{"name":"napari-blender","display_name":"Blender Visualization","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-blender.get_reader","title":"Open data with Blender Visualization","python_name":"napari_blender._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.write_multiple","title":"Save multi-layer data with Blender Visualization","python_name":"napari_blender._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.write_single_image","title":"Save image data with Blender Visualization","python_name":"napari_blender._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_sample_data","title":"Load sample data from Blender Visualization","python_name":"napari_blender._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_container_widget","title":"Make threshold Container widget","python_name":"napari_blender:ImageThreshold","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_transparant_widget","title":"Make widget to compare two images","python_name":"napari_blender:transparant_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_microscopy_widget","title":"Make widget to compare two images using microscopy input","python_name":"napari_blender:microscopy_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_gradient_widget","title":"Make widget to compare two images","python_name":"napari_blender:gradient_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_tracked_widget","title":"Make widget to display single image","python_name":"napari_blender:tracked_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_timelapse_widget","title":"Make widget to display single image","python_name":"napari_blender:timelapse_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-blender.make_video_loader_widget","title":"Make widget to display video","python_name":"napari_blender:video_loader_widget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-blender.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-blender.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-blender.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-blender.make_transparant_widget","display_name":"Transparent Overlay","autogenerate":false},{"command":"napari-blender.make_microscopy_widget","display_name":"Microscopy Overlay","autogenerate":false},{"command":"napari-blender.make_gradient_widget","display_name":"Gradient Overlay","autogenerate":false},{"command":"napari-blender.make_tracked_widget","display_name":"Tracked Nuclei","autogenerate":false},{"command":"napari-blender.make_timelapse_widget","display_name":"Timelapse Mode","autogenerate":false},{"command":"napari-blender.make_video_loader_widget","display_name":"Video Loader","autogenerate":false}],"sample_data":[{"command":"napari-blender.make_sample_data","key":"unique_id.1","display_name":"Blender Visualization"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-blender","version":"1.0.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plug-in to help visualize and analyze organoid segmentation using Blender","description":"# napari-blender\n\nnapari-blender is a plugin for napari that allows you to render 3D scenes using Blender.\n\nThis is a system that combines optical validation of model predictions by having different 3D visualizations and quantitative evaluation. Utilizing Blender’s rendering capabilities for deepening the understanding of nuclei segmentation for users with different levels of expertise. Examples are time-lapse animations (aimed to be generated from label data), opaque ground truth visualizations with solid prediction objects to compare prediction quality optically and 3D images where nuclei are coloured according to their prediction quality. To facilitate meaningful quantitative evaluation, different metrics are calculated for these predictions and displayed within the animation, such as the Jaccard index, Intersection over Union and the F1-score. The emphasis in this system is on operating it with limited technical knowledge, allowing for bridging between researchers and developers; but includes metrics that allow for a deeper understanding of performance for expert users.\n\nDocumentation can be found at https://living-technologies.github.io/napari-blender/\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nThe installation of `napari-blender` is made easier by the inclusion of a virtual environment containing specified versions of each library. These versions should be followed, since dependencies could otherwise break the build. \n\nDownload the [environment.yml], and navigate to the directory of the file. Install by:\n\n    conda env create -f environment.yml\n    conda activate napari-blender-env\n\nNow you can install the plug-in using:\n\n    pip install napari-blender\n\nNote:\n\nIn Windows, an error might occur in the installation of the `mathutils` package, stating 'Microsoft Visual C++ 14.0 or greater is required'. A fix can be found on[StackOverflow].\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/Living-Technologies/napari-blender.git\n\n## License\n\nDistributed under the terms of the [Mozilla Public License 2.0] license,\n\"napari-blender\" 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[environment.yml]: https://github.com/Living-Technologies/napari-blender/blob/main/environment.yml\n[StackOverflow]: https://stackoverflow.com/questions/64261546/how-to-solve-error-microsoft-visual-c-14-0-or-greater-is-required-when-inst\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\n[file an issue]: https://github.com/Living-Technologies/napari-blender/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":null,"author_email":"\"Krijn H. van der Steen\" <k.h.vandersteen@gmail.com>","maintainer":null,"maintainer_email":null,"license":"Mozilla Public License Version 2.0","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","napari-video","tifffile","bpy >=4.0.0","trimesh","opencv-python","scipy","pathlib","mathutils","pandas"],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/Living-Technologies/napari-blender/issues","Documentation, https://living-technologies.github.io/napari-blender/index.html","Source Code, https://github.com/Living-Technologies/napari-blender","User Support, https://github.com/Living-Technologies/napari-blender/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}