nicolai -3d visualizationucce.ucdavis.edu/files/datastore/234-2480.pdf · 2013. 3. 11. · lewis...
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AutoCAD autoModellenCFDSystembuild
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Applying new visualization techniques to construct 3-D geometrical plant models
B. Nicolaï
University of Leuven - Belgium
Antoni van Leeuwenhoek1632-1723
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Techniques• X-ray (micro) Computed Tomography• Magnetic Resonance Imaging (MRI)• Neutron tomography• Confocal microscopy( CLSM)• Optical coherence tomography (OCT)• Ultrasound tomography• …
X-ray tomography: principle X-ray generation
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http://www.celnav.de/hv/hv5.htm
Detection of X-rays• Photographic plate• Geiger counters• Scintillators
o Materials such as NaI convert X-ray photon to VIS photon
o VIS photon amplified using photomultiplier• Scintillator screens
o Imaging using line or CCD camera
Interaction with matter• Absorption depends on
o Compositiono Sizeo Energy level
• Beer’s law
with I : intensity of beam at position x
I0 : intensity of beamμ : linear attenuation coefficient
0 exp( )I I xμ= −
I
I0
x
3-D reconstruction
Intensity
3-D reconstruction
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3-D reconstruction
Intensity
+ + = Reconstruction
Real
Types of X-ray equipment• Radiography (2D)• CT scanners (3D)• X-ray computed micro-tomography (3D > 1μm)• Synchrotron radiation X-ray tomography (3D < 1μm)
Examples of (μ)CT• CT images obtained with medical CT scanner
o Fast scan times !o Low res
Els Herremans, unpublished
• Changes of internal air space during fruit development
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• Vascular system in apple • Disorders in apple during commercial storage
Braeburn browning disorder Verde doncella watercore
Nov. Dec. Jan. W.coreSound
Herremans et al. (2013) Postharvest Biol. Technol. 75
ESRF (France)
sample
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Verboven et al. Plant Physiol. 2008;147:518-527
Apple Pear
140 μm
• Individual apple cello Purple: cello Yellow: air space
300 μm
Pear Apple
• Rice stem
Complete image of an internode (nodes are indicated with the arrows)
Image of the aerenchymachannels (blue) and spongy tissue (cyan) across the internode
Detail of the aerenchyma (blue) and spongy tissue (cyan) at a node
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Central cavities (blue) in the internodes
Spongy tissue (cyan) in the node
Stem aerenchyma (blue) connecting with spongy
tissue (green) of internode
Geometric macroscale models
Geometric microscale models
Mebatsion et al. (2009) Journal of Food Engineering 93 (2009) 141–148
Geometric model (pear parenchyma) Synchrotron microtomography
Geometric model (pear intercellular space)
Synchrotron microtomography
Mebatsion et al. (2009) Journal of Food Engineering 93 (2009) 141–148
Cell growth models
Parenchyma tissue Intercellular space
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symplast + cell wall air space pear cortex+ =
Virtual skin apple tissue Synchrotron tomography of apple skin tissue
Application: gas transport in apple
Ho et al. (2008) PLoS Comp Biol 4 (3), art.nr. e1000023, -.Ho et al. (2011) Plant Phys 155 (3), 1158-1168
Conclusions• 3-D essential for certain geometrical features• X-ray micro and nano CT perfect for micrometer resolution
3-D imaging• Submicron resolution now possible with benchtop micro CT• Synchrotron CT necessary when fast imaging, very high
resolution or phase contrast imaging is required• Image processing very time consuming• Reconstructed images basis for engineering computations
Acknowledgements• Metadel Abera• Thijs Defraeye• Els Herremans• Hibru Mebatsion• Quang Tri Ho• Maarten Hertog• Pieter Verboven
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'What is the use of a book', thought Alice, 'without pictures or conversations?'
LEWIS CARROLL, Alice in Wonderland