{"name":"allencell-segmenter-ml","display_name":"allencell-segmenter-ml","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"allencell-segmenter-ml.make_qwidget","title":"Allen Cell Segmenter - ML","python_name":"allencell_ml_segmenter.main.main_widget:MainWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"allencell-segmenter-ml.make_qwidget","display_name":"Allen Cell Segmenter - ML","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"allencell-segmenter-ml","version":"1.0.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to leverage ML segmentation in napari","description":"# Allencell-segmenter-ml\n\n[![Test and lint](https://github.com/AllenCell/allencell-segmenter-ml/actions/workflows/test_lint.yaml/badge.svg?branch=main&event=push)](https://github.com/AllenCell/allencell-segmenter-ml/actions/workflows/test_lint_pr.yaml)\n\n\n## What is Allen Cell Segmenter ML\nA napari plugin for deep-learning based segmentation of cellular structures.\n\n![SegmenterML-plugin_fig1_output.png](docs%2Fuser_docs%2Fimages%2FSegmenterML-plugin_fig1_output.png)\n\n- **Available at no cost** — available on PyPI\n- **User-friendly** — leverage napari as a fast 3D viewer with interactive plugin interface\n- **Beginner-friendly** — new to machine learning? This plugin simplifies the application of machine learning in the segmentation process through the 3 main modules:\n  - **Curation**: curate training datasets\n  - **Training**: iteratively train custom segmentation model(s) (UNET) to target cellular structure with wide morphological variability\n  - **Prediction & Thresholding**: generate segmentation prediction on 2D and 3D cell image data\n\n\n##  📰 News\n\n - **[2024.09.24]** :tada: Initial release of the plugin and Megaseg models!\n - **[2024.05.29]** :tada: v1.0.0 Released on PyPi\n\n\n## User Documentation\n[See our full user documentation on our github pages site.](https://allencell.github.io/allencell-segmenter-ml/index.html)\n\n\n## 🛠️ Installation\n\n### System and Data Requirements\n\n[Please click here to check out our latest System and Data requirements.](https://allencell.github.io/allencell-segmenter-ml/1_Get-started/1_prerequisites.html)\n\n\n### Installation Steps\n[Please click here for our latest installation steps.](https://allencell.github.io/allencell-segmenter-ml/1_Get-started/2_installation.html)\n\n\n## Models\n[More information about the pre-trained models we provide with our plugin, and citation information, can be found here.](https://allencell.github.io/allencell-segmenter-ml/1_Get-started/4_pretrained-models.html)\n\n## License\n\nDistributed under the terms of the [Allen Institute Software License].\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[@napari]: https://github.com/napari\n[Allen Institute Software License]: https://github.com/AllenCell/allencell-segmenter-ml/blob/main/LICENSE\n[file an issue]: https://github.com/AllenCell/allencell-ml-segmenter/issues\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[PyTorch]: https://pytorch.org/get-started/locally/\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":"Allen Institute Software License – This software license is the 2-clause BSD license plus clause a third clause that\nprohibits redistribution for commercial purposes without further permission.\n\nCopyright © 2024. Allen Institute.  All rights reserved.\n\n\n\nRedistribution and use in source and binary forms, with or without modification, are permitted provided that the\nfollowing conditions are met:\n\n1. Redistributions of source code must retain the above copyright notice, this list of conditions\nand the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions\nand the following disclaimer in the documentation and/or other materials provided with the distribution.\n\n3. Redistributions for commercial purposes are not permitted without the Allen Institute’s written permission.\nFor purposes of this license, commercial purposes is the incorporation of the Allen Institute's software into\nanything for which you will charge fees or other compensation.\nContact terms@alleninstitute.org for commercial licensing opportunities.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES,\nINCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\nARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,\nINCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE\nGOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY\nOF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY\nOUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Science/Research","License :: Other/Proprietary License","License :: Free for non-commercial use","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["npe2>=0.6.2","numpy","hydra-core==1.3.2","bioio==1.1.0","bioio-base==1.0.4","tifffile<2025.2.18,>=2023.4.12","watchdog","cyto-dl>=0.4.5","scikit-image!=0.23.0","napari>=0.4.18; extra == \"napari\"","pyqt5; extra == \"napari\"","pytest<8.0.0; extra == \"test-lint\"","pytest-cov; extra == \"test-lint\"","pytest-qt; extra == \"test-lint\"","qtpy; extra == \"test-lint\"","pyqt5; extra == \"test-lint\"","black>=24.2.0; extra == \"test-lint\"","pytest-xvfb; sys_platform == \"linux\" and extra == \"test-lint\"","responses; extra == \"test-lint\"","mypy; extra == \"test-lint\"","toml; extra == \"test-lint\"","bumpver; extra == \"test-lint\"","napari>=0.4.18; extra == \"test-lint\"","magicgui; extra == \"test-lint\"","black>=24.2.0; extra == \"dev\"","coverage>=7.2.2; extra == \"dev\"","flake8>=6.0.0; extra == \"dev\"","pytest<8.0.0,>=7.2.2; extra == \"dev\"","pytest-qt>=3.3.0; extra == \"dev\"","pytest-cov>=2.6.1; extra == \"dev\"","pyqt5>=5.15.9; extra == \"dev\"","bumpver>=2023.1129; extra == \"dev\"","build>=1.0.3; extra == \"dev\"","twine>=5.0.0; extra == \"dev\"","responses; extra == \"dev\"","mypy; extra == \"dev\"","linkify-it-py; extra == \"sphinx-docs\"","sphinx; extra == \"sphinx-docs\"","furo; extra == \"sphinx-docs\"","sphinxext-opengraph; extra == \"sphinx-docs\"","sphinx_inline_tabs; extra == \"sphinx-docs\"","sphinx_copybutton; extra == \"sphinx-docs\"","myst_parser; extra == \"sphinx-docs\"","sphinx_togglebutton; extra == \"sphinx-docs\"","sphinx_design; extra == \"sphinx-docs\""],"requires_python":"<3.11,>=3.9","requires_external":null,"project_url":["Homepage, https://github.com/AllenCell/allencell-ml-segmenter","Bug Tracker, https://github.com/AllenCell/allencell-ml-segmenter/issues","Documentation, https://github.com/AllenCell/allencell-ml-segmenter#README.md","User Support, https://github.com/AllenCell/allencell-ml-segmenter/issues"],"provides_extra":["napari","test-lint","dev","sphinx-docs"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}