epicure.json

{
  "name": "epicure",
  "display_name": "EpiCure",
  "visibility": "public",
  "icon": "",
  "categories": [
    "Annotation",
    "Segmentation"
  ],
  "schema_version": "0.2.1",
  "on_activate": null,
  "on_deactivate": null,
  "contributions": {
    "commands": [
      {
        "id": "epicure.start",
        "title": "Start",
        "python_name": "epicure.start_epicuring:start_epicure",
        "short_title": null,
        "category": null,
        "icon": null,
        "enablement": null
      },
      {
        "id": "epicure.concatenate",
        "title": "Concatenate",
        "python_name": "epicure.concatenate_movie:concatenate_movies",
        "short_title": null,
        "category": null,
        "icon": null,
        "enablement": null
      },
      {
        "id": "epicure.doc",
        "title": "Documentation",
        "python_name": "epicure.Utils:show_documentation",
        "short_title": null,
        "category": null,
        "icon": null,
        "enablement": null
      },
      {
        "id": "epicure.preferences",
        "title": "Preferences",
        "python_name": "epicure.preferences:edit_preferences",
        "short_title": null,
        "category": null,
        "icon": null,
        "enablement": null
      }
    ],
    "readers": null,
    "writers": null,
    "widgets": [
      {
        "command": "epicure.start",
        "display_name": "Start EpiCure",
        "autogenerate": false
      },
      {
        "command": "epicure.concatenate",
        "display_name": "Concatenate EpiCured movies",
        "autogenerate": false
      },
      {
        "command": "epicure.doc",
        "display_name": "Open EpiCure documentation",
        "autogenerate": false
      },
      {
        "command": "epicure.preferences",
        "display_name": "Edit Preferences",
        "autogenerate": false
      }
    ],
    "sample_data": null,
    "themes": null,
    "menus": {},
    "submenus": null,
    "keybindings": null,
    "configuration": []
  },
  "package_metadata": {
    "metadata_version": "2.2",
    "name": "epicure",
    "version": "0.2.5",
    "dynamic": null,
    "platform": null,
    "supported_platform": null,
    "summary": "Napari plugin to manually correct epithelia segmentation in movies",
    "description": "# EpiCure\n\n[![License BSD-3](https://img.shields.io/pypi/l/epicure.svg?color=green)](https://gitlab.pasteur.fr/gletort/epicure/-/blob/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/epicure.svg?color=green)](https://pypi.org/project/epicure)\n[![Python Version](https://img.shields.io/pypi/pyversions/epicure.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/epicure)](https://napari-hub.org/plugins/epicure)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13952184.svg)](https://doi.org/10.5281/zenodo.13952184)\n\n![EpiCure logo](https://gitlab.pasteur.fr/gletort/epicure/-/raw/main/imgs/epicure_logo.png?raw=True \"EpiCure logo\")\n\n**Napari plugin to ease manual correction of epithelia segmentation in movies.**\n\nTo analyse individual cell trajectory from epithelia movies marked for cell-cell junctions, a very precise segmentation and tracking is required.\nSeveral tools such as TissuAnalyzer, Epyseg, CellPose or Dist2Net perform very good segmentation (~5% of errors). \nHowever, this still implies a high amount of cells to correct manually. \nEpiCure allows to decrease the burden of this task. \nSeveral features are proposed to ease the manual correction of the segmented movies, such as error detection, numerous shortcuts for editing the segmentation, option for tracking, display and measure/export options.\nEpiCure detect segmentation errors by taking advantage of temporal information. \nWhen a correction is done at a given frame, EpiCure relink the track to adjust for the changes.\n\n\n > **Documentation in the [wiki](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Home)**\n\n<p align=\"center\">\n![EpiCure interface](https://gitlab.pasteur.fr/gletort/epicure/-/raw/main/imgs/EpiGen.png?raw=True \"EpiCure interface\")\n</p>\n\n## Installation\n\n### Install plugin\nTo install EpiCure on a fresh python virtual environment, type inside the environement:\n```\npip install epicure\n``` \n\nThen launch `Napari`, and the plugin should be visible in the `Plugins` list.\n\nIf you already have an environment with `Napari` installed, you can also install it directly in `Napari>Plugins>Install/Uninstall plugins`\n\n### Install code\nTo have the code to be able to modify it, clone this repository. You can use `pip install -e .` so that everytime you update the code, the plugin will be updated. \n\n## Dependencies\n\nThe input files of EpiCure can be already tracked or not.\nTracking options are proposed in EpiCure:\n* Laptrack centroids\n* Laptrack overlaps\n\n## Usage\nRefer to the [wiki](https://gitlab.pasteur.fr/gletort/epicure/-/wikis/Home) for documentation of the different steps possible in the pipeline.\n\n## References\n\nIf you use EpiCure, thank you for citing our work: \n\nEpiCure is not published yet, you can cite it using Zenodo for now: https://doi.org/10.5281/zenodo.13952184\n\n\n## Issues\nIssues have been disactivated to avoid spammed issues. To report an issue or ask for development, please contact us directly by email.\n\n\nThis [napari] plugin was initialized with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[file an issue]: https://github.com/gletort/epicure/issues\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://gitlab.pasteur.fr/gletort/epicure",
    "download_url": null,
    "author": "Ga\u00eblle Letort",
    "author_email": null,
    "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 :: 3.8",
      "Programming Language :: Python :: 3.9",
      "Programming Language :: Python :: 3.10",
      "Topic :: Scientific/Engineering :: Image Processing"
    ],
    "requires_dist": [
      "napari<=0.4.19",
      "numpy",
      "magicgui",
      "qtpy",
      "scikit-image",
      "opencv_python_headless",
      "roifile",
      "xlsxwriter",
      "laptrack",
      "matplotlib",
      "imagecodecs",
      "edt",
      "tox; extra == \"testing\"",
      "pytest; extra == \"testing\"",
      "pytest-cov; extra == \"testing\"",
      "pytest-qt; extra == \"testing\"",
      "napari; extra == \"testing\"",
      "pyqt5; extra == \"testing\""
    ],
    "requires_python": ">=3.8",
    "requires_external": null,
    "project_url": [
      "Bug Tracker, https://gitlab.pasteur.fr/gletort/epicure/issues",
      "Documentation, https://gitlab.pasteur.fr/gletort/epicure#README.md",
      "Source Code, https://gitlab.pasteur.fr/gletort/epicure",
      "User Support, https://gitlab.pasteur.fr/gletort/epicure/issues"
    ],
    "provides_extra": [
      "testing"
    ],
    "provides_dist": null,
    "obsoletes_dist": null
  },
  "npe1_shim": false
}