{"name":"napari-rosettasciio","display_name":"RosettaSciIO Reader/Writer","visibility":"public","icon":"","categories":["IO"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-rosettasciio.get_reader","title":"Open scientific data with RosettaSciIO","python_name":"napari_rosettasciio._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-rosettasciio.write_multiple","title":"Save multi-layer data with RosettaSciIO","python_name":"napari_rosettasciio._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-rosettasciio.write_single_image","title":"Save image data with RosettaSciIO","python_name":"napari_rosettasciio._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-rosettasciio.get_reader","filename_patterns":["*.hspy","*.hdf5","*.h5","*.zspy","*.dm3","*.dm4","*.emd","*.ser","*.emi","*.mrc","*.mrcs","*.st","*.mrcz","*.map","*.rec","*.ali","*.bcf","*.edaxh5","*.spc","*.spd","*.sur","*.pro","*.raw","*.rpl","*.pts","*.tvf","*.tvips","*.nxs","*.nc","*.msa","*.emsa","*.img","*.cpr","*.csv","*.wdf","*.txt"],"accepts_directories":false}],"writers":[{"command":"napari-rosettasciio.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[".hspy",".zspy",".hdf5",".h5"],"display_name":""},{"command":"napari-rosettasciio.write_single_image","layer_types":["image"],"filename_extensions":[".hspy",".zspy",".hdf5",".h5",".rpl",".nxs",".sur",".pro",".prz",".msa",".emsa",".emd",".blo",".tvips",".unf"],"display_name":""},{"command":"napari-rosettasciio.write_single_image","layer_types":["labels"],"filename_extensions":[".hspy",".zspy",".hdf5",".h5",".mrcz",".rpl",".nxs",".sur",".pro",".prz",".msa",".emsa",".emd",".blo",".tvips",".unf"],"display_name":""}],"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-rosettasciio","version":"0.1.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A napari plugin to read and write scientific data formats using RosettaSciIO","description":"# napari-rosettasciio\n\n[![License MIT](https://img.shields.io/pypi/l/napari-rosettasciio.svg?color=green)](https://github.com/jules-vanaret/napari-rosettasciio/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-rosettasciio.svg?color=green)](https://pypi.org/project/napari-rosettasciio)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-rosettasciio.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-rosettasciio)](https://napari-hub.org/plugins/napari-rosettasciio)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n\nA napari plugin to read and write scientific data formats using [RosettaSciIO].\n\n----------------------------------\n\n## Overview\n\nThis plugin integrates [RosettaSciIO] with [napari], enabling napari to read and write a wide range of scientific data formats, particularly those used in electron microscopy and spectroscopy.\n\n**Note:** This plugin focuses on scientific data formats not natively supported by napari. Standard image formats (PNG, JPEG, TIFF, BMP, GIF) and NumPy arrays are handled by napari's built-in readers and are excluded from this plugin to avoid conflicts.\n\n### Supported File Formats\n\nRosettaSciIO supports many scientific data formats including:\n\n- **HDF5-based formats**: HyperSpy (`.hspy`), EMD (`.emd`), NeXus (`.nxs`), USID\n- **Microscopy formats**: Digital Micrograph (`.dm3`, `.dm4`), MRC (`.mrc`), FEI/TIA (`.ser`, `.emi`)\n- **Spectroscopy formats**: EDAX (`.spc`, `.spd`), Bruker (`.bcf`), Renishaw WiRE (`.wdf`)\n- And many more specialized scientific formats...\n\nFor a complete list of supported formats, see the [RosettaSciIO documentation].\n\n## Installation\n\nYou can install `napari-rosettasciio` via [pip]:\n\n```bash\npip install napari-rosettasciio\n```\n\n### Optional Dependencies\n\nTo enable support for specific file formats, you can install with optional dependencies:\n\n```bash\n# For HDF5 formats (HyperSpy, EMD, NeXus, etc.)\npip install \"napari-rosettasciio[hdf5]\"\n\n# For image formats (PNG, JPEG, etc.)\npip install \"napari-rosettasciio[image]\"\n\n# For Zarr-based formats\npip install \"napari-rosettasciio[zspy]\"\n\n# For all formats\npip install \"napari-rosettasciio[all]\"\n```\n\n## Usage\n\nOnce installed, the plugin will automatically register with napari. You can then:\n\n1. **Open files**: Use `File > Open` or drag and drop files into napari\n2. **Save files**: Use `File > Save` and select the desired format\n\nThe plugin will automatically detect and use the appropriate reader/writer based on the file extension.\n\n### Preserving Metadata\n\nThe plugin preserves metadata from the original files, including:\n- Axes scales and units\n- Original metadata structures\n- Custom attributes\n\nThis metadata is stored in the layer metadata and can be preserved when saving to formats that support it (e.g., HDF5, Zarr).\n\n### Format Limitations\n\nSome formats have specific requirements:\n- **MRCZ** (`.mrcz`): Only supports 3D volumetric data. This format is currently excluded from the writer capabilities as it cannot handle 2D images.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-rosettasciio\" 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## Acknowledgements\n\nThis plugin is built on top of [RosettaSciIO], which originated from the [HyperSpy] project. \nWe are grateful to all contributors to these projects.\n\n[napari]: https://github.com/napari/napari\n[RosettaSciIO]: https://github.com/hyperspy/rosettasciio\n[RosettaSciIO documentation]: https://hyperspy.org/rosettasciio/supported_formats/index.html\n[HyperSpy]: https://hyperspy.org\n[MIT]: http://opensource.org/licenses/MIT\n[pip]: https://pypi.org/project/pip/\n[file an issue]: https://github.com/jules-vanaret/napari-rosettasciio/issues\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Jules Vanaret","author_email":"jules.vanaret@epfl.ch","maintainer":null,"maintainer_email":null,"license":"The MIT License (MIT)\n\nCopyright (c) 2026 jules-vanaret\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Developers","Intended Audience :: Science/Research","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy>=1.22","rosettasciio>=0.1","PyQt5","qtpy","rosettasciio[all]; extra == \"all\"","rosettasciio[hdf5]; extra == \"hdf5\"","rosettasciio[image]; extra == \"image\"","rosettasciio[zspy]; extra == \"zspy\"","rosettasciio[mrcz]; extra == \"mrcz\"","rosettasciio[usid]; extra == \"usid\""],"requires_python":">=3.10","requires_external":null,"project_url":null,"provides_extra":["all","hdf5","image","zspy","mrcz","usid"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}