{"name":"napari-ome-arrow","display_name":"OME-Arrow","visibility":"public","icon":null,"categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-ome-arrow.get_reader","title":"Open OME-Arrow data","python_name":"napari_ome_arrow._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-ome-arrow.get_reader","filename_patterns":["*.ome-arrow","*.ome.parquet","*.parquet","*.pq","*.ome.vortex","*.vortex","*.ome.tif","*.ome.tiff","*.tif","*.tiff","*.ome.zarr","*.zarr"],"accepts_directories":true}],"writers":null,"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-ome-arrow","version":"0.0.6","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A Napari plugin for OME-Arrow and OME-Parquet bioimage data","description":"# napari-ome-arrow\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-ome-arrow.svg?color=green)](https://github.com/wayscience/napari-ome-arrow/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-ome-arrow.svg?color=green)](https://pypi.org/project/napari-ome-arrow)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-ome-arrow.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ome-arrow)](https://napari-hub.org/plugins/napari-ome-arrow)\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[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17613571.svg)](https://doi.org/10.5281/zenodo.17613571)\n\n`napari-ome-arrow` opens OME image data in [napari] using the [OME-Arrow](https://github.com/wayscience/ome-arrow) library.\n\n## Supported inputs\n\n- Typed OME-Arrow dataset directories (`*.ome-arrow`)\n- Nested OME-Arrow tables in Parquet (`*.ome.parquet`, `*.parquet`, `*.pq`)\n- OME-Vortex files (`*.ome.vortex`, `*.vortex`)\n- OME-TIFF and TIFF files (`*.ome.tif`, `*.ome.tiff`, `*.tif`, `*.tiff`)\n- OME-Zarr stores (`*.ome.zarr`, `*.zarr`)\n- Numbered image stacks and stack patterns containing `<`, `>`, or `*`\n- NumPy arrays (`*.npy`)\n\nMulti-image OME-Arrow datasets and multi-row nested tables are loaded as multiple napari layers.\n\n## Installation\n\nPython 3.11 or newer is required.\n\nInstall the plugin into an existing napari environment:\n\n```bash\npip install napari-ome-arrow\n```\n\nOr install napari with a Qt backend at the same time:\n\n```bash\npip install \"napari-ome-arrow[pyqt6]\"\n```\n\nOME-Vortex support requires one additional extra:\n\n```bash\npip install \"napari-ome-arrow[vortex]\"\n```\n\n## Usage\n\nOpen napari, then drag a supported file or directory into the viewer.\nYou can also start napari with a path:\n\n```bash\nnapari sample.ome.parquet\nnapari images.ome-arrow\n```\n\nThe plugin loads data as either image or labels layers.\nIt chooses the layer type in this order:\n\n1. `NAPARI_OME_ARROW_LAYER_TYPE`, when set to `image` or `labels`.\n1. OME-Arrow `image_type` metadata, when available.\n1. A napari prompt.\n1. `image` when running without a Qt application.\n\nSet the mode explicitly for scripts or repeatable commands:\n\n```bash\nNAPARI_OME_ARROW_LAYER_TYPE=labels napari segmentation.ome.parquet\n```\n\nFor a numbered stack, select the files together or provide a pattern:\n\n```bash\nnapari \"stack/z<000-120>.tif\"\n```\n\n## Configuration\n\n| Environment variable              | Purpose                                      |\n| --------------------------------- | -------------------------------------------- |\n| `NAPARI_OME_ARROW_LAYER_TYPE`     | Load as `image` or `labels`                  |\n| `NAPARI_OME_ARROW_PARQUET_COLUMN` | Select an OME-Arrow struct column in Parquet |\n| `NAPARI_OME_ARROW_VORTEX_COLUMN`  | Select an OME-Arrow struct column in Vortex  |\n| `NAPARI_OME_ARROW_STACK_SCALE`    | Set stack spacing as `Z,Y,X` or `T,C,Z,Y,X`  |\n\nMultiple rows are displayed in napari's grid view.\nImage stacks with a real Z dimension open in 3D.\nIf stack spacing is missing, the plugin can prompt for it when a Qt application is available.\n\n## Development\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for setup and test instructions.\n\n## License\n\nThis project uses the BSD 3-Clause License.\nSee [LICENSE](LICENSE).\n\nReport problems through the [issue tracker].\n\n[issue tracker]: https://github.com/wayscience/napari-ome-arrow/issues\n[napari]: https://napari.org\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":null,"maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Dave Bunten\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Programming Language :: Python :: 3.14","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["magicgui","numpy","ome-arrow>=0.0.10","qtpy>=2.4","scikit-image","napari; extra == \"all\"","qtpy>=2.4; extra == \"all\"","napari[pyqt6]; extra == \"pyqt6\"","pyqt6>=6.6; extra == \"pyqt6\"","qtpy>=2.4; extra == \"pyqt6\"","napari[pyside6]; extra == \"pyside6\"","pyside6>=6.6; extra == \"pyside6\"","qtpy>=2.4; extra == \"pyside6\"","vortex-data; extra == \"vortex\""],"requires_python":">=3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/wayscience/napari-ome-arrow/issues","Source Code, https://github.com/wayscience/napari-ome-arrow","User Support, https://github.com/wayscience/napari-ome-arrow/issues","Documentation, https://github.com/wayscience/napari-ome-arrow#README.md"],"provides_extra":["all","pyqt6","pyside6","vortex"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}