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X-Ray Âľ-Computed Tomography for Plant Root Phenotyping Stefan Mairhofer, Susan Zappala, Saoirse R. Tracy, Craig Sturrock, Malcolm Bennett, Sacha J. Mooney, and Tony Pridmore

University of Nottingham, UK.

X-Ray µ-Computed Tomography • General purpose sensor capable of providing rich descriptions of complex objects/situations • Images values reflect target density • Non-destructive • Captures root systems in three-dimensional space • Can visualise roots and soil simultaneously

Imaging Issues: Sample Exposure • Typical dose for modern scans of plant and soil samples is 0.1 – 20 Gy • Most evaluative studies on seeds • 10Gy at germination reduces shoot elongation and flowering (Johnson 1936) • BUT Plants show much higher tolerance after germination • Repeated exposure over 10 days at 7+ Gy produced no effect (Tracy et al, in prep)

Imaging Issues: Water Content • Increased water content makes root and soil density similar, what is the ideal water content for root/soil segmentation? • Samples were scanned over 9 days while drying from saturation

• (Manually) segmented volumes compared with root washing – At saturation root and soil become (near-) indistinguishable – In dry soil, air pockets add image noise – Root volume was most accurately recovered after 3 days drainage: at approximately field capacity Zappala et al, under review

Image Analysis Challenges • Similar density of roots, water and pore spaces Roots

Pore space

Pore space Root material Soil Soil Maize in loamy sand, resolution 44.23Âľm

Intensity Variation of Roots

Soil depth



Maize in loamy sand, resolution 44.23Âľm

Greyscale intensity distribution


Threshold-based Segmentation

Wheat in sand, resolution 28.75Âľm

A Tracking Approach • Volumetric dataset is stored in a three-dimensional grid of voxels • Can be considered as a stack of images that are traversed from top to bottom • Allows analysis to be focussed and adaptive

Root Shape Detection • Level set method • Implicit representation of an object‘s shape • Interface motion is controlled by a properly defined velocity function


Outside F

Example of Moving Interface

Root Tracking • Statistical analysis based on Jensen-Shannon divergence

• Compute the distance between two probability density functions – Root model – Actual data in the current image

t +1 =



Wheat Rice Tomato

Downwards Growing Roots

Upwards Growing Roots


Root Systems of a Tomato

Mairhofer et al, submitted

Coming Soon....

Coming Soon....

Coming Soon....

The Rhizosphere Facility

The Rhizosphere Facility • £4M of investment • Three scanners • Scans from 0.5 µm to 5 mm resolution • Samples up to 25 cm diameter & 1 m length • Automated sampling system enabling 4-D visualisation • Automated root imaging via RooTrak

New Building opening early 2013

European Plant Phenotyping Network Partner 7: UNOTT

WP11 Transnational access

Installation 1: Vertical Confocal

Installation 2: RootTrace

Installation 3: MicroCT

Installation 4: SCREENGlasshouse

Installation 5: SCREENField

Unit of Access: 1/2 day Min Access: 70

Unit of Access: 1 day Min. Access: 45 days

Unit of Access: 1 day Min. Access: 70 days

Unit of Access: 1 day Min. Access: 75 days

Unit of Access: 1 day Min. Access: 75 days

RootTrace is software and associated image acquisition robots forming together a highthroughput device for analysing root system structure and growth in agar plates with a size of 12 or 24 cm (Capacity: 400 plants)

High Resolution X-ray microComputed Tomography for 4D phenotyping of root geometries and soil properties

Installation with a highthroughput large plant root analysis system in glasshouses with a capacity of 100 – 250 plants for root architecture in soil-filled columns (15 cm diam x 100 cm) to confirm root architecture from seedling screens

Installation for root assessments on a plot-scale in field experiments from soil cores of 42 mm width and 120 cm length extracted using a hydraulic soil corer

Installation for confocal microscopy specially developed for non-invasive, high resolution analysis of live root cells and tissues growing vertically on agar plates(12 or 24 cm)

X-Ray mu-computed tomography for plant root phenotyping  

PDF of the talk at the PhenoDays 2012 in Wageningen, NL