{"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":"0.0.14","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":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":["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","tifffile<=2024.12.12","numpy","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\"","napari[all]<=0.6.5; extra == \"napari\"","magicgui; extra == \"napari\"","pillow; extra == \"napari\""],"requires_python":"<3.11","requires_external":null,"project_url":["Homepage, https://github.com/Image-Analysis-Hub/napari-epyseg","Documentation, https://github.com/Image-Analysis-Hub/napari-epyseg#README.md","Source code, https://github.com/Image-Analysis-Hub/napari-epyseg","Bug Tracker, https://github.com/Image-Analysis-Hub/napari-epyseg/issues","User Support, https://github.com/Image-Analysis-Hub/napari-epyseg/issues"],"provides_extra":["testing","napari"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}