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morphometrics.json
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morphometrics.json
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{
"name": "morphometrics",
"display_name": "morphometrics",
"visibility": "public",
"icon": "",
"categories": [],
"schema_version": "0.2.1",
"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<!--\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/plugins/stable/index.html\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 <path/to/downloaded/environment.yml>\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<table border=\"0\">\n<tr><td>\n\n\n<img src=\"https://github.com/kevinyamauchi/morphometrics/raw/main/resources/surface_distance_measurement.gif\"\nwidth=\"300\"/>\n\n</td><td>\n\n[measure the distance between surfaces](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/surface_distance_measurement.ipynb)\n\n</td></tr><tr><td>\n\n<img src=\"https://github.com/kevinyamauchi/morphometrics/raw/main/resources/region_props_plugin.png\"\nwidth=\"300\"/>\n\n</td><td>\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</td></tr><tr><td>\n\n<img src=\"https://github.com/kevinyamauchi/morphometrics/raw/main/resources/object_classification.png\"\nwidth=\"300\"/>\n\n</td><td>\n\n[object classification](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/object_classification.ipynb)\n\n</td></tr><tr><td>\n\n<img src=\"https://github.com/kevinyamauchi/morphometrics/raw/main/resources/mesh_object.png\"\nwidth=\"300\"/>\n\n</td><td>\n\n[mesh binary mask](https://github.com/kevinyamauchi/morphometrics/blob/main/examples/mesh_binary_mask.ipynb)\n\n\n</td></tr></table>\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": "[email protected]",
"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
}