{"name":"napari-bioformats","display_name":"napari-bioformats","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-bioformats.napari_get_reader","title":"napari_get_reader","python_name":"napari_bioformats._core:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-bioformats.napari_get_reader","filename_patterns":["*"],"accepts_directories":true}],"writers":null,"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-bioformats","version":"0.2.1","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"Bioformats for napari, using pims","description":"# napari-bioformats\n\n[![License](https://img.shields.io/pypi/l/napari-bioformats.svg?color=green)](https://github.com/napari/napari-bioformats/raw/master/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-bioformats.svg?color=green)](https://pypi.org/project/napari-bioformats)\n[![Conda](https://img.shields.io/conda/v/conda-forge/napari-bioformats)](https://anaconda.org/conda-forge/napari-bioformats)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-bioformats.svg?color=green)](https://python.org)\n[![tests](https://github.com/tlambert03/napari-bioformats/workflows/tests/badge.svg)](https://github.com/tlambert03/napari-bioformats/actions)\n[![codecov](https://codecov.io/gh/tlambert03/napari-bioformats/branch/master/graph/badge.svg)](https://codecov.io/gh/tlambert03/napari-bioformats)\n\nBioformats plugin for napari using\n[pims-bioformats](http://soft-matter.github.io/pims/v0.5/bioformats.html)\n\n----------------------------------\n\n## Use this plugin as a fallback!\n\nAnyone coming to napari from the Fiji/ImageJ world will likely be aware of the\n_incredible_ [Bio-Formats](https://docs.openmicroscopy.org/bio-formats/6.6.1/index.html)\nlibrary.  A heroic effort, built over years, to read\n[more than a 100 file formats](https://docs.openmicroscopy.org/bio-formats/6.6.1/supported-formats.html).  Naturally, we want some of that goodness for `napari` ... hence this plugin.\n\n**However:** it's important to note that this plugin _still_\nrequires having a java runtime engine installed.  This is easy enough to do\n(the plugin will ask to install it for you if you're in a `conda` environment), but\nit definitely makes for a more complicated environment setup, it's not very\n\"pythonic\", and the performance will likely not feel as snappy as a native \"pure\"\npython module.\n\nSo, before you reflexively install this plugin to fill that bio-formats\nsized hole in your python heart, consider trying some of the other pure-python\nplugins designed to read your format of interest:\n\n- **Zeiss (.czi)**: [napari-aicsimageio](https://github.com/AllenCellModeling/napari-aicsimageio), [napari-czifile2](https://github.com/BodenmillerGroup/napari-czifile2)\n- **Nikon (.nd2)**: [napari-nikon-nd2](https://github.com/cwood1967/napari-nikon-nd2), [nd2-dask](https://github.com/DragaDoncila/nd2-dask)\n- **Leica (.lif)**: [napari-aicsimageio](https://github.com/AllenCellModeling/napari-aicsimageio)\n- **Olympus (.oif)**: no plugin?  (but see [oiffile](https://pypi.org/project/oiffile/) )\n- **DeltaVision (.dv, .mrc)**: [napari-dv](https://github.com/tlambert03/napari-dv)\n\n> *if you have a pure-python reader for a bio-formats-supported file format that\nyou'd like to see added to this list, please open an issue*\n\n## Installation\n\nThe easiest way to install `napari-bioformats` is via [conda], from the\n[conda-forge] channel:\n\n    conda install -c conda-forge napari-bioformats\n\nIt is also possible to install via [pip], but you will need to have a working\nJVM installed, and may need to set the `JAVA_HOME` environment variable\n\n    pip install napari-bioformats\n\n### First Usage\n\nThe first time you attempt to open a file with napari-bioformats, you will\nlikely notice a long delay as pims downloads the `loci_tools.jar` (speed will\ndepend on your internet connection). Subsequent files should open more quickly.\n\n## License\n\nDistributed under the terms of the [GPLv3] license,\n\"napari-bioformats\" 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_This [napari] plugin was generated with [Cookiecutter] using with [@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[GPLv3]: https://opensource.org/licenses/GPL-3.0\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[file an issue]: https://github.com/tlambert03/napari-bioformats/issues\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[conda]: https://docs.conda.io/en/latest/\n[conda-forge]: https://conda-forge.org\n[PyPI]: https://pypi.org/\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/tlambert03/napari-bioformats","download_url":null,"author":"Talley Lambert","author_email":"talley.lambert@gmail.com","maintainer":null,"maintainer_email":null,"license":"GPL-3.0","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: GNU General Public License v3 (GPLv3)","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Topic :: Software Development :: Testing"],"requires_dist":["jpype1","napari-plugin-engine (>=0.1.4)","numpy","ome-types","pims","requests","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'"],"requires_python":">=3.7","requires_external":null,"project_url":["Bug Tracker, https://github.com/tlambert03/napari-bioformats/issues","Documentation, https://github.com/tlambert03/napari-bioformats#README.md","Source Code, https://github.com/tlambert03/napari-bioformats","User Support, https://github.com/tlambert03/napari-bioformats/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}