Basic Concepts: FOOD, U. Copenhagen, Denmark. WWW - Models.life - Ku.dk

19/11/2017
Introduction
Basic concepts
FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk
IMAGES
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Images
Chemical Image Definition
A chemical image is any image that gives chemical information
Medical Image Definition
A medical image is any image that gives medical information
Image Definition
An image is a representation of the external form of an object
Images
Images
Images are spatial (bi-dimensional) representations of an action or objects
The spatial dimensions are sub-divided by pixels
Every pixel is an entity (individual) that is influence:

- By its value
- By the values of the surrounding pixels
6 7 8 7 6
7 8.5 9 8.5 7
8 9 10 9 8
7 8.5 9 8.5 7
6 7 8 7 6
Where does that value come from?
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Images
Images
Images are spatial (bi-dimensional) representations of an action or objects
The spatial dimensions are sub-divided by pixels
Every pixel is an entity (individual) that is influence:

- By its value
- By the values of the surrounding pixels
Spatial Resolution
It is the length of the pixel IN BOTH SPATIAL DIRECTIONS
It is also important to consider the relative spatial resolution (area or length)
=
Images
Values on the pixels. Scientific information

Single channel images
Every pixel contains only one value
Usually ranged between limits
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Images

Color-space images. RGB images
Every pixel contains three values
Ranged between limits depending on the storage
The three values are combined to form real colors
Images

Multi-band images. Multi-spectral images
Every pixel contains a discrete number of values usually higher than 4
The values come from different types of sources
The sources are usually discrete wavelengths
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Images

Hyperspectral images
Every pixel contains a important number of values. Usually a spectrum
The values usually come from the same spectral source
Spectral resolution: Separation between wavelengths
Multiband images are also hyperspectral images
RGB Images
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Red Green Blue images
The visible radiation (400 – 750 nm)

The only radiation that we can perceive
The visible radiation (400 – 750 nm)

The human eye is sensitive to visible light at different rates depending of
day/night radiation
Day vision (cone sensors) Night vision (rod sensors)
BLUE GREEN RED GREEN
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Red, Green and Blue channels

Our digital cameras are based on human eye perception
Red, Green and Blue channels Blue

cyan
magenta
Green
Red yellow
GRAYSCALE
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Red, Green and Blue channels Blue

cyan
magenta
Green
Red yellow
FALSE COLOR PICTURES
RED GREEN BLUE
Color = Intensity
Red, Green and Blue channels

Every channel contains a maximum of fixed amount of values
It depends on the precision of the numbers and the storage capability
8 bites pictures  28 levels per channel  256 levels  2563 = 16777216 colors
Pure red = [255 0 0]

Pure green = [0 255 0]
Pure blue = [0 0 255]
16 bites pictures  216 levels per channel  65536 levels  655363 colors
There are many other precisions. This is known as color depth
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Other color spaces

There are many different ways of coding color
HSV (Hue – Saturation – value) and HSL (Hue – Saturation – Luminescence)
*Source: Wikipedia
Other color spaces

Lab (Luminosity – Red to Green – Blue gradient)
*Source: Wikipedia
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Other color spaces

YCbCr (Luma – croma in blue – croma in red)
What is JPEG:
*Source: Wikipedia
Some examples
Digital cameras
 High spatial resolution
 Problems with focal distance
 Problems with illumination
Flat-bed scanners
 High spatial resolution
 Fixed focal distance
 Fixed light source (tunable)
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The data and the analysis

There are three channels of information
Their combinations are analyzed
C1 = R – G
C2 = R – B
C3 = G – B
Mostly based on the Digital Imaging methods
Example: Detecting specific areas on an image and measuring properties
Steak_example.m
Sevilla_flower_example.m
MULTISPECTRAL IMAGING
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Multispectral images
Between RGB and Hyperspectral
Non-continuous spectrum
200
Specific spectral channels
Intensity (a.u.)
150
100
50
500 600 700 800 900
Wavelengths (nm.)
Multispectral technologies
Filter based cameras
Filter-based signals
Attenuation
Bandwidth
Easy to change the filters
From UV to NIR
Illumination issues
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Multi-objectives based cameras
Filter-based signals
Attenuation
Bandwidth
NOT easy to change the filters
Illumination issues
LEDs based cameras

LED system Acquiring the image
Ultra Blue 430nm Chlorophyll A
Blue 450nm Riboflavin, Chlorophyll B, Beta-carotene
Blue 470nm RGB Blue
Blue Green 505nm RGB green, Metmyoglobