orseg

Segtree is a plugin designed for the segmentation of individual trees from imagery. It isolates tree in ovelapping tree context.

How it works

The user provides as input a color image and, optionally, a trunk detector mask. With a single click, the plugin automatically places prompt points on the detected trunk labels. These prompts are then used by SAM2 HQ (Segment Anything Model v2, High Quality mode) to segment the tree foliage associated with each trunk.

Article : Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering

METUAREA, Herearii, LAURENS, François, GUERRA, Walter, et al. Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering. Sensors, 2025, vol. 25, no 15, p. 4721.

Citing segtree

If you find segtree useful in your research, please star ⭐ this repository and consider citing 📝:

@article{metuarea2025individual,
  title={Individual Segmentation of Intertwined Apple Trees in a Row via Prompt Engineering},
  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},
  journal={Sensors},
  volume={25},
  number={15},
  pages={4721},
  year={2025},
  publisher={MDPI}
}

Installation

You can install orseg via pip:

pip install orseg

If napari is not already installed, you can install orseg with napari and Qt via:

pip install "orseg[all]"

To install latest development version :

pip install git+https://github.com/hereariim/orseg.git

Contact

Imhorphen team, bioimaging research group

42 rue George Morel, Angers, France

• Pr David Rousseau, david.rousseau@univ-angers.fr
• Herearii Metuarea, herearii.metuarea@univ-angers.fr

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "orseg" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.