{"name":"orseg","display_name":"Orseg","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"orseg.ind_segm","title":"Tree Segmentation","python_name":"orseg:individual_tree","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"orseg.ind_segm","display_name":"Individual Tree Segmentation","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"orseg","version":"0.0.2","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Segtree is a plugin designed for the segmentation of individual trees from imagery. It isolates tree in ovelapping tree context.","description":"# orseg\n\n[![License BSD-3](https://img.shields.io/pypi/l/orseg.svg?color=green)](https://github.com/hereariim/orseg/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/orseg.svg?color=green)](https://pypi.org/project/orseg)\n[![Python Version](https://img.shields.io/pypi/pyversions/orseg.svg?color=green)](https://python.org)\n[![tests](https://github.com/hereariim/orseg/workflows/tests/badge.svg)](https://github.com/hereariim/orseg/actions)\n[![codecov](https://codecov.io/gh/hereariim/orseg/branch/main/graph/badge.svg)](https://codecov.io/gh/hereariim/orseg)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/orseg)](https://napari-hub.org/plugins/orseg)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\nSegtree is a plugin designed for the segmentation of individual trees from imagery. It isolates tree in ovelapping tree context.\n\n![alt text](<src/orseg/Screenshot from 2025-09-10 17-01-24.png>)\n\n## How it works\n\nThe user provides as input a **color image** and, optionally, a **trunk detector mask**.\nWith a single click, the plugin automatically places prompt points on the detected trunk labels. These prompts are then used by [SAM2 HQ](https://github.com/SysCV/sam-hq/blob/main/sam-hq2/README.md#citing-hq-sam-2) (Segment Anything Model v2, High Quality mode) to segment the tree foliage associated with each trunk.\n![alt text](<src/orseg/Screenshot from 2025-09-10 15-30-09.png>)\n\n## Article : Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering\n\nMETUAREA, Herearii, LAURENS, François, GUERRA, Walter, et al. [Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering](https://www.mdpi.com/1424-8220/25/15/4721). Sensors, 2025, vol. 25, no 15, p. 4721.\n\n## Citing segtree\n\nIf you find segtree useful in your research, please star ⭐ this repository and consider citing 📝:\n\n```\n@article{metuarea2025individual,\n  title={Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering},\n  author={Metuarea, Herearii and Laurens, Fran{\\c{c}}ois and Guerra, Walter and Lozano, Lidia and Patocchi, Andrea and Van Hoye, Shauny and Dutagaci, Helin and Labrosse, Jeremy and Rasti, Pejman and Rousseau, David},\n  journal={Sensors},\n  volume={25},\n  number={15},\n  pages={4721},\n  year={2025},\n  publisher={MDPI}\n}\n```\n\n## Installation\n\nYou can install `orseg` via [pip]:\n\n```\npip install orseg\n```\n\nIf napari is not already installed, you can install `orseg` with napari and Qt via:\n\n```\npip install \"orseg[all]\"\n```\n\n\nTo install latest development version :\n\n```\npip install git+https://github.com/hereariim/orseg.git\n```\n\n## Contact\n\nImhorphen team, bioimaging research group\n\n42 rue George Morel, Angers, France\n\n- Pr David Rousseau, david.rousseau@univ-angers.fr\n- Herearii Metuarea, herearii.metuarea@univ-angers.fr\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"orseg\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[copier]: https://copier.readthedocs.io/en/stable/\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n\n[file an issue]: https://github.com/hereariim/orseg/issues\n\n[napari]: https://github.com/napari/napari\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":null,"download_url":null,"author":"Herearii Metuarea","author_email":"herearii.metuarea@univ-angers.fr","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Herearii Metuarea\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* 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\n* Neither the name of 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 :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["torch>=2.3.1","torchvision>=0.18.1","numpy","magicgui","qtpy","aiofiles==23.2.1","altair==5.5.0","annotated-types==0.7.0","antlr4-python3-runtime==4.9.3","anyio==4.9.0","attrs==25.3.0","certifi==2025.1.31","charset-normalizer==3.4.1","click==8.1.8","coloredlogs==15.0.1","contourpy==1.3.1","cycler==0.12.1","fastapi==0.115.12","ffmpy==0.5.0","filelock==3.18.0","flatbuffers==25.2.10","fonttools==4.56.0","fsspec==2025.3.2","gradio==4.29.0","gradio-client==0.16.1","gradio-imageslider==0.0.20","h11==0.14.0","httpcore==1.0.7","httpx==0.28.1","huggingface-hub==0.30.1","humanfriendly==10.0","hydra-core==1.3.2","idna==3.10","imageio==2.37.0","importlib-resources==6.5.2","iopath==0.1.10","jinja2==3.1.6","joblib==1.4.2","jsonschema==4.23.0","jsonschema-specifications==2024.10.1","kiwisolver==1.4.8","lazy-loader==0.4","markdown-it-py==3.0.0","markupsafe==2.1.5","matplotlib==3.10.1","mdurl==0.1.2","mpmath==1.3.0","narwhals==1.33.0","networkx==3.4.2","numpy==1.26.4","omegaconf==2.3.0","onnx==1.17.0","onnxruntime==1.21.0","opencv-python==4.11.0.86","orjson==3.10.16","pandas==2.2.3","pillow==10.4.0","portalocker==3.1.1","protobuf==6.30.2","py-cpuinfo==9.0.0","pycocotools==2.0.8","pydantic==2.11.1","pydantic-core==2.33.0","pydub==0.25.1","pyparsing==3.2.3","pyreadline3==3.5.4","python-multipart==0.0.20","pytz==2025.2","pyyaml==6.0.2","referencing==0.36.2","regex==2024.11.6","requests==2.32.3","rich==14.0.0","rpds-py==0.24.0","ruff==0.11.2","safetensors==0.5.3","scikit-image==0.25.2","scikit-learn==1.6.1","scipy==1.15.2","seaborn==0.13.2","semantic-version==2.10.0","shellingham==1.5.4","sniffio==1.3.1","starlette==0.46.1","sympy==1.13.1","threadpoolctl==3.6.0","tifffile==2025.3.30","timm==1.0.15","tokenizers==0.21.1","tomlkit==0.12.0","tqdm==4.67.1","transformers==4.50.3","typer==0.15.2","typing-inspection==0.4.0","tzdata==2025.2","ultralytics==8.3.99","ultralytics-thop==2.0.14","urllib3==2.3.0","uvicorn==0.34.0","websockets==11.0.3","napari[all]; extra == \"all\""],"requires_python":">=3.10.16","requires_external":null,"project_url":["Bug Tracker, https://github.com/hereariim/orseg/issues","Documentation, https://github.com/hereariim/orseg#README.md","Source Code, https://github.com/hereariim/orseg","User Support, https://github.com/hereariim/orseg/issues"],"provides_extra":["all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}