{"name":"napari-himena","display_name":"Himena","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-himena.make_qwidget","title":"Make example QWidget","python_name":"napari_himena:QNapariHimenaPipeline","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-himena.make_qwidget","display_name":"Napari-Himena Pipeline","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-himena","version":"0.0.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Pipeline between napari and himena","description":"# napari-himena\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-himena.svg?color=green)](https://github.com/hanjinliu/napari-himena/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-himena.svg?color=green)](https://pypi.org/project/napari-himena)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-himena.svg?color=green)](https://python.org)\n[![tests](https://github.com/hanjinliu/napari-himena/workflows/tests/badge.svg)](https://github.com/hanjinliu/napari-himena/actions)\n[![codecov](https://codecov.io/gh/hanjinliu/napari-himena/branch/main/graph/badge.svg)](https://codecov.io/gh/hanjinliu/napari-himena)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-himena)](https://napari-hub.org/plugins/napari-himena)\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\nPipeline between [`napari`](https://github.com/napari/napari) and [`himena`](https://github.com/hanjinliu/himena).\n\n`napari` is a great tool for visualization, annotation and analysis of multi-dimensional\nimages. On the other hand, `himena` has a powerful plugin system that allows users to\ntechnically do anything, such as editing table and plotting.\n\n`napari-himena` connects these two ecosystems together, enabling users to send data\nback and forth, extending the functionality of the both packages.\n\n## Examples\n\n#### 1. Sending image layers to `himena` for ImageJ-like multi-measurement and Excel-like plotting.\n\nMeasuring time-course change in the image intensity with [`himena-image`](https://github.com/hanjinliu/himena-image) plugin, and plot the result using the built-in plot functions using `matplotlib`.\n\n![](https://github.com/hanjinliu/napari-himena/blob/main/assets/image-plot.gif)\n\n#### 2. Sending points and their features to `himena` for seaborn plotting.\n\nFeature dataframe can be directly sent to `himena` for `seaborn` plotting using [`himena-seaborn`](https://github.com/hanjinliu/himena-seaborn) plugin.\n\n![](https://github.com/hanjinliu/napari-himena/blob/main/assets/feature-sns.gif)\n\n## Usage\n\n#### Starting from `napari`\n\nOpen the `napari-himena` dock widget from the \"Plugin\" menu, connect to one of the\n`himena` profile (only \"default\" is available by default), and that's it!\n\n![](https://github.com/hanjinliu/napari-himena/blob/main/assets/from-napari.png)\n\n#### Starting from `himena`\n\nTo use this plugin from `himena`, you need to first register this plugin to the `himena`\nprofile\n\n```shell\n# install to the default profile\nhimena --install napari-himena\n\n# or install to a specific profile\nhimena <my-profile> --install napari-himena\n```\n\nThen all the commands will be available in `himena` and a napari viewer will be launched\nwhen it is needed. You don't need to do this if you always launch `himena` from `napari`\nplugin; it automatically register this package in the beginning.\n\n![](https://github.com/hanjinliu/napari-himena/blob/main/assets/from-himena.png)\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n## Installation\n\nYou can install `napari-himena` via [pip]:\n\n    pip install napari-himena\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/hanjinliu/napari-himena.git\n\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 [BSD-3] license,\n\"napari-himena\" 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[file an issue]: https://github.com/hanjinliu/napari-himena/issues\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":"Hanjin Liu","author_email":"liuhanjin.sc@gmail.com","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Hanjin Liu\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 :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["himena","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt6; extra == \"testing\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/hanjinliu/napari-himena/issues","Documentation, https://github.com/hanjinliu/napari-himena#README.md","Source Code, https://github.com/hanjinliu/napari-himena","User Support, https://github.com/hanjinliu/napari-himena/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}