{"name":"napari-imaref","display_name":"Napari ImaRef","visibility":"public","icon":null,"categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.3.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-imaref.get_reader","title":"Open data with Napari Stereotyping","python_name":"napari_imaref._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-imaref.write_multiple","title":"Save multi-layer data with Napari Stereotyping","python_name":"napari_imaref._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-imaref.write_single_image","title":"Save image data with Napari Stereotyping","python_name":"napari_imaref._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-imaref.make_stereotyping_widget","title":"Stereotyping Widget","python_name":"napari_imaref._widget:StereotypingWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-imaref.make_points_transformation_widget","title":"Coordinates Transformation Widget","python_name":"napari_imaref._points_transformation_widget:CoordinateTransformationWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-imaref.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-imaref.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-imaref.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-imaref.make_stereotyping_widget","display_name":"Stereotyping Widget","autogenerate":false,"default_dock_area":"right","tabify":false},{"command":"napari-imaref.make_points_transformation_widget","display_name":"Coordinates Transformation Widget","autogenerate":false,"default_dock_area":"right","tabify":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configurations":{}},"package_metadata":{"metadata_version":"2.4","name":"napari-imaref","version":"1.1.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Stereotyping zebrafish embryos by manually setting a reference frame","description":"# napari-imaref \n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-imaref.svg?color=green)](https://github.com/koopa31/napari-imaref/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-imaref.svg?color=green)](https://pypi.org/project/napari-imaref)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-imaref.svg?color=green)](https://python.org)\n[![tests](https://github.com/koopa31/napari-imaref/workflows/tests/badge.svg)](https://github.com/koopa31/napari-imaref/actions)\n[![codecov](https://codecov.io/gh/koopa31/napari-imaref/branch/main/graph/badge.svg)](https://codecov.io/gh/koopa31/napari-imaref)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-imaref)](https://napari-hub.org/plugins/napari-imaref)\n\nStereotyping 3D images of the zebrafish olfactory system by defining a reproducible reference frame. \nThe method relies on ellipsoid fitting based on manually placed landmark points.\n\n\n![](https://github.com/koopa31/ImaRef_doc/blob/main/docs/images/placer_points.gif?raw=true)\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n## Installation\n\nYou can install `napari-imaref` via [pip] following these steps:\n\n1) First create a Conda environment\n\n conda create -n napari_stereotyping python=3.11\n2) Activate the Conda environment\n \n conda activate napari_stereotyping\n3) Then install Napari (Napari versions after 0.6.6 are not compatible with the plugin.)\n\n pip install \"napari[all]\"==0.6.6\n4) Install the plugin \n \n pip install napari-imaref\n\n\n## Documentation\n\nA [documentation] is available to understand how to effectively learn how to use the plugin. \n\n\n## Contributing\n\nContributions are very welcome. If you manage to apply this method to other sample types, we’d love to hear about it! \nAnd if you’re considering adapting it to different biological systems but feel that a few modifications might be necessary,\ndon’t hesitate to reach out.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-imaref\" 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 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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[documentation]: https://imaref-doc.readthedocs.io/en/latest/\n[file an issue]: https://github.com/koopa31/napari-imaref/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":"Clément Cazorla, Vincent Demont","author_email":"clement.cazorla31@gmail.com","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2024, Clément Cazorla, Vincent Demont\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==2.1.0","magicgui==0.9.1","qtpy==2.4.1","scikit-image==0.23.2","pandas==2.2.2","scipy==1.13.1","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Documentation, https://imaref-doc.readthedocs.io/en/latest/","Bug Tracker, https://github.com/koopa31/napari-imaref/issues","Source Code, https://github.com/koopa31/napari-imaref","User Support, https://forum.image.sc/"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}