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RhizoVision Analyzer v1: Software for high-throughput measurements from images of crop root crowns (deprecated)

Anand Seethepalli; Larry York

PLEASE READ. Note this is the original version of RhizoVision Analyzer and has been replaced by RhizoVisionExplorer which is highly recommended to use instead. This version will be maintained for reproducibility reasons for any work that has used it, but access will be restricted to avoid confusion. Results from the Whole root mode in RhizoVisionExplorer will match RhizoVision Analyzer very closely. Simply request access to RhizoVision Analyzer and it will be granted.

This is a batch processor only for root crowns as described below and has fewer GUI elements and options than the new version. Please contact me for access to a beta of RVA 2, or watch this space for the public release of the new version within a month or two. 

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. [Update 10-16-2020: the source code for Analyzer is available as an archival ZIP file on GitHub for v1]

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.

RhizoVision Analyzer was developed at Noble Research Institute, LLC. Anand Seethepalli was the lead programmer and Dr. Larry York was the principal investigator.

When publishing or presenting data generated using this software, please provide the citation for both this repository and the associated manuscript

Restricted Access

You may request access to the files in this upload, provided that you fulfil the conditions below. The decision whether to grant/deny access is solely under the responsibility of the record owner.

By requesting access, you are acknowledging you are aware this is older software that has been deprecated and replaced by RhizoVisionExplorer, which is recommended for future use. Analyzer should only be requested for reproducibility reasons.

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