August 28, 2019 Dataset Open Access

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

York, Larry; Anand Seethepalli; Haichao Guo

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.

Manuscript title: RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping

Authors: Anand Seethepalli, Haichao Guo, Xiuwei Liu, Marcus Griffiths, Hussien Almtarfi, Zenglu Li, Shuyu Liu, Alina Zare, Felix B. Fritschi, Elison B. Blancaflor, Xue-Feng Ma, Larry M. York

Preprint: https://www.biorxiv.org/content/10.1101/569707v2

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 conducted with RhizoVision Analyzer software available at:

https://zenodo.org/record/2585892#.XWgN8eNKiUk

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.

⇒ 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.