RT Journal Article
SR Electronic
T1 RhizoVision Explorer: Open-source software for root image analysis and measurement standardization
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.11.439359
DO 10.1101/2021.04.11.439359
A1 Anand Seethepalli
A1 Kundan Dhakal
A1 Marcus Griffiths
A1 Haichao Guo
A1 Gregoire T. Freschet
A1 Larry M. York
YR 2021
UL http://biorxiv.org/content/early/2021/04/11/2021.04.11.439359.abstract
AB Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter, and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing, and reliable measurements. The default broken roots mode is intended for roots sampled from pots or soil cores, washed, and typically scanned on a flatbed scanner, and provides measurements like length, diameter, and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth, and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest, and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a novel copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous, and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements, and provide a foundation for collaborative improvement and reliable access to all.Competing Interest StatementThe authors have declared no competing interest.