{"id":13716658,"url":"https://github.com/kreshuklab/plant-seg","last_synced_at":"2025-12-24T12:32:10.785Z","repository":{"id":36455448,"uuid":"216003952","full_name":"kreshuklab/plant-seg","owner":"kreshuklab","description":" A tool for cell instance aware segmentation in densely packed 3D volumetric images 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science"],"sub_categories":[],"readme":"# PlantSeg  \u003c!-- omit in toc --\u003e\n\n![alt text](docs/logos/logo.png)\n\n[![Conda Build and Test](https://github.com/kreshuklab/plant-seg/actions/workflows/build-and-test-package.yml/badge.svg)](https://github.com/kreshuklab/plant-seg/actions/workflows/build-and-test-package.yml)\n[![Docs Build and Publish](https://github.com/kreshuklab/plant-seg/actions/workflows/build-and-publish-docs.yml/badge.svg)](https://github.com/kreshuklab/plant-seg/actions/workflows/build-and-publish-docs.yml)\n\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plant-seg/badges/version.svg)](https://anaconda.org/conda-forge/plant-seg)\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plant-seg/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/plant-seg)\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plant-seg/badges/downloads.svg)](https://anaconda.org/conda-forge/plant-seg)\n[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plant-seg/badges/license.svg)](https://anaconda.org/conda-forge/plant-seg)\n\n![Illustration of Pipeline](../assets/images/main_figure_nologo.png)\n\n[PlantSeg](plantseg) is a tool for cell instance aware segmentation in densely packed 3D volumetric images.\nThe pipeline uses a two stages segmentation strategy (Neural Network + Segmentation).\nThe pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy.\nPre-trained models are provided.\n\n## Table of Contents  \u003c!-- omit in toc --\u003e\n\n* [Getting Started](#getting-started)\n* [Installation](#installation)\n* [Repository Index](#repository-index)\n* [Citation](#citation)\n\n## Getting Started\n\nCheckout the [**documentation** 📖](https://kreshuklab.github.io/plant-seg/latest/chapters/getting_started/) for more details.\n\nhttps://github.com/user-attachments/assets/9551210b-0ed6-4f06-b1d1-4059aadecd11\n\n\n## Installation\n\nThe easiest way to get PlantSeg is using the installer. [**Download it here**](https://heibox.uni-heidelberg.de/d/72b4bd3ba5f14409bfee/)\n\nThe installer comes with python and conda.\nPlease go to the [documentation](https://kreshuklab.github.io/plant-seg/latest/chapters/getting_started/installation/) for more detailed instructions.\n\nFor development, we recommend to clone the repo and install using:\n\n```bash\nconda env create -f environment-dev.yaml\n```\n\nThe above command will create new conda environment `plant-seg-dev` together with all required dependencies.\n\n## Repository Index\n\nThe PlantSeg repository is organised as follows:\n\n* **plantseg**: Contains the source code of PlantSeg.\n* **docs**: Contains the documentation of PlantSeg.\n* **examples**: Contains the files required to test PlantSeg.\n* **tests**: Contains automated tests that ensures the PlantSeg functionality are not compromised during an update.\n* **evaluation**: Contains all script required to reproduce the quantitative evaluation in\n[Wolny et al.](https://doi.org/10.7554/eLife.57613).\n* **conda-reicpe**: Contains all necessary code and configuration to create the anaconda package.\n* **constructor**: Contains scripts for the installer creation.\n* **Menu**: Contains scripts for OS Menu entries\n\n## Citation\n\n```text\n@article{wolny2020accurate,\n  title={Accurate and versatile 3D segmentation of plant tissues at cellular resolution},\n  author={Wolny, Adrian and Cerrone, Lorenzo and Vijayan, Athul and Tofanelli, Rachele and Barro, Amaya Vilches and Louveaux, Marion and Wenzl, Christian and Strauss, S{\\\"o}ren and Wilson-S{\\'a}nchez, David and Lymbouridou, Rena and others},\n  journal={Elife},\n  volume={9},\n  pages={e57613},\n  year={2020},\n  publisher={eLife Sciences Publications Limited}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkreshuklab%2Fplant-seg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkreshuklab%2Fplant-seg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkreshuklab%2Fplant-seg/lists"}