on the development of predictive models of light
TRANSCRIPT
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On the Development of
Predictive Models of Light Interaction with
Organic and Inorganic Materials
Lecture Series
Gladimir V. G. Baranoski
Natural Phenomena Simulation Group
School of Computer Science
University of Waterloo, Canada
National Institute of Informatics -Tokyo - 2012
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Schedule of Lectures
Predictability: Benefits and Costs
Data Collection: Finding the Pieces of Jigsaw Puzzles
Model Design: Balancing Reality and Abstraction
Evaluation: The Key for Assessing “Real” Contributions
Interdisciplinary Applications: Technical and Political Barriers
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Data Collection: Finding the Pieces of Jigsaw Puzzles
Lecture 2
Gladimir V. G. Baranoski
Natural Phenomena Simulation Group
School of Computer Science
University of Waterloo, Canada
National Institute of Informatics -Tokyo - 2012
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Outline
What data?
Biophysical Data Constraints
Characterization Data Constraints
Evaluation Data Constraints
Getting Our Own Data
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What data?
What are the main steps leading to predictive models?
• The crossing of field boundaries
• The use of scientifically sound development frameworks
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“Good science requires both theory and data –
one is of little use without the other.”
G. Ward (1992)
In our case, what data?
• Biophysical data Refractive indices, absorption coefficients, etc …
• Characterization data Thickness, concentration of pigments, etc …
• Evaluation data Reflectance, transmittance, etc …
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Outline
What data?
Biophysical Data Constraints
Characterization Data Constraints
Evaluation Data Constraints
Getting Our Own Data
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Biophysical Data Constraints
Scarcity
• Spectral refractive indices (real and complex)
Example: simulation of light interactions with sand
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Often, only average single values are available in the literature
for example, mesophyll of soy leaves = 1.42
Leaf Cross-Section
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Although Gladstone and Dale law can be used to obtain spectral indices, it also suffers from data unavailability issues
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• Specific absorption coefficients
Example: “the chlorophyll case”
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Measured (LOPEX)
Modeled (LAS) Modeled (DFA)
Modeled (PAS)
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Light Absorption Spectroscopy (LAS)
Light Absorption Spectra
(Zscheile and Comar, Botanical Gazette 1941,
Zscheile et al., Plant Physiology 1942)
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Measured (LOPEX)
Modeled (LAS)
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Data Fitting Approach (DFA)
DFA Absorption Spectra for chlorophyll a+b
(Jacquemoud et al., Remote Sensing of Environment 1996)
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Measured (LOPEX)
Modeled (LAS) Modeled (DFA)
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Photoacoustic Absorption Spectroscopy (PAS)
Photoacoustic Spectrometer
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Photoacoustic Absorption Spectra
(Nagel et al., Biological Role of Plant Lipids 1989)
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Measured (LOPEX)
Modeled (LAS) Modeled (DFA)
Modeled (PAS)
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Remark: same issues apply to the carotenoids ...
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… and are worse for tannins and anthocyanins
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Reliability issues: in vivo vs. in vitro
→
In vivo
pigments
In vitro
pigments
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• Sieve and detour effects
• Spectral shifts
chloroplast
Cross-Section of a Plant Leaf Chlorophyll Solution
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• Biophysical data derived from inversion procedures
Inversion procedure: a way to derive biochemical and optical
properties from in situ and non-invasive measurements
“Inversion” implies a reversal of the usual process of calculating
reflection and transmission
Was the model fully evaluated?
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Outline
What data?
