tomatowur 1.3.7

About

Official implementation of TomatoWUR dataset:

An annotated dataset of tomato plants to quantitatively evaluate segmentation, skeletonisation, and plant trait extraction algorithms for 3D plant phenotyping

The dataset is related to the paper:

• 3D plant segmentation: Comparing a 2D-to-3D segmentation method with state-of-the-art 3D segmentation algorithms
• From point clouds to plant traits: investigation of a pipeline for phenotyping of tomato plants using skeletonisation

Changes:

• 2025-11-14 published original TomatoWUR repo --> release tag: original_tomatowur_paper
• 2026-05-27 In point cloud to plant traits paper 4 annotations errors were found. These annotations are added to the 4TU dataset version 3.
• 2026-07-31 Added updates of point cloud to plant traits paper in this REPO. This includes.
  • Improved skeleton evaluation method
  • Additional skeletonisation methods.
  • deprecated CLI interface -> only config files instead. python3 wurTomato.py --config config.yaml For reproduceability of Point clouds to plait traits paper we recommend git related to that publication.
• 2026-07-31: created pyproject. TODO check pc_skeletor dependency

Installation

This software is tested on Python 3.11. To install the dependencies, run:

pip install tomatowur

OR to work locally and use pc_skeletor as well:

git clone https://github.com/WUR-ABE/TomatoWUR.git
cd tomatowur
conda create --name tomatowur python=3.11
conda activate tomatowur
pip install -e .
## for laplacian skeletonisation also install pc_skeletor
# pip install -e src/tomatowur/skeletonisation_methods/pc_skeletor/.
## verify installation with
python3 -c "import tomatowur"

Usage

Make sure to extract and download the dataset, this will be done automatically if path can not be found:

wurtomato --config config.yaml run_mode=["visualise"]

For more examples have a look at the example_notebook.ipynb

Settings are described in config file

Citation

If you only use the TomatoWUR dataset, please use the citation below. If your work also uses components from the 2D-to-3D segmentation or the point cloud to plant traits papers, please cite those as well.

@article{VANMARREWIJK2025111852,
title = {TomatoWUR: An annotated dataset of tomato plants to quantitatively evaluate segmentation, skeletonisation, and plant-trait extraction algorithms for 3D plant phenotyping},
journal = {Data in Brief},
volume = {61},
pages = {111852},
year = {2025},
issn = {2352-3409},
doi = {https://doi.org/10.1016/j.dib.2025.111852},
url = {https://www.sciencedirect.com/science/article/pii/S2352340925005773},
author = {Bart M. {van Marrewijk} and Tim {van Daalen} and Katarína Smoleňová and Bolai Xin and Gerrit Polder and Gert Kootstra},
}

Related research

• 2Dto3D segmentation
• Point cloud to plant traits

Funding

This research is part of AgrifoodTEF: Test and Experiment Facilities for the Agri-Food Domain (101100622)