RhizoVision Analyzer


Noble Institute

Overview

Measured variables length, surface, shape, count, convex-hull
Operating system windows
Licence open-source, freeware
Automation level automated
Plant requirements any
Export formats csv
Other information

Scientific article(s)

RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping
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
Plant Phenomics, 2020 View paper

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Description

RhizoVision Analyzer was developed for use with the RhizoVision Crown phenotyping platform. The hardware platform suspends root crowns in front of a backlight with a monochrome camera facing the light in order to capture the root crown silhouette as a greyscale image. Analyzer has no other dependencies, simply download the ZIP file, extract to a folder on your local drive, and run the executable. Analyzer is designed for Windows 10 systems with a 64-bit processor. RhizoVision Analyzer is open-source and released under the GPL 3 license. The source code is available on GitHub. A folder of greyscale images is batch processed by Analyzer using a user-defined greyscale thresholding value. The user may optionally choose to invert the image, save the segmented image, save a feature image that graphically overlays some of the measured features on the segmented image, provide the 'pixels per mm' for conversion of pixel units to physical units, and to set diameter thresholds for fine, medium, and coarse roots. Overall, 27 extracted features are output to a CSV file ready for data analysis. In addition, a metadata CSV file is output that contains all user-defined settings for that batch process. While intended for use with the RhizoVision Crown platform for root crown phenotyping, users should have no problems using Analyzer for any 'complete' root system greyscale or segmented image. Note that Analyzer is designed to only analyze the largest component in the image (the root crown), and is therefore not suitable for disconnected scanned roots. A manual is included in the ZIP file.

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