Data

Tools

Indexes

Applications

Experiments

Open Source Science

phenotrack3d

Phenotyping Maize over time

https://github.com/openalea/phenotrack3d

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary

Keywords

maize openalea organs phenotyping tracking
Last synced: 6 months ago · JSON representation

Repository

Phenotyping Maize over time

Basic Info
  • Host: GitHub
  • Owner: openalea
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 111 MB
Statistics
  • Stars: 10
  • Watchers: 3
  • Forks: 3
  • Open Issues: 4
  • Releases: 2
Topics
maize openalea organs phenotyping tracking
Created over 3 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation Authors

README.md

PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

PhenoTrack3D can be used to track leaf organs over time, in a time-series of 3D maize plant reconstructions. Such 3D reconstructions can be obtained from sets of RGB images with the Phenomenal pipeline (https://github.com/openalea/phenomenal)

Maintainers

  • Daviet Benoit (benoit.daviet@inrae.fr)
  • Fournier Christian (christian.fournier@inrae.fr)
  • Pradal Christophe (christophe.pradal@cirad.fr)

License

Our code is released under Cecill-C (https://cecill.info/licences/LicenceCeCILLV1.1-US.txt) licence. See LICENSE file for details.

Install

install dependencies with conda:

conda create -n phenotrack -c conda-forge -c openalea3 openalea.phenomenal skan=0.10 pytest numpy skimage
conda activate phenotrack

Clone repo and run setup

git clone https://github.com/openalea/phenotrack3d.git
cd phenotrack3d

References

If you use PhenoTrack3D to your research, cite:

Daviet, B., Fernandez, R., Cabrera-Bosquet, L. et al. PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time. Plant Methods 18, 130 (2022). https://doi.org/10.1186/s13007-022-00961-4

```latex @article {daviet22, author = {Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c c} and Pradal, Christophe and Fournier, Christian}, title = {PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time}, elocation-id = @article{daviet2022phenotrack3d, title={PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time}, author={Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c{c}} and Pradal, Christophe and Fournier, Christian}, journal={Plant Methods}, volume={18}, number={1}, pages={1--14}, year={2022}, publisher={Springer} }

```

Owner

  • Name: OpenAlea
  • Login: openalea
  • Kind: organization

OpenAlea is an open source project aimed at the plant research community. It includes modules to analyse and model growth and functioning of plant architectures

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 1
  • Watch event: 2
  • Push event: 3
  • Pull request event: 1
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 1
  • Watch event: 2
  • Push event: 3
  • Pull request event: 1

Dependencies

setup.py pypi