{"name":"napari-align-annotator","display_name":"ALIGN Annotator","visibility":"public","icon":null,"categories":["Annotation","Segmentation"],"schema_version":"0.3.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-align-annotator.project_creator","title":"ALIGN Annotator","python_name":"napari_align_annotator.project_creator:ALIGNAnnotatorWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-align-annotator.project_creator","display_name":"ALIGN Annotator","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configurations":{}},"package_metadata":{"metadata_version":"2.4","name":"napari-align-annotator","version":"0.1.0","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"An annotator plugin to use with align_pipeline","description":"# napari-align-annotator\n\n[![License BSD-3](https://img.shields.io/github/license/spsalmon/napari-align-annotator?color=green)](https://github.com/spsalmon/napari-align-annotator/blob/main/LICENSE)\n[![Python Version](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)](https://python.org)\n[![tests](https://github.com/spsalmon/napari-align-annotator/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/spsalmon/napari-align-annotator/actions/workflows/tests.yml)\n[![codecov](https://codecov.io/gh/spsalmon/napari-align-annotator/branch/main/graph/badge.svg)](https://codecov.io/gh/spsalmon/napari-align-annotator)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\nA [napari] plugin for building annotated datasets for\n[ALIGN](https://github.com/spsalmon/align_pipeline).\nAnnotation work is organised into *projects*: a directory holding a\n`project.yaml` descriptor and a master annotation CSV, so a session can be\nclosed and resumed at any time.\n\n----------------------------------\n\n## Installation\n\nInstall the plugin into an environment that has napari and a Qt binding:\n\n    pip install napari-align-annotator\n\nor, to get napari and PyQt together:\n\n    pip install \"napari-align-annotator[all]\"\n\nThe plugin can also be installed from napari's plugin manager\n(`Plugins > Install/Uninstall Plugins...`).\n\nTo install the latest development version:\n\n    pip install git+https://github.com/spsalmon/napari-align-annotator.git\n\n## Usage\n\nOpen napari and start the widget from\n`Plugins > ALIGN Annotator`. From there you can either\n**Create Project** or **Load Project** (pick a directory containing a\n`project.yaml`).\n\nWhen creating a project you choose a name, a location, the image type\n(multichannel, z-stack or time series), the data directories, and\noptionally whether the data should be copied into the project. Two project\ntypes are currently supported:\n\n### Classification\n\nAssign one class to each whole image.\n\n- Define the list of classes, and choose whether to display the image, its\n  mask, or both (masks require mask directories).\n- Click a class button to label the current image and move to the next\n  one. **Ignore** removes the current image from the project.\n- Labels are written to `annotations/annotations.csv`, with one row per\n  image (`ImagePath`, `MaskPath`, `Class`).\n\n### Panoptic\n\nAssign a class to each segmented instance of an image.\n\n- Requires raw image directories and matching segmentation (label)\n  directories, plus a list of classes.\n- Select a class, then place a point on an instance to label it. For\n  z-stacks, instances are linked across planes (stitched by IoU, threshold\n  adjustable with **Re-stitch**) so a label placed on one plane propagates to\n  the rest of the object.\n- Keyboard shortcuts: `J` next image, `H` previous image, `S` save.\n- The master CSV lists `Reference`, `Segmentation` and `Annotation` paths;\n  each per-image annotation file has one row per labelled instance\n  (`Label`, `ClassID`, `Class`, plus `Z` and `InstanceID` for z-stacks).\n  `Label` is the value of the instance in the segmentation file.\n\nThe *Keypoint* project type is shown in the creator but is not supported\nyet.\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox] or directly with\n`pytest` after `pip install -e \".[testing]\"`; please ensure the coverage at\nleast stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-align-annotator\" is free and open source software.\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed\ndescription.\n\nThis [napari] plugin was generated with [copier] using the\n[napari-plugin-template].\n\n[napari]: https://github.com/napari/napari\n[copier]: https://copier.readthedocs.io/en/stable/\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n[file an issue]: https://github.com/spsalmon/napari-align-annotator/issues\n[tox]: https://tox.readthedocs.io/en/latest/\n","description_content_type":"text/markdown","keywords":"napari,annotation,segmentation,classification,microscopy","home_page":null,"download_url":null,"author":null,"author_email":"Sacha Psalmon <sacha.psalmon@unibe.ch>","maintainer":null,"maintainer_email":null,"license":null,"classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Science/Research","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","pandas","napari_guitils","natsort","pyyaml","qtpy","scikit-image","scipy","tifffile","imageio","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","napari; extra == \"testing\"","pyqt6; extra == \"testing\"","napari[all]; extra == \"all\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/spsalmon/napari-align-annotator/issues","Documentation, https://github.com/spsalmon/napari-align-annotator#readme","Source Code, https://github.com/spsalmon/napari-align-annotator","User Support, https://github.com/spsalmon/napari-align-annotator/issues"],"provides_extra":["testing","all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}