From 40444f4f53ab76a1266816e299334f241b9b77a1 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 14 Nov 2024 12:01:37 +0000 Subject: [PATCH] [bot] BigQuery update --- public/classifiers.json | 13 +- public/pypi/PartSeg.json | 2 + public/pypi/Partial-Aligner.json | 2 + public/pypi/brainways.json | 857 ++++++++++++++++++ public/pypi/cellpose-napari.json | 2 - public/pypi/elastix-napari.json | 2 - public/pypi/fish-scan.json | 2 + public/pypi/imaxt-multiscale-plugin.json | 2 + public/pypi/in-silico-fate-mapping.json | 2 + public/pypi/midi-app-controller.json | 2 + public/pypi/morphometrics-engine.json | 2 - public/pypi/napari-bil-data-viewer.json | 2 - public/pypi/napari-checkerboard.json | 2 + public/pypi/napari-generic-SIMulator.json | 2 + public/pypi/napari-graph.json | 2 - public/pypi/napari-nd-cropper.json | 2 - public/pypi/napari-prism.json | 186 ++++ public/pypi/napari-tomoslice.json | 2 + public/pypi/napari-vesicles-segmentation.json | 2 + public/pypi/napari-workflow-inspector.json | 2 + public/pypi/napari-wsireg.json | 2 + public/pypi/platelet-unet-watershed.json | 2 + public/pypi/pssr.json | 2 + public/pypi/skan.json | 2 + 24 files changed, 1083 insertions(+), 15 deletions(-) create mode 100644 public/pypi/brainways.json create mode 100644 public/pypi/napari-prism.json diff --git a/public/classifiers.json b/public/classifiers.json index e1e7b8680e..1966724d21 100644 --- a/public/classifiers.json +++ b/public/classifiers.json @@ -192,6 +192,9 @@ "0.0.2", "0.0.1" ], + "brainways": [ + "0.1.15" + ], "btrack": [ "0.6.5", "0.6.4", @@ -1984,9 +1987,6 @@ "0.0.3", "0.0.2" ], - 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Pre-Alpha", + "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 :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: Implementation :: CPython", + "Topic :: Scientific/Engineering :: Image Processing" + ], + "description": "# Brainways\n\n[![DOI](https://img.shields.io/badge/DOI-10.1101/2023.05.25.542252-green.svg)](https://doi.org/10.1101/2023.05.25.542252)\n[![License GNU GPL v3.0](https://img.shields.io/pypi/l/brainways.svg?color=green)](https://github.com/bkntr/brainways/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/brainways.svg?color=green)](https://pypi.org/project/brainways)\n[![Python Version](https://img.shields.io/pypi/pyversions/brainways.svg?color=green)](https://python.org)\n[![tests](https://github.com/bkntr/brainways/workflows/tests/badge.svg)](https://github.com/bkntr/brainways/actions)\n[![codecov](https://codecov.io/gh/bkntr/brainways/branch/main/graph/badge.svg)](https://codecov.io/gh/bkntr/brainways)\n[![Documentation Status](https://readthedocs.org/projects/brainways/badge/?version=latest)](https://brainways.readthedocs.io/en/latest/?badge=latest)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/brainways)](https://napari-hub.org/plugins/brainways)\n\n\n## What Is Brainways?\n\n\nBrainways is an AI-based tool for automated registration, quantification and generation of brain-wide activity networks based on fluorescence in coronal slices.\n\n![Brainways UI](docs/assets/brainways-ui.gif)\n\n\n## Why Brainways?\n\n\nCoronal slice registration, cell quantification and whole-brain contrast analysis between experimental conditions should be made easily accessible from a single software, without requiring programming experience.\nCustomization should be made easy by having a highly flexible pythonic backend.\n\n## Getting Started\n\nTo install and run brainways, run the following in your python environment:\n\n```bash\npip install brainways\nbrainways ui\n```\n\nFollow our [getting started guide](https://brainways.readthedocs.io/en/latest/getting_started/) for more details.\n\n## How it works\n\nBrainways allows users to register, quantify and provide statistical contrast analysis by following several simple steps:\n\n1. Rigid registration of coronal slices to a 3D atlas.\n1. Non-rigid registration of coronal slices to a 3D atlas, to account for individual difference and imperfections in acquisition procedure.\n1. Cell detection (using [StarDist](https://github.com/stardist/stardist)).\n1. Quantification of cell counts per brain region.\n1. Statistical analysis:\n * ANOVA contrast analysis.\n * PLS (Partial Least Square) analysis.\n * Network graph creation.\n\n\n\n## Architecture\n\nBrainways is implemented as three modules. `brainways.ui` contains the GUI implementation as a [napari](https://napari.org/stable/) plugin. `brainways.ui` is using `brainways` as its backend. All of the functionality is implemented in the brainways package. This separation was done to guarantee that brainways is a GUI-agnostic software, and can be fully accessed and manipulated through python code to allow custom complex usage scenarios. The code that was used to train, evaluate and run the automatic registration model resides in `brainways-reg-model`.\n\n## Development Status\n\nBrainways is being actively developed by Ben Kantor of Bartal lab, Tel Aviv University, Israel. Our releases can be found [here](https://github.com/bkntr/brainways/releases).\n\n## Citation\n\nIf you use brainways, please cite [Kantor and Bartal (2023)](https://doi.org/10.1101/2023.05.25.542252):\n\n @article{kantor2023brainways,\n title={Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent Markers on Coronal Brain Slices},\n author={Kantor, Ben and Ben-Ami Bartal, Inbal},\n journal={bioRxiv},\n pages={2023--05},\n year={2023},\n publisher={Cold Spring Harbor Laboratory}\n }\n\n## License\n\nDistributed under the terms of the [GNU GPL v3.0] license,\n\"brainways\" 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[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\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 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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 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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", + "description_content_type": "text/markdown", + "docs_url": null, + "download_url": null, + "downloads": { + "last_day": -1, + "last_month": -1, + "last_week": -1 + }, + "dynamic": null, + "home_page": "https://github.com/clinicalomx/napari-prism", + "keywords": null, + "license": "MIT", + "license_expression": null, + "license_files": null, + "maintainer": null, + "maintainer_email": null, + "name": "napari-prism", + "package_url": "https://pypi.org/project/napari-prism/", + "platform": null, + "project_url": "https://pypi.org/project/napari-prism/", + "project_urls": { + "Bug Tracker": "https://github.com/clinicalomx/napari-prism/issues", + "Documentation": 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