Root crown images of soybean and wheat and statistical analysis for RhizoVision Crown

This repository contains raw image data of root crowns imaged using the backlit RhizoVision Crown platform of soybean and wheat plants phenotyped in Missouri and Oklahoma, respectively, as described in the below manuscript. Data files and the R scripts are included for complete statistical analysis associated with the imaged root crown set as well as validation using images of copper wires and simulated root images. We request any reuse of this data to both cite this repository and also the publication given below.

Citation:

Seethepalli, A., Guo, H., Liu, X., Griffiths. M. G., Almtarfi, H., Li, Z., Liu, S., Zare, A., Fritschi, F., Blancaflor, E., Ma, X., and York, L. M. (2020). RhizoVision Crown: An integrated hardware and software platform for root crown phenotyping. Plant Phenomics.  doi:10.34133/2020/3074916

Link: https://spj.sciencemag.org/plantphenomics/2020/3074916/

Root crown images were acquired using the RhizoVision Imager software available at:

https://zenodo.org/record/2585882#.XWgOAeNKiUk

Image analysis of physical wires, simulated dicot and monocot root systems, and soybean and wheat root crowns was originally conducted with RhizoVision Analyzer. However, Analyzer has been replaced by RhizoVision Explorer that uses the same underlying algorithms and the analysis can be recreated using the 'whole root' mode of Explorer, available here:

https://zenodo.org/record/4095629

Image Files

physical_validation_wires.zip - A set for validation of physical units using 10 images of 2 individual wires of 5 gauges (10, 16, 22, 28, 32) in PNG format acquired using the RhizoVision Crown hardware platform. Includes a CSV file containing measured length and diameters as well as those from image analysis using RhizoVision Analyzer.

Soybean_RVC_RootCrowns.zip - 2,778 greyscale images in PNG format of field excavated soybean root crowns.

Wheat_RVC_RootCrowns.zip - 1,754 greyscale images in PNG format of field excavated wheat root crowns.

metadata_Analyzer_allImageSets.zip - CSV files with the metadata files output by the RhizoVision Analyzer software for the physical validation, validation of simulated dicots and monocots (described in preprint), and the soybean and wheat root crown images. Useful to see thresholding and physical resolution settings.

The simulated monocot and dicot root systems images and associated data are described in the preprint and available from Lobet et al. here:

Lobet, Guillaume, Koevoets, Iko, Noll, Manuel, Tocquin, Pierre, Meyer, Patrick E, Pagès, Loic, & Périlleux, Claire. (2016). Library of simulated root images, with different noise levels [Data set]. Zenodo.

https://zenodo.org/record/208214

Statistical Analysis

Rcode_allData.zip - Contains a single .R text file with code to reproduce all statistics and data figures. Contains several .CSV data files used by the R code. Assumption for running is that R code and data files are in the same working directory and setwd() is set there. Also, libraries needed are called at the top of the script and need to be previously installed.

Hardware Plans

RhizoVision_Crown_Hardware_Plans_Details.pdf  - For completeness, hardware plans for the RhizoVision Crown platform as described in the manuscript are included. Currently, we recommend the following camera and lens to use in this system:

Basler 5472 monochrome usb camera

https://graftek.biz/products/basler-aca5472-17um

This Moritex 25 mm lens:

https://graftek.biz/products/moritex-ml-u2515sr-18c?

⇒ Version 2 of this repository includes updates based on peer-review of the manuscript. New versions of physical_validation_wires.zip and Rcode_allData.zip were uploaded.

⇒ Version 3 of this repository includes updates based on peer-review of the manuscript. A new version of Rcode_allData.zip was uploaded.