{"name":"napari-epyseg","display_name":"Napari-EpySeg","visibility":"public","icon":"","categories":["Segmentation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-epyseg.start","title":"Start","python_name":"napari_epyseg.start_epyseg:start_epyseg","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-epyseg.start","display_name":"Napari-EpySeg","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-epyseg","version":"0.0.10","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Napari plugin to segment epithelia with EpySeg","description":"[![DOI](https://zenodo.org/badge/931444556.svg)](https://doi.org/10.5281/zenodo.16910935)\n[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)\n\n# napari-epyseg\n\nPlugin to run [EpySeg](https://github.com/baigouy/EPySeg) directly in [Napari](https://napari.org/stable/).\nCan handle temporal data (movie) or single time point (image).\n\n## Installation\n\nTo install it from Napari, go into the `Plugins` menu, select `Install/Uninstall Plugins..` and look for napari-epyseg in the plugins list.\n\nTo install it directly outside of napari, create/reuse and activate a python environement, e.g `epyseg_env` and install it with `pip`:\n```\npip install napari-epyseg\n```\n\n> [!IMPORTANT]\n> `epyseg` is compatible until python 3.10 (included), but not for versions of python above. Thus, `napari-epyseg` is also compatible with python versions until 3.10\n\n## Usage\n\nIn Napari, go to `Plugins>napari-epyseg` to start it.\nIt will open an interface in the left part of the main window.\n\n![interface_image](./imgs/napepy-interface.png)\n\nYou must select the layer (image or movie, single color channel) on which to run `EpySeg`.\nFor this, in the `Pick an Image` parameter, select the corresponding layer (you should open the image/movie independantly of the plugin).\n\nTo run `EpySeg` with default parameters, press directly `Segment` once you have selected the image.\nWhen processing is finished, a new layer called `Segmentation` will be added in the right panel of the interface.\nYou can save the result with the `Save segmentation` button that appears on the left part of the interface. \nChoose where to save the file and the file name with the `Segmentation filename` parameter, and click the button to save it.\n\n![results_image](./imgs/result.png)\n\n## Remark\n\nThis plugin was tested on python 3.10, with epyseg version 0.1.52, napari version 0.4.19, tensorflow 2.14\n\n## Troubleshooting\n\n* On Linux Ubuntu, python 3.10, epyseg don't run with tensorflow 2.15 and output the error: `DNN not found`. Downgrading tensorflow to 2.14 worked.\n* `tifffile versions` compability: some versions of tifffile where not compatible with epyseg, but recent versions are now fine. `tifffile <= 2021.11.2` are fine and `tifffile==2025.1.10` also.\n\n## License\n\nThis plugin is distributed under the BDS-3 license.\nIf you use this plugin, please cite [Epyseg](https://journals.biologists.com/dev/article/147/24/dev194589/226105/EPySeg-a-coding-free-solution-for-automated) and the plugin with its doi: [![DOI](https://zenodo.org/badge/931444556.svg)](https://doi.org/10.5281/zenodo.16910935)\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/Image-Analysis-Hub/napari-epyseg","download_url":null,"author":"Gaëlle 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":["epyseg","napari<=0.6.5","numpy","magicgui","tifffile<=2024.12.12","pillow","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":"<3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/Image-Analysis-Hub/napari-epyseg/issues","Documentation, https://github.com/Image-Analysis-Hub/napari-epyseg#README.md","Source Code, https://github.com/Image-Analysis-Hub/napari-epyseg","User Support, https://github.com/Image-Analysis-Hib/napari-epyseg/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}