An image processing and analysis tool for identifying and analysing complex plant root systems in 3D soil using non-destructive analysis: Root1

Richard J. Flavel, Chris N. Guppy, Sheikh M.R. Rabbi, Iain M. Young

Research output: Contribution to journalArticlepeer-review

51 Scopus citations

Abstract

The objective of this study was to develop a flexible and free image processing and analysis solution, based on the Public Domain ImageJ platform, for the segmentation and analysis of complex biological plant root systems in soil from x-ray tomography 3D images. Contrasting root architectures from wheat, barley and chickpea root systems were grown in soil and scanned using a high resolution micro-tomography system. A macro (Root1) was developed that reliably identified with good to high accuracy complex root systems (10% overestimation for chickpea, 1% underestimation for wheat, 8% underestimation for barley) and provided analysis of root length and angle. In-built flexibility allowed the user interaction to (a) amend any aspect of the macro to account for specific user preferences, and (b) take account of computational limitations of the platform. The platform is free, flexible and accurate in analysing root system metrics.

Original languageEnglish (US)
Article numbere0176433
JournalPloS one
Volume12
Issue number5
DOIs
StatePublished - May 1 2017

Bibliographical note

Publisher Copyright:
© 2017 Flavel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences

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