tomatowur
TomatoWUR; a comprehensive dataset for 3D plant phenotyping
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: sciencedirect.com -
○Academic email domains
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○Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary
Keywords
Repository
TomatoWUR; a comprehensive dataset for 3D plant phenotyping
Basic Info
- Host: GitHub
- Owner: WUR-ABE
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: http://doi.org/10.4121/e2c59841-4653-45de-a75e-4994b2766a2f.v1
- Size: 16.1 MB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
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
Installation
This software is tested on Python 3.11. To install the dependencies, run:
pip install -r requirements.txt
Usage
Make sure to extract and download the dataset, this will be done automatically if path can not be found:
python3 wurTomato.py --visualise 0
For more examples have a look at the example_notebook.ipynb
Settings are described in config file
Citation
@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
Funding
This research is part of AgrifoodTEF: Test and Experiment Facilities for the Agri-Food Domain (101100622)
Owner
- Name: Wageningen University & Research - Agricultural Biosystems Engineering
- Login: WUR-ABE
- Kind: organization
- Location: Netherlands
- Website: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/agricultural-biosystems-engineering.htm
- Repositories: 1
- Profile: https://github.com/WUR-ABE
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite the preferred-citation.
authors:
- family-names: van Marrewijk
given-names: Bart M.
orcid: "https://orcid.org/0000-0003-3681-8114"
- family-names: van Daalen
given-names: Tim
orcid: "https://orcid.org/0009-0003-0308-1969"
- family-names: Smoleňová
given-names: Katarína
orcid: "https://orcid.org/0009-0008-3164-0955"
- family-names: Xin
given-names: Bolai
- family-names: Polder
given-names: Gerrit
orcid: "https://orcid.org/0000-0003-4896-4776"
- family-names: Kootstra
given-names: Gert
orcid: "https://orcid.org/0000-0002-2579-4324"
title: "TomatoWUR: An annotated dataset of tomato plants to quantitatively evaluate segmentation, skeletonisation, and plant-trait extraction algorithms for 3D plant phenotyping"
version: 1.0.0
url: https://doi.org/10.1016/j.dib.2025.111852
preferred-citation:
authors:
- family-names: van Marrewijk
given-names: Bart M.
orcid: "https://orcid.org/0000-0003-3681-8114"
- family-names: van Daalen
given-names: Tim
orcid: "https://orcid.org/0009-0003-0308-1969"
- family-names: Smoleňová
given-names: Katarína
orcid: "https://orcid.org/0009-0008-3164-0955"
- family-names: Xin
given-names: Bolai
- family-names: Polder
given-names: Gerrit
orcid: "https://orcid.org/0000-0003-4896-4776"
- family-names: Kootstra
given-names: Gert
orcid: "https://orcid.org/0000-0002-2579-4324"
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
start: 111852
issn: "2352-3409"
doi: "10.1016/j.dib.2025.111852"
type: article
year: 2025
GitHub Events
Total
- Watch event: 6
- Push event: 10
- Public event: 1
- Pull request event: 1
- Fork event: 2
Last Year
- Watch event: 6
- Push event: 10
- Public event: 1
- Pull request event: 1
- Fork event: 2
Dependencies
- actions/checkout v4 composite
- actions/checkout v4 composite
- ipykernel *
- matplotlib *
- natsort *
- omegaconf *
- pandas *
- polyscope *
- requests *
- scikit-learn *
- scipy *
- torch *
- tqdm *