openalea / phenotrack3d Goto Github PK

Phenotyping Maize over time

License: Other

Python 100.00%

maize openalea organs phenotyping tracking

phenotrack3d's Introduction

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 ([email protected])
Fournier Christian ([email protected])
Pradal Christophe ([email protected])

License

Our code is released under Cecill-C (https://cecill.info/licences/Licence_CeCILL_V1.1-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=0.9
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

@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}
}

phenotrack3d's People

Contributors

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Watchers

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pradal rocsg

phenotrack3d's Issues

Conda packaging and CI

Create a conda package
Update it automatically on openalea3 channel using Github Continuous Integration

ModuleNotFoundError: No module named 'openalea.maizetrack'

Hi,

When I try
(phenotrack) C:\Users\twang\phenotrack3d\examples>python tutorial_leaf_extension.py
I got
ModuleNotFoundError: No module named 'openalea.maizetrack'
I can see maizetrack.py is in the folder of src in this repository but still failed to import.

Any clue?
Thanks.
Tien

Add Citation.cff and connect repository to Zenodo

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TypeError: leaf_extension() got an unexpected keyword argument 'display_angle'

Hi,
I got new error from
(phm) C:\Users\twang\phenotrack3d>python examples/tutorial_leaf_extension.py

Traceback (most recent call last):
  File "examples/tutorial_leaf_extension.py", line 28, in <module>
TypeError: leaf_extension() got an unexpected keyword argument 'display_angle'

PackagesNotFoundError: - openalea.phenomenal

Hi,
Romain suggested me to try this package. I would be appreicated if you can help me with the installation.

I have tried to create the conda environment based on
conda create -n phenotrack -c conda-forge -c openalea3 openalea.phenomenal skan=0.9
And I got

`Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

openalea.phenomenal

Current channels:

https://conda.anaconda.org/conda-forge/win-64

https://conda.anaconda.org/conda-forge/noarch

https://conda.anaconda.org/openalea3/win-64

https://conda.anaconda.org/openalea3/noarch

https://repo.anaconda.com/pkgs/main/win-64

https://repo.anaconda.com/pkgs/main/noarch

https://repo.anaconda.com/pkgs/r/win-64

https://repo.anaconda.com/pkgs/r/noarch

https://repo.anaconda.com/pkgs/msys2/win-64

https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.`

Any thought?
Thank you in advance.
Best,
Tien-Cheng

ModuleNotFoundError: No module named 'alinea'

Hi,

When I try
(phenotrack) C:\Users\HAIER\phenotrack3d\examples>python tutorial_leaf_extension.py
I got
ModuleNotFoundError: No module named 'alinea'
I can see maizetrack.py is in the folder of src in this repository but still failed to import.

Thanks.