{"name":"napari-segselect","display_name":"SegSelect","visibility":"public","icon":"","categories":["Annotation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-segselect.read_mrc","title":"Read \".mrc\" files","python_name":"napari_segselect._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-segselect.write_segmentation","title":"Write segmentation to \".mrc\"","python_name":"napari_segselect._writer:write_segmentation","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-segselect.select_label","title":"Select labels","python_name":"napari_segselect._widget:select_label_widget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-segselect.read_mrc","filename_patterns":["*.mrc"],"accepts_directories":false}],"writers":[{"command":"napari-segselect.write_segmentation","layer_types":["labels+"],"filename_extensions":[".mrc"],"display_name":""}],"widgets":[{"command":"napari-segselect.select_label","display_name":"Select Label","autogenerate":true}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.2","name":"napari-segselect","version":"0.1.3","dynamic":null,"platform":null,"supported_platform":null,"summary":"Select a connected component from a membrain-seg segmentation.","description":"# napari-segselect\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-segselect.svg?color=green)](https://github.com/bwmr/napari-segselect/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-segselect.svg?color=green)](https://pypi.org/project/napari-segselect)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-segselect.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-segselect)](https://napari-hub.org/plugins/napari-segselect)\n\nSelect a connected component from a [membrain-seg](https://github.com/teamtomo/membrain-seg) segmentation.\n\n## Usage\n\n1. Run `membrain-seg` with the `--store-connected-components` flag (optional, otherwise connected components will be calculated while opening)\n2. Open the segmentation in Napari, find out which component numbers correspond to your feature.\n    ![Label Layer](images/image2.png)\n3. Enter these numbers and a feature name in the widget, press run. \n    ![Widget](images/image3.png)\n4. Save the resulting layer using naparis built-in dialog. \n5. Now you have a standalone binary segmentation of your feature of interest.\n    ![Output](images/image4.png)\n\n\n## Installation\n\nYou can install `napari-segselect` via [pip]:\n\n    pip install napari-segselect\n   \nOr directly from GitHub:\n\n    pip install git+https://github.com/bwmr/napari-segselect.git\n\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-segselect\" 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\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n\n[napari]: https://github.com/napari/napari\n[copier]: https://copier.readthedocs.io/en/stable/\n[@napari]: https://github.com/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n\n[file an issue]: https://github.com/bwmr/napari-segselect/issues\n\n[napari]: https://github.com/napari/napari\n[pip]: https://pypi.org/project/pip/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Benedikt Wimmer","author_email":"b.wimmer@bioc.uzh.ch","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Benedikt Wimmer\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","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","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","mrcfile","scipy","napari; extra == \"testing\"","ruff; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/bwmr/napari-segselect/issues","Documentation, https://github.com/bwmr/napari-segselect#README.md","Source Code, https://github.com/bwmr/napari-segselect","User Support, https://github.com/bwmr/napari-segselect/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}