{"name":"morphometrics","display_name":"morphometrics","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"morphometrics.make_simple_labeled_cube","title":"Load sample labeled cube from morphometrics","python_name":"morphometrics._sample_data:make_simple_labeled_cube","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"morphometrics.make_random_3d_image","title":"Load sample 3D intensity image from morphometrics","python_name":"morphometrics._sample_data:make_random_3d_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"morphometrics.make_cylinders_and_spheres","title":"Load sample 3D label image with cylinders and spheres","python_name":"morphometrics._sample_data:make_cylinders_and_spheres","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"morphometrics.QtMeasurementWidget","title":"Make region properties measurement widget","python_name":"morphometrics._gui._qt.measurement_widgets:QtMeasurementWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"morphometrics.QtClusterAnnotatorWidget","title":"Make cluster annotation widget","python_name":"morphometrics._gui._qt.annotation_widgets:QtClusterAnnotatorWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"morphometrics.QtLabelingWidget","title":"Make label curation widget","python_name":"morphometrics._gui._qt.labeling_widgets:QtLabelingWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"morphometrics.QtMeasurementWidget","display_name":"Measure region properties","autogenerate":false},{"command":"morphometrics.QtClusterAnnotatorWidget","display_name":"Annotate clustered features","autogenerate":false},{"command":"morphometrics.QtLabelingWidget","display_name":"Curate labels","autogenerate":false}],"sample_data":[{"command":"morphometrics.make_simple_labeled_cube","key":"morphometrics_labeled_cube","display_name":"simple labeled cube"},{"command":"morphometrics.make_random_3d_image","key":"morphometrics_3d_intensity_image","display_name":"random 3D intensity image"},{"command":"morphometrics.make_cylinders_and_spheres","key":"morphometrics_cylinders_and_spheres","display_name":"3D cylinders and spheres"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"morphometrics","version":"0.0.8","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plugin for quantifying shape and neighborhoods from images.","description":"# morphometrics\n\n[![License](https://img.shields.io/pypi/l/morphometrics.svg?color=green)](https://github.com/morphometrics/morphometrics/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/morphometrics.svg?color=green)](https://pypi.org/project/morphometrics)\n[![Python Version](https://img.shields.io/pypi/pyversions/morphometrics.svg?color=green)](https://python.org)\n[![tests](https://github.com/morphometrics/morphometrics/workflows/tests/badge.svg)](https://github.com/morphometrics/morphometrics/actions)\n[![codecov](https://codecov.io/gh/morphometrics/morphometrics/branch/main/graph/badge.svg)](https://codecov.io/gh/morphometrics/morphometrics)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/morphometrics)](https://napari-hub.org/plugins/morphometrics)\n\nA plugin for quantifying shape and neighborhoods from images.\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n## Installation\n\n### conda environment file\nYou can install `morphometrics` via our conda environment file. To do so, first install anaconda or miniconda on\nyour computer. Then, download the [`environment.yml file`](https://raw.githubusercontent.com/kevinyamauchi/morphometrics/master/environment.yml) (right click the link and \"Save as...\"). In your terminal,\nnavigate to the directory you downloaded the `environment.yml` file to:\n\n```bash\ncd \n```\n\nThen create the `morphometrics` environment using\n\n```bash\nconda env create -f environment.yml\n```\n\nOnce the environment has been created, you can activate it and use `morphometrics` as described below.\n\n```bash\nconda activate morphometrics\n```\n\nIf you are on Mac OS or Linux install the following:\n\nMac:\n\n```bash\nconda install -c conda-forge ocl_icd_wrapper_apple\n```\n\nLinux:\n\n```bash\nconda install -c conda-forge ocl-icd-system\n```\n\n\n### Development installation\n\nTo install latest development version :\n\n pip install git+https://github.com/kevinyamauchi/morphometrics.git\n\n## Example applications\n\n
\n\n\n\n\n\n\n[measure the distance between surfaces](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/surface_distance_measurement.ipynb)\n\n
\n\n\n\n\n\n[napari plugin for measuring properties of segmented objects (regionprops)](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/measure_with_widget.py)\n\n
\n\n\n\n\n\n[object classification](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/object_classification.ipynb)\n\n
\n\n\n\n\n\n[mesh binary mask](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/mesh_binary_mask.ipynb)\n\n\n
\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\"morphometrics\" 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\n[file an issue]: https://github.com/kevinyamauchi/morphometrics/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":"https://github.com/kevinyamauchi/morphometrics","download_url":null,"author":"Kevin Yamauchi","author_email":"kevin.yamauchi@gmail.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","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","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["glasbey","imageio (!=2.11.0,!=2.22.1,>=2.5.0)","leidenalg","napari-skimage-regionprops","napari","numba","numpy","qtpy","pandas","pooch","pyclesperanto-prototype (>=0.8.0)","pymeshfix","pyqtgraph","scanpy","scikit-image (>0.19.0)","scikit-learn (>=0.24.2)","tqdm","trimesh[easy]","pre-commit ; extra == 'dev'","pytest ; extra == 'dev'","pytest-qt ; extra == 'dev'"],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/kevinyamauchi/morphometrics/issues","Documentation, https://github.com/kevinyamauchi/morphometrics#README.md","Source Code, https://github.com/kevinyamauchi/morphometrics","User Support, https://github.com/kevinyamauchi/morphometrics/issues"],"provides_extra":["dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}