Images and statistical analysis of alfalfa root crowns from inside and outside disease rings caused by cotton root rot

This repository contains raw image data of root crowns imaged using the backlit RhizoVision Crown platform of alfalfa plants from either inside or outside disease rings caused by cotton root rot for a manuscript to be submitted. Data files and the R scripts are included for complete statistical analysis associated with the imaged root crown set.

Please cite both this repository and below journal article if reusing this data for a publication.

Manuscript Title: Digital imaging to evaluate root system architectural changes associated with soil biotic factors

Authors: Chakradhar Mattupalli, Anand Seethepalli, Larry M. York, Carolyn A. Young

Journal Article: https://doi.org/10.1094/PBIOMES-12-18-0062-R (open access)

Image Files

afalfa_roots_raw_images.zip - 264 images in PNG format directly from a monochrome camera with gamma at 3.9 to make near-segmented raw images in greyscale

alfalfa_feature_images.zip - 264 images in PNG format with a subset of computed features overlaid

alfalfa_segmented_images.zip - 264 black and white, binary images in PNG format that result from simple thresholding of the raw images

I_scale_1.png - an image of a 6 inch ruler for extracting pixel to physical unit conversion

metadata.csv  - metadata output from RhizoVision Analyzer with diameter ranges and other options used for image analysis

Statistical Analysis

alfalfaCRR_features_10012018.csv - extracted features from RhizoVision Analyzer v1.0.3 - called by name in R script

RootArchitectureFieldStudyimagetoIDmap.csv - mapping of image file names to plot identity - called by name in R script

manuscript complete root rot RVC analysis.R - R script with all analysis that used the data from the imaged root crowns