{"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_plate_browser","title":"Plate Browser","python_name":"napari_ome_zarr_navigator:PlateBrowser","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_plate_browser","display_name":"Plate 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":"0.3.0","dynamic":null,"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\n### Plate Browser\n\nThe Plate Browser loads an OME-Zarr plate from the local filesystem or via authenticated HTTPS (e.g. a [Fractal Server](https://fractal-analytics-platform.github.io/) instance). It also auto-detects plates opened via [napari-ome-zarr](https://github.com/ome/napari-ome-zarr).\n\n![\"navigator_plate_browser\"](\"https://github.com/user-attachments/assets/ed1f1c13-1055-4b21-a3e6-100279f64f5b\")
\n\nThe Plate Browser lets you zoom to a selected well (\"Go to well\"), which draws a bounding box and centers the camera on that well.\n\n![\"plate_browser_go_to_well\"](\"https://github.com/user-attachments/assets/c83c1daf-a5d2-41b7-8685-564f80eb0122\")
\n\nUsing [ngio condition tables](https://biovisioncenter.github.io/ngio/stable/table_specs/table_types/condition_table/), the Plate Browser can filter the well list to any subset defined by one or more conditions. Plate-level condition tables (fast) and image-level condition tables (slower, aggregated on the fly) are both supported.\n\n![\"plate_browser_filtering\"](\"https://github.com/user-attachments/assets/7938ed80-31ee-4e58-b896-20ed92ea6508\")
\n\n### ROI Loader\n\nThe ROI Loader can be launched directly from napari's *Plugins* menu (standalone) or by selecting a well in the Plate Browser (\"Select ROI to load\"). It supports:\n\n- Loading images from different multiplexing cycles / acquisitions\n- Loading any ROI from [ROI tables](https://biovisioncenter.github.io/ngio/stable/table_specs/table_types/roi_table/), or the whole image when no ROI table is selected\n- Loading label images\n- Loading feature measurements from [feature tables](https://biovisioncenter.github.io/ngio/stable/table_specs/table_types/feature_table/)\n- **Multi-resolution (lazy)** mode — streams a full dask pyramid, optimal for large images and remote data\n- **Fixed resolution** mode — loads a single numpy array, optimal for 3D images and downstream tools in napari that don't handle multi-resolution layers (e.g. the label layer needs to be loaded as fixed resolution for using it in the classifier)\n\nOnce a ROI has been loaded for one well, \"Load selected ROI for additional well(s)\" reuses the same settings for any further wells selected in the Plate Browser.\n\n![\"roi_loader\"](\"https://github.com/user-attachments/assets/ddd8268f-52ae-4a43-9c00-f52df4422ba3\")
\n\nThis plugin is tested with OME-Zarr files generated by [Fractal](https://fractal-analytics-platform.github.io/) and is designed to work with any OME-Zarr ≥ v0.4. The feature loading workflow is optimised for use with the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier).\n\n----------------------------------\n\n\n## Test data\n\nTest & sample data is available at https://zenodo.org/records/20429951\n\n\n## Installation\n\n### Via pixi (recommended)\n\n[pixi](https://pixi.sh) manages all Python and system dependencies in a single step:\n\n```bash\ngit clone https://github.com/fractal-napari-plugins-collection/napari-ome-zarr-navigator\ncd napari-ome-zarr-navigator\npixi run napari\n```\n\nTo launch with the full feature-analysis environment (adds [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier) and [napari-feature-visualization](https://github.com/fractal-napari-plugins-collection/napari-feature-visualization)):\n\n```bash\npixi run napari-fractal\n```\n\n### Via pip\n\nInstall into an existing Python ≥ 3.11 environment with [napari] already present:\n\n```bash\npip install napari-ome-zarr-navigator\n```\n\nFor a fresh environment we recommend [miniforge](https://github.com/conda-forge/miniforge):\n\n```bash\nconda create -n napari-ome-zarr python=3.12 napari pyqt -c conda-forge\nconda activate napari-ome-zarr\npip install napari-ome-zarr-navigator\nnapari\n```\n\nOptionally also install additional plugins like `napari-feature-classifier` and `napari-feature-visualization`, as in:\n```bash\npip install napari-feature-classifier napari-feature-visualization\n```\n\n## Contributing\n\nContributions are very welcome. Tests can be run with `pixi run test`; please ensure coverage stays the same before submitting 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\n[napari]: https://github.com/napari/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[file an issue]: https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator/issues\n[pip]: https://pypi.org/project/pip/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Fabio Steffen , Joel Luethi ","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 :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["magicgui","napari-ome-zarr<0.8","ngio<0.6,>=0.5","numcodecs!=0.14.0,!=0.14.1,!=0.16","numpy","ome-zarr","qtpy","scikit-image","wget","napari; extra == 'testing'","pytest; extra == 'testing'","pytest-cov; extra == 'testing'","pytest-qt; extra == 'testing'","qtpy; extra == 'testing'"],"requires_python":"<3.13,>=3.11","requires_external":null,"project_url":["Homepage, https://github.com/fractal-analytics-platform/napari-ome-zarr-navigator","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}