Biophysical Data Constraints
Characterization Data Constraints
Evaluation Data Constraints
Getting Our Own Data
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Characterization Data Constraints
Scarcity
• Structural parameters affecting light and matter interactions
Skin Surface
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venation systems and hairs
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sand grains (dimensions, shape and roundness)
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red blood cells (volume and contour)
RBCs (SEM)
RBC Cross-Section (sketch)
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tissue thickness
Leaf Cross-Section
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Human Skin Diagram
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• Pigment contents
Example: in human skin, light absorption comes mostly from
a natural pigment, melanin, found in organelles (melanosomes)
inside cells (melanocytes) located in the epidermis
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Melanin is produced by the melanocytes through
a photobiological process: melanogenesis
The amount of melanin produced is determined by
both genetic factors and exposure to sunlight (UV)
Melanin absorption level depends on the number
of melanosomes per unit volume
e.g., 1.3% for lightly
pigmented specimens
e.g., 43% for darkly
pigmented specimens
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Types of melanin present in the epidermis
red/yellow phaeomelanin
brown/back eumelanin
b-carotene is also present in the epidermis
(Jacques, Tech. Rep. OMLC 2001)
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The dermis layer can be divided into two main layers:
the papillary dermis (smaller blood vessels)
the reticular dermis (larger blood vessels)
Absorption comes from blood borne pigments:
hemoglobin, bilirubin and b-carotene
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The two types of hemoglobin (oxygenated and deoxygenated)
give blood its reddish color
Volume fraction of blood in the dermal tissues can vary roughly in
the range 0.2-7% range
(Prahl, Tech. Rep. OMLC 1999)
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Bilirubin
an orange-yellow pigment derived from the degradation of
hemoglobin during the normal and abnormal destruction
of red blood cells
excessive amounts in the characteristic
jaundice (yellowish) appearance
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• Subsurface scattering data
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Scattering data is usually limited to a few wavelengths
Example: skin subsurface measurements performed by
Bruls and van der Leun (1984)
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Stratum corneum
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Epidermis
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Outline
What data?
Biophysical Data Constraints
Characterization Data Constraints
Evaluation Data Constraints
Getting Our Own Data
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Evaluation Data Constraints
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Scarcity
• Spectral databases rarely include the specimen’s
characterization data
Noteworthy example: Leaf Optical Experiments 1993 (LOPEX’93)
thickness
fresh and dry weights
concentration of absorbers (chlorophylls, carotenoids,
cellulose, lignin and protein)
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Reflectance Curves of a Corn Leaf
LOPEX
ABM-U
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Qualitative descriptions
• How these descriptions really relate to material parameters?
Example: human subjects and pigmentation
African
Caucasian
Indian
Asian
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African Indian
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Caucasian Asian
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How about tanned specimens?
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How about blood flow conditions?
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Measurements are usually limited to a few incidence and
collection geometries
Reflectance and Transmittance Measurement Geometries
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Scattering measurements are usually limited to a few
representative cases
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Often, the following pieces of measurement related information
are omitted from publications:
• angle of incidence
• collection geometry
• spectral resolution (for reflectance and transmittance)
• wavelength of interest (for scattering measurements)
• spectral characteristics of the light source
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Measured data is rarely available electronically
Blood Scattering Data at 613 nm
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How can we extract this data?
BRDF Data for a Soybean Leaf
(Woolley, Plant Physiology 1971)
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Outline
What data?
Biophysical Data Constraints
Characterization Data Constraints
Evaluation Data Constraints
Getting Our Own Data
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Getting Our Own Data
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• Investments
Equipment
Space
Time
• Benefits
Control
Contributions
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• Investments
Equipment
Space
Time
• Benefits
Control
Contributions
(Chen and Baranoski, Optics Express 2008)
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• Investments and benefits may increase considerably when
it comes to scattering measurements
BTDF and BRDF Measurement Arrangements
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• Investments and benefits can increase even more when
comes to human data
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Iridal Spectral Data
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In our search for data, we cannot lose sight of something
even more fundamental:
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This concludes Lecture 2!
Thanks!
Questions?
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Credits: Images and Photos
• J. Rokne
• D. Yim
• B. W. Kimmel
• A. Krishnaswamy
• T.F. Chen
• D. Eng
• L. Northam
• A. Baranoski
• S. Jacquemoud
• F. Imai
• C. Carvalho
• M. Oliveira
• V. Pamplona