Applications realised

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Platforms (M3P)
Montpellier Plant Phenotyping Platforms (M3P)
PhenoArch
Applications realised

Applications realised

EarTrack

An imaging library to detect and track future position of ear on maize plants.

EarTrack is released under a Cecill-C license.

Contents

Documentation

The documentation is available at https://eartrack.readthedocs.io

Tutorials are available as Jupyter notebook :

Installation with Miniconda

Miniconda installation

Follow official website instruction to install miniconda : http://conda.pydata.org/miniconda.html

To create conda environment and activate it :

conda create -n eartrack python=2.7
source activate eartrack #just "activate eartrack" on windows
User installation

Available for linux, Windows and Mac OSX on 64 bits.

conda install -c conda-forge -c openalea openalea.eartrack
Source code installation

Please follow documentation installation page https://eartrack.readthedocs.io/en/latest/source/install/index.html.

Help and Support

Please open an Issue if you need support or that you run into any error (Installation, Runtime, etc.).

We'll try to resolve it as soon as possible.

Authors
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To cite in publications, use:

Brichet N, Fournier C, Turc O, Strauss O, Artzet S, Pradal C, Welcker C, Tardieu F, Cabrera-Bosquet L. 2017. A robot-assisted imaging pipeline for tracking the growths of maize ear and silks in a high-throughput phenotyping platform. Plant Methods 13:96 doi:10.1186/s13007-017-0246-7

SunPathGen

SunPathGen is an R-based interactive web application based on the R Shiny package (http://shiny.rstudio.com/) that provides advanced visualization and statistical computing. It allows calculation of sun paths and light transmission on hemispherical images under a user-friendly environment. The App does not require any previous knowledge on R programming, just an updated version of most current browsers (e.g. Mozilla, IE). The web application has three main features:

  • Sun path calculator: It allows simulating sun paths and astronomical related parameters depending on the user inputs (day of year and latitude/ longitude coordinates)
  • Light transmission calculator: It allows calculating the transmission of diffuse and direct light based on user inputs (binarised hemispherical images, day of year and latitude). A csv file containing the obtained results can be downloaded.
  • Gallery: A video file of the direct light transmission over one year in our greenhouse together with a gallery of the PhenoArch platform is available.

The application is available at the following link:

http://web.supagro.inra.fr/lepse-shiny/SunPathGen/

Shiny_reference

To cite in publications, use:

Cabrera-Bosquet L, Fournier C, Brichet N, Welcker C, Suard B, Tardieu F. 2016. High throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform. New Phytologist, 212: 269-281. http://onlinelibrary.wiley.com/doi/10.1111/nph.14027/full

Modification date : 17 July 2023 | Publication date : 17 June 2021 | Redactor : Aurélien Ausset