{"name":"napari-stitcher","display_name":"napari-stitcher","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-stitcher.get_reader","title":"Open data with Stitcher","python_name":"napari_stitcher._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.write_multiple","title":"Save multi-layer data with Stitcher","python_name":"napari_stitcher._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.write_single_image","title":"Save image data with Stitcher","python_name":"napari_stitcher._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.make_sample_data","title":"Load sample data from Stitcher","python_name":"napari_stitcher._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.drifting_timelapse_with_stage_shifts_no_overlap_2d","title":"Load sample data from Stitcher","python_name":"napari_stitcher._sample_data:drifting_timelapse_with_stage_shifts_no_overlap_2d","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.timelapse_with_stage_shifts_with_overlap_3d","title":"Load sample data from Stitcher","python_name":"napari_stitcher._sample_data:timelapse_with_stage_shifts_with_overlap_3d","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.make_qwidget","title":"Make Stitcher QWidget","python_name":"napari_stitcher._stitcher_widget:StitcherQWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-stitcher.make_mosaic","title":"Make Stitcher Mosaic","python_name":"napari_stitcher._mosaic_widget:MosaicQWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-stitcher.get_reader","filename_patterns":["*.czi"],"accepts_directories":false}],"writers":[{"command":"napari-stitcher.write_multiple","layer_types":["image+"],"filename_extensions":[".tif"],"display_name":""}],"widgets":[{"command":"napari-stitcher.make_qwidget","display_name":"Stitcher","autogenerate":false},{"command":"napari-stitcher.make_mosaic","display_name":"Mosaic arrangement","autogenerate":false}],"sample_data":[{"command":"napari-stitcher.make_sample_data","key":"unique_id.1","display_name":"Mosaic"},{"command":"napari-stitcher.drifting_timelapse_with_stage_shifts_no_overlap_2d","key":"unique_id.2","display_name":"2D drifting timelapse with stage shifts and no overlap"},{"command":"napari-stitcher.timelapse_with_stage_shifts_with_overlap_3d","key":"unique_id.3","display_name":"3D timelapse with stage shifts and overlap"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-stitcher","version":"0.1.4","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Stitch napari image layers in 2-3D+t","description":"[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-stitcher)](https://napari-hub.org/plugins/napari-stitcher)\n[![License {{cookiecutter.license}}](https://img.shields.io/pypi/l/napari-stitcher.svg?color=green)](https://github.com/multiview-stitcher/napari-stitcher/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-stitcher.svg?color=green)](https://pypi.org/project/napari-stitcher)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-stitcher.svg?color=green)](https://python.org)\n[![tests](https://github.com/multiview-stitcher/napari-stitcher/actions/workflows/test_and_deploy.yml/badge.svg)](https://github.com/multiview-stitcher/napari-stitcher/actions)\n[![codecov](https://codecov.io/gh/multiview-stitcher/napari-stitcher/branch/main/graph/badge.svg)](https://codecov.io/gh/multiview-stitcher/napari-stitcher)\n[![DOI](https://zenodo.org/badge/697999800.svg)](https://zenodo.org/doi/10.5281/zenodo.14176362)\n\n\n# napari-stitcher\n\nA napari plugin for stitching large multi-positioning datasets in 2/3D+t using [`multiview-stitcher`](https://github.com/multiview-stitcher/multiview-stitcher).\n\n![](docs/images/napari-stitcher-loaded-mosaic-annotated.png)\n<small>Image data by Arthur Michaut @ Jérôme Gros Lab @ Institut Pasteur.</small>\n\n#### Quick guide:\n\n1. Directly stitch napari layers: Use napari to load, visualize and [preposition](prearrangement.md) the tiles to be stitched.\n2. When working with multi-channel data, stick to the following [naming convention](naming_convention.md): `{tile} :: {channel}`.\n3. Load either all or just a subset of the layers into the plugin.\n4. Choose registration options: registration channel, binning and more.\n5. Stitching = registration (refining the positions, optional) + fusion (joining the tiles into a single image).\n6. The registration result is shown in the viewer and the fused channels are added as new layers.\n\n## Demo\n\nhttps://github.com/user-attachments/assets/8773e49f-af18-4ff3-ab2f-2a5f1b1cadf2\n\n<small>This demo uses the awesome [`napari-threedee`](https://github.com/napari-threedee/napari-threedee) for prepositioning the tiles. Image data: [BigStitcher](https://imagej.net/plugins/bigstitcher/).</small>\n\n## Documentation\n\nHead over to the [user guide](https://multiview-stitcher.github.io/napari-stitcher/main/) for more details.\n\n## Installation\n\nYou can install `napari-stitcher` via `pip`:\n\n```bash\npip install napari-stitcher\n```\n\nFor more installation options, see the [installation docs](https://multiview-stitcher.github.io/napari-stitcher/main/installation/).\n\n## Contributing\n\nContributions are very welcome. Tests can be run with `tox`.\n\n## License\n\nDistributed under the terms of the [BSD-3] license, \"napari-stitcher\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue](https://github.com/multiview-stitcher/napari-stitcher/issues) along with a detailed description.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Marvin Albert","author_email":"marvin.albert@gmail.com","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":["dask","magicgui","multiscale_spatial_image","multiview-stitcher[czi,itk-elastix]>=0.1.49","napari","numpy>=1.18","qtpy","spatial_image","tifffile>=2022.7.28","tqdm","xarray","tox; extra == \"testing-no-gui\"","multiview-stitcher[czi]>=0.1.47; extra == \"testing-no-gui\"","pytest; extra == \"testing-no-gui\"","pytest-cov; extra == \"testing-no-gui\"","pytest-qt; extra == \"testing-no-gui\"","tox; extra == \"testing\"","multiview-stitcher[czi]>=0.1.47; 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/multiview-stitcher/napari-stitcher/issues","Documentation, https://multiview-stitcher.github.io/napari-stitcher/","Source Code, https://github.com/multiview-stitcher/napari-stitcher","User Support, https://github.com/multiview-stitcher/napari-stitcher/issues"],"provides_extra":["testing-no-gui","testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}