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| { | ||
| "info": { | ||
| "author": "Rafael Tubelleza", | ||
| "author_email": "[email protected]", | ||
| "bugtrack_url": null, | ||
| "classifiers": [ | ||
| "Development Status :: 2 - Pre-Alpha", | ||
| "Framework :: napari", | ||
| "Intended Audience :: Science/Research", | ||
| "License :: OSI Approved :: MIT License", | ||
| "Operating System :: OS Independent", | ||
| "Programming Language :: Python", | ||
| "Programming Language :: Python :: 3", | ||
| "Programming Language :: Python :: 3.10", | ||
| "Topic :: Scientific/Engineering :: Image Processing" | ||
| ], | ||
| "description": "# PRISM: A **P**ython package for the inte**R**active and **I**ntegrated analy**S**is of **M**ultiplexed tissue microarrays\n\n<!--\n#FUTURE: package logo\n-->\n\n[](https://github.com/clinicalomx/napari-prism/raw/main/LICENSE)\n[](https://pypi.org/project/napari-prism)\n[](https://python.org)\n[](https://github.com/clinicalomx/napari-prism/actions)\n[](https://codecov.io/gh/clinicalomx/napari-prism)\n[](https://napari-hub.org/plugins/napari-prism)\n\n**NOTE: PRISM is still in heavy development.**\nPRISM or napari-prism is a package and [napari] plugin designed for interactive processing, analysing and visualising multiplxed tissue microarrays.\n\nCurrently, end-to-end capabilities (i.e. starting from importing the raw image file, to basic spatial analysis of annotated cells) are available for images generated from the\nAkoya Phenocycler\u2122-Fusion platform. However, the modular structure of the\npackage allows for usage at any stage of processing and/or analysis, given a pre-built SpatialData object using readers from either\n[spatialdata-io] or [sopa].\n\nPRISM uses [spatialdata] as the core data framework, allowing for:\n\n1. The rich integration of tools from the ([scverse]) Python bioinformatics ecosystem with highly interactive graphical user interfaces from [napari] and [napari-spatialdata].\n2. The storage of images, shapes, annotations and their linked `AnnData` objects in a standardized, FAIR-compliant data structure, addressing the non-standard and fragmented organization of files before, during, and after a multiplexed image analysis pipeline.\n\nThe package was designed to be used completely within the [napari] application and therefore require little to no knowledge of Python programming. Therefore, documentation for usage via the API is currently in progress.\n\n## Installation\n\nInstall this package via [pip]:\n\n```bash\npip install napari-prism\n```\n\nInstall the latest development version:\n\n```bash\npip install git+https://github.com/clinicalomx/napari-prism.git@main\n```\n\n## Getting Started\n\nTo start using `PRISM`, please see the [tutorials](https://napari-prism.readthedocs.io/en/latest/notebooks/getting_started.html#):\n\n- [Getting started](https://napari-prism.readthedocs.io/en/latest/notebooks/getting_started.html)\n- To learn how to interactively analyse raw .qptiff TMAs, see [TMA Image Analysis](https://napari-prism.readthedocs.io/en/latest/notebooks/tma_usage.html)\n- To learn how to interactively analyse AnnData-contained SpatialData objects, see [Anndata Analysis](https://napari-prism.readthedocs.io/en/latest/notebooks/adata_usage.html)\n\n## GPU Acceleration\n\n\\*\\*In-progress/Testing\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-prism\" 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## Citation\n\n\\*\\*tba\n\n[napari]: https://github.com/napari/napari\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[file an issue]: https://github.com/clinicalomx/prism/issues\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[spatialdata]: https://github.com/scverse/spatialdata/tree/main\n[napari-spatialdata]: https://github.com/scverse/napari-spatialdata/tree/main\n[spatialdata-io]: https://github.com/scverse/spatialdata-io\n[sopa]: https://github.com/gustaveroussy/sopa\n[scverse]: https://scverse.org/\n", | ||
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