Rhizo-II Root Biometrics Suite

The Rhizo-II Root Biometrics Suite

[The EZ-Root-VIS Pipeline]

The Rhizo-II Root Biometrics Suite is a software package for Windows platforms that includes both a new version of the popular EZ-Rhizo program and Root-VIS, an application for visualisation and analysis of root system architecture (RSA) data acquired by EZ-Rhizo.

The software is ideally suited for developmental and phenotypic descriptions of individual plants and plant species, accessions, and mutants, and of growth under varying nutritional and environmental conditions. It facilitates new research perspectives in the areas of functional genomics, breeding and QTL analysis, and in predictive analysis of plant performance.

The two programs share a common graphical user interface (GUI) and data can easily be shared between them using databases built using XML.

Background

The EZ-Rhizo application enables the analysis of images of roots grown on two-dimensional media such as agar plates. The program provides a semi-automated system for root detection, measurement of multiple parameters relevant to the root architecture, data storage and data analysis.

The Root-VIS application provides rapid and informative visualisations of comparative averages extracted from RSA datasets acquired by the EZ-Rhizo program (and other software); the program also produces numerical output, in a choice of formats, which can be used as source data for more detailed analysis elsewhere.

Download/Installation

You can download the software installers from either of the following links, depending on your operating system:

For 32-Bit Windows: https://www.psrg.org.uk/download/Rhizo-32.msi
For 64-Bit Windows: https://www.psrg.org.uk/download/Rhizo-64.msi

Note: For Windows running on ARM64 machines, you will need to install the 32-Bit Package

(If you’re not sure which type of Windows you have, then try the 64-bit installer first: this will not work if your platform is 32-bit! However, the 32-bit version will install on 64-bit platforms, but with lower overall performance.) The files are Microsoft Installer Packages; either “Save” the relevant one to your local PC then double-click, or you can “Run” from the website (if your browser gives you the option). The software should work on any version of Windows from XP (Service Pack 3) onwards: Vista, 7, 8.1 and 10 (in ‘Classic Desktop’ mode). There is not (yet) a version for Mac OSX but the software should run under “Parallels” (Windows on Mac). Note: If you have problems running the installer (MSI) package, then there may be a problem with your Windows system settings; in such cases, you can try this fixer tool from Microsoft.

For help, general enquiries or further information, please feel free to contact the EZ-Rhizo team at the following e-mail: ez-rhizo@psrg.org.uk.

The Rhizo-II Root Biometrics Suite is available free of charge for use in academic research institutions; however, registration/activation of the software is required. When publishing data collected, or analyses made, using the software, please cite:

Zaigham Shahzad, Fabian Kellermeier, Emily M. Armstrong, Simon Rogers, Guillaume Lobet, Anna Amtmann and Adrian Hills: “EZ-Root-VIS – A Software Pipeline for the Visual Reconstruction of Averaged Root System Architecture” Plant Physiology, 2018, 177:1368–1381 (DOI: 10.1104/pp.18.00217; PMID: 29895611).

Release Notes

V-2.4.4.3 (June, 2018): Initial publication of the Rhizo-II Root Biometrics Suite.

V-2.4.4.12 (July, 2018): Fixed issue in XL-Orate (single variant trait table with ‘separate worksheet’ option had no output data). Added the “Files and Folders” Settings Property Page. Added preliminary database editing options. Addressed issues with Windows XP (32-bit) and improved performance on Windows 8.1 and 10 (64-bit) platforms.

V-2.4.5.10 (August, 2018): Fixed issues with the Print, Print Setup and Print Preview dialogue boxes. Moved the development platform entirely to Visual Studio 2017 (MFC V-14.0).

V-2.4.6.2 (September, 2018): Fixed (hopefully) issues with importing data from RSML files, for plants with lateral roots. Also, added the Box/Plate “Rescale” command for database editing.

V-2.4.6.4 (October, 2018): Removed some minor bugs from the “Settings” property sheets and added “Save” and “Load” options thereto.

V-2.4.6.6 (January, 2019): Significant performance improvements by adopting new features of the ISO C++ 2017 standard. Better visual interface on Windows 8.1 and 10, especially with high-resoultion screens (‘DPI Aware’). A new (faster, more robust) “Skeletonisation” algorithm, adapted from that provided by Image-J (there is an option to continue using the original method).

V-2.4.7.1 (May, 2019): Reported problems with the “Image Editing” tools (such as crashes/hangs caused by memory allocation issues) have been addressed. Also, much of the code for processing editing operations has been made substantially quicker.

V-2.4.8.3 (July, 2019): A number of database display options have been made more efficient, as has the process of creating new analyses from database entries, in the Root-VIS program. We continue to add improvements in the visual presentation, especially when using newer, ‘High DPI’ screen displays.

V-2.4.9.6 (September, 2020): A number of 'minor' bugs and discrepancies in the user interface have been addressed, along with some underlying issues caused by upgrading to a newer version of the MSVC compiler. Also, there is now an updated Digital Certificate in use for code-signing the programs and the installer package.

V-2.5.0.4 (March, 2021): This release fixes a significant bug whereby creation of Collection Analyses in the Root-VIS program would sometimes merge two or more genotypes or media types. It also adds a number of minor corrections and improvements to the general code base (incorporating improvements to conform to more modern C++ coding practices).

V-2.5.2.4 (Christmas, 2021): In this release, the way that the XL-Orate plug-in handles different default file formats has been improved. Also, the ‘saved location’ of the pop-up dialogue boxes in the EZ-Rhizo program is checked, to ensure that it is available/visible on the current desktop.

V-2.5.4.0 (Summer, 2022): This release fixes an issue that prevented plug-in modules from working properly on 32-bit platforms, and also consolidates a number of minor corrections and some significant efficiency improvements. It was built using a major update of the Visual Studio toolchain.

V-2.5.6.3 (Summer, 2023): A bug in determining file creation/modification times – which caused the program(s) to crash when attempting to export analyses to RSML format – has been fixed.

V-2.5.8.0 (Winter, 2023): The bug that was preventing activation codes generated for one version of the software from working with (some) newer versions has (hopefully) been addressed.

V-2.6.1.6 (Summer, 2024): This release is, essentially, a ‘consolidation’ of a number of minor, internal changes and (hopefully) improvements. These are largely matters of ‘style’ changes that make the source code more conformant to modern C++ programmiong standards and more ‘compatible’ with newer versions of Microsoft Visual Studio and Windows operting systems.