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Title: An image processing and analysis tool for identifying and analysing complex plant root systems in 3D soil using non-destructive analysis: Root1
Contributor(s): Flavel, Richard  (author)orcid ; Guppy, Christopher  (author)orcid ; Rabbi, Sheikh M R (author); Young, Iain  (author)
Publication Date: 2017
Open Access: Yes
DOI: 10.1371/journal.pone.0176433Open Access Link
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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.
Publication Type: Journal Article
Source of Publication: PLoS One, 12(5), p. 1-18
Publisher: Public Library of Science (PLoS)
Place of Publication: United States
ISSN: 1932-6203
Field of Research (FOR): 080106 Image Processing
070306 Crop and Pasture Nutrition
080306 Open Software
Socio-Economic Outcome Codes: 961402 Farmland, Arable Cropland and Permanent Cropland Soils
820507 Wheat
820503 Grain Legumes
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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Appears in Collections:Journal Article
School of Environmental and Rural Science

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