{"name":"segment-any-confocal-images","display_name":"Segment Any Confocal Images","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"segment-any-confocal-images.widget","title":"Segment Any Confocal Images","python_name":"segment_any_confocal_images._widget:SegmentConfocalWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"segment-any-confocal-images.write_single","title":"Save layer with metadata","python_name":"segment_any_confocal_images._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":[{"command":"segment-any-confocal-images.write_single","layer_types":["image","labels"],"filename_extensions":[".tif",".tiff",".png",".jpg",".jpeg"],"display_name":"Save layer with metadata"}],"widgets":[{"command":"segment-any-confocal-images.widget","display_name":"Segment Any Confocal Images","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"segment-any-confocal-images","version":"0.0.8","dynamic":null,"platform":null,"supported_platform":null,"summary":"Segment Any Confocal Images is a flexible and high-performance plugin designed for segmentation of confocal microscopy data. It supports both 2D and 3D image stacks, enabling users to identify and extract cellular or subcellular structures with minimal manual effort.","description":"# segment-any-confocal-images\n\n[![License MIT](https://img.shields.io/pypi/l/segment-any-confocal-images.svg?color=green)](https://github.com/fenghuibao/segment-any-confocal-images/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/segment-any-confocal-images.svg?color=green)](https://pypi.org/project/segment-any-confocal-images)\n[![Python Version](https://img.shields.io/pypi/pyversions/segment-any-confocal-images.svg?color=green)](https://python.org)\n[![tests](https://github.com/fenghuibao/segment-any-confocal-images/workflows/tests/badge.svg)](https://github.com/fenghuibao/segment-any-confocal-images/actions)\n[![codecov](https://codecov.io/gh/fenghuibao/segment-any-confocal-images/branch/main/graph/badge.svg)](https://codecov.io/gh/fenghuibao/segment-any-confocal-images)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/segment-any-confocal-images)](https://napari-hub.org/plugins/segment-any-confocal-images)\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[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\nSegment Any Confocal Images is a flexible and high-performance plugin designed for segmentation of confocal microscopy data. It supports both 2D and 3D image stacks, enabling users to identify and extract cellular or subcellular structures with minimal manual effort.\n\n## Supported inputs\n\nThe widget currently supports standard image formats only:\n\n- `*.tif`, `*.tiff`\n- `*.png`\n- `*.jpg`, `*.jpeg`\n\nMicroscope-specific container formats such as `czi`, `nd2`, `lif`, and `lsm` are not loaded by the widget anymore.\n\nLoaded images are normalized into the widget's internal `TCZYX` layout:\n\n- 2D grayscale images become `1 x 1 x 1 x Y x X`\n- grayscale stacks become `1 x 1 x Z x Y x X`\n- RGB/RGBA images become `1 x 3 x 1 x Y x X`\n- RGB/RGBA stacks become `1 x 3 x Z x Y x X`\n\nPhysical pixel size metadata is no longer auto-imported from source files. Standard images default to pixel size `1.0`.\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template] (None).\n\n\n\n## Installation\n\nYou can install `segment-any-confocal-images` via [pip]:\n\n```\npip install segment-any-confocal-images\n```\n\nIf napari is not already installed, you can install `segment-any-confocal-images` with napari and Qt via:\n\n```\npip install \"segment-any-confocal-images[all]\"\n```\n\nCore runtime dependencies include `numpy`, `qtpy`, `magicgui`, `superqt`, and `scikit-image`.\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\"segment-any-confocal-images\" 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[copier]: https://copier.readthedocs.io/en/stable/\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[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n\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","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Huibao Feng","author_email":"fenghuibao@gmail.com","maintainer":null,"maintainer_email":null,"license":"<<<<<<< HEAD\nMIT License\n\nCopyright (c) 2025 fenghuibao\n=======\n\nThe MIT License (MIT)\n\nCopyright (c) 2025 Huibao Feng\n>>>>>>> 8d6afec (initial commit)\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\n<<<<<<< HEAD\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n=======\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n>>>>>>> 8d6afec (initial commit)\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n<<<<<<< HEAD\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n=======\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n>>>>>>> 8d6afec (initial commit)\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","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 :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["matplotlib","numpy","openpyxl","magicgui","qtpy","scikit-image","napari[all] ; extra == 'all'"],"requires_python":">=3.10","requires_external":null,"project_url":null,"provides_extra":["all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}