Dataset Open Access

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

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

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

 

 

Files (128.1 MB)
Name Size
afalfa_roots_raw_images.zip
md5:d3cde92063dd6870903c1aedb94d1741
77.6 MB Download
alfalfa_feature_images.zip
md5:a8d9233b30f103e5a1c15d980110ff54
42.2 MB Download
alfalfa_segmented_images.zip
md5:3b715b8bed7367e75722c9f4026c8b40
7.8 MB Download
alfalfaCRR_features_10012018.csv
md5:87b527de7152c4409d8fd0ed68c44a8f
57.8 kB Download
I_scale_1.png
md5:5e6c105a847ea49313daab038e30516d
379.7 kB Download
manuscript complete root rot RVC analysis.R
md5:8fc20254a7a6fa3f92c192ce2126eb12
26.6 kB Download
metadata.csv
md5:b13f95440c64f19435b1d9ac1e466fa1
417 Bytes Download
RootArchitectureFieldStudyimagetoIDmap.csv
md5:e493a06af49374c77956f6f325be9614
9.8 kB Download
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