\n\nNapari plugin to ease manual correction of epithelia segmentation in movies.
\n\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](https://github.com/baigouy/EPySeg), [CellPose](https://www.cellpose.org/) or [Dist2Net](https://github.com/jeanollion/distnet2d) perform very good segmentation (~5% of errors). \nHowever, this still implies a high amount of cells to correct manually. \n\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 > **See the full [documentation here](https://image-analysis-hub.github.io/Epicure/)**\n\n![EpiCure interface](https://github.com/Image-Analysis-Hub/Epicure/blob/main/docs/imgs/EpiGen.png \"EpiCure interface\")\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 [documentation](https://image-analysis-hub.github.io/Epicure/) 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## Contributing and Feedback\nEpiCure is mainly developed in CNRS UMR3738, in the [Developmental and Stem Cell Biology Department](https://research.pasteur.fr/en/department/developmental-stem-cell-biology/) of Institut Pasteur.\nIf you have a question on using EpiCure or ask to add a feature, either file an issue or write in the [imagesc forum](https://forum.image.sc/).\n\nAny contribution is most welcome. \nDo not hesitate to contact us beforehand through [filing an issue](https://github.com/Image-Analysis-Hub/epicure/issues/) (choose \"Other questions/comments\" type).\nTo suggest the addition of a new feature, you can also contact us by filing an issue choosing the \"Feature request\" option.\n\nIf you encounter a code related issue using EpiCure, please [file an issue](https://github.com/Image-Analysis-Hub/epicure/issues) in this repository.\n\n\n[napari]: https://github.com/napari/napari\n[file an issue]: https://github.com/Image-Analysis-Hub/epicure/issues\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Gaëlle Letort","author_email":null,"maintainer":null,"maintainer_email":null,"license":"BSD 3-Clause License\n\nCopyright (c) 2025, Gaelle Letort\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n1. Redistributions of source code must retain the above copyright notice, this\n list of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\n this list of conditions and the following disclaimer in the documentation\n and/or other materials provided with the distribution.\n\n3. Neither the name of the copyright holder nor the names of its\n contributors may be used to endorse or promote products derived from\n this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Framework :: napari","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["napari","numpy","qtpy","bioio","bioio-bioformats","bioio-tifffile","scikit-image","opencv-python-headless<4.9.0","roifile","pyqtwebengine","magicgui","scipy","xlsxwriter","plotly","kaleido","imagecodecs","edt","packaging","laptrack>=0.15.0","joblib","appose"],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/Image-Analysis-Hub/Epicure/issues","Documentation, https://image-analysis-hub.github.io/Epicure/","Source Code, https://github.com/Image-Analysis-Hub/Epicure","User Support, https://github.com/Image-Analysis-Hub/Epicure/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}