-4c55-9388-c818bb94bbc3\")
\n\nThis plugin is meant to work well for OME-Zarr files generated by [Fractal](https://fractal-analytics-platform.github.io/).\n\n----------------------------------\n\n\n## Test data\n\nTest data is available at https://zenodo.org/records/11262587\n\n\n## Installation\n\nYou can install `napari-ome-zarr-navigator` via [pip]:\n\n pip install napari-ome-zarr-navigator\n\n\n\nTo install latest development version :\n\n pip install git+https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator.git\n\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 [BSD-3] license,\n\"napari-ome-zarr-navigator\" 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\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\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/fractal-analytics-platform/napari-ome-zarr-navigator/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":"https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator","download_url":null,"author":"Fabio Steffen and Joel Luethi","author_email":"fabio.steffen@uzh.ch","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","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","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","napari-ome-zarr","ome-zarr","wget","ngio<0.5,>=0.4.0","numcodecs!=0.14.0,!=0.14.1,!=0.16","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator/issues","Documentation, https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator#README.md","Source Code, https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator","User Support, https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}