arabidopsis-segmentation-model

Arabidopsis Segmentation Model

This is a pre-trained nnU-Net v2 model for root segmentation in Arabidopsis images. This model is a further finetuned model forked from ChronoRoot 2.0 part of the ChronoRoot 2.0 framework for high-throughput phenotyping of plant root systems. This finetuned model is now capable of segmenting etiolated Arabidopsis plants

For more information about the application and framework for this model, please refer to the associated website

Please cite the following paper if you use this model in your research:

@article{gaggion2026chronoroot,
  title={ChronoRoot 2.0: An Open AI-Powered Platform for 2D Temporal Plant Phenotyping}, 
  author={Nicolás Gaggion and Noelia A. Boccardo and Rodrigo Bonazzola and María Florencia Legascue and María Florencia Mammarella and Florencia Sol Rodriguez and Federico Emanuel Aballay and Florencia Belén Catulo and Andana Barrios and Luciano J. Santoro and Franco Accavallo and Santiago Nahuel Villarreal and Leonardo I. Pereyra-Bistrain and Moussa Benhamed and Martin Crespi and Martiniano María Ricardi and Ezequiel Petrillo and Thomas Blein and Federico Ariel and Enzo Ferrante},
  journal={arXiv preprint arXiv:2504.14736},
  year={2026}
}