{"name":"napari-pram","display_name":"napari PRAM","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-pram.get_img_reader","title":"Open PRAM image with napari PRAM","python_name":"napari_pram._reader:reader_pram_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.get_vgg_annot_reader","title":"Open VGG annotation with napari PRAM","python_name":"napari_pram._reader:reader_vgg_annot","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.write_multiple","title":"Save multi-layer data with napari PRAM","python_name":"napari_pram._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.write_single_image","title":"Save image data with napari PRAM","python_name":"napari_pram._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.make_sample_data","title":"Load sample data from napari PRAM","python_name":"napari_pram._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.make_qwidget","title":"Make example QWidget","python_name":"napari_pram._widget:ExampleQWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-pram.open_panel","title":"Show PRAM toolbox","python_name":"napari_pram.main_napari:PramQWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-pram.get_img_reader","filename_patterns":["*.png"],"accepts_directories":false},{"command":"napari-pram.get_vgg_annot_reader","filename_patterns":["*.json"],"accepts_directories":false}],"writers":[{"command":"napari-pram.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-pram.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-pram.open_panel","display_name":"Open PRAM's toolbox","autogenerate":false}],"sample_data":[{"command":"napari-pram.make_sample_data","key":"unique_id.1","display_name":"napari PRAM"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-pram","version":"0.1.3","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"plugin for PRAM data annotation and processing","description":"# napari-pram\n\n[![License](https://img.shields.io/pypi/l/napari-pram.svg?color=green)](https://github.com/hthieu166/napari-pram/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-pram.svg?color=green)](https://pypi.org/project/napari-pram)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-pram.svg?color=green)](https://python.org)\n[![tests](https://github.com/hthieu166/napari-pram/workflows/tests/badge.svg)](https://github.com/hthieu166/napari-pram/actions)\n[![codecov](https://codecov.io/gh/hthieu166/napari-pram/branch/main/graph/badge.svg)](https://codecov.io/gh/hthieu166/napari-pram)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-pram)](https://napari-hub.org/plugins/napari-pram)\n\nPlugin for PRAM data annotation and processing.\n\n![PRAM Demo](https://raw.githubusercontent.com/hthieu166/napari-pram/main/docs/figs/demo.jpg)\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## Usage\n\n### Open `napari-pram` toolbox:\n\nOn the toolbar, select ``[Plugins] > napari-pram: Open PRAM's toolbox``\n\n### Load PRAM image and annotations:\n\nPress <kbd>Command/Control</kbd> + <kbd>O</kbd>: \n- Select `*.json` files for annotations (from either [VGG Annotator](https://www.robots.ox.ac.uk/~vgg/software/via/) or `napari-pram`)\n- Select `*.png` files for PRAM image\n\n### Annotate\n- Press <kbd>Annotate</kbd>\n- Click the plus-in-circle icon on the top-left panel and start editing\n\n### Run PRAM particles detector\n- Select a proper threshold between 1 (ultra sensitive) - 10 (less sensitive)\n- Press <kbd>Run Detector</kbd>\n\n### Evaluate\n- Press <kbd>Evaluate</kbd>\n- Hide/Unhide true positive/ false postive/false negative layers\n\n### Load new image\n- Press <kbd>Clear All</kbd> to remove all layers\n\n### Export to JSON\n- Press <kbd>Save to File</kbd> to export all annotations, predictions from the algorithm to a JSON file\n## Installation\nFollowing this [tutorial](https://napari.org/tutorials/fundamentals/quick_start.html) to install `napari`. \n\nAlternatively, you can follow my instructions as follows:\n\nYou will need a python environment. I recommend [Conda](https://docs.conda.io/en/latest/miniconda.html). Create a new environment, for example:\n    \n    conda create --name napari-env python=3.7 pip \n\nActivate the new environment:\n\n    conda activate napari-env \n\nInstall [napari](https://napari.org/tutorials/fundamentals/installation) via [pip]:\n\n    pip install napari[all]\n\nThen you can finally install our plugin `napari-pram` via [pip]:\n\n    pip install napari-pram\n\nAlternatively, the plugin can be installed using napari-GUI\n\n``[Plugins] > Install/Uninstall Plugins`` and search for `napari-pram`\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 [MIT] license,\n\"napari-pram\" 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[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\n\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Hieu Hoang","author_email":"hthieu@illinois.edu","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Development Status :: 2 - Pre-Alpha","Intended Audience :: Developers","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: MIT License"],"requires_dist":["numpy","magicgui","qtpy","opencv-python","scipy","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.7","requires_external":null,"project_url":null,"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}