Biometrics Software


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.


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.


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, In Press (DOI: 10.1104/pp.18.00217; PMID: 29895611)

For enquiries and further information about EZ-RHIZO, please e-mail


EZ-Rhizogenerates a large amount of morphological parameters for main root and all orders lateral roots. Thus, EZ-Rhizo works best with MySQL and the database buttons allow the user to add data (txt files), and to query measured and derived RSA parameters (saved as csv files). However, for R users, a direct communication between the R interface and the database is possible; for this purpose, the DBI and RMySQL packages need to loaded. Then use the following script:

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

V- (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.

V- (July, 2018): Added preliminary database editing options. Addressed issues with Windows XP (32-bit) and improved performance on Windows 8.1 and 10 (64-bit) platforms.

(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 will run under “Parallels” (Windows on Mac).