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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

0

z

Maize in loamy sand, resolution 44.23Âľm

Greyscale intensity distribution

255


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

Inside

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 =

?

t=


Wheat Rice Tomato


Downwards Growing Roots


Upwards Growing Roots


Back-Tracking


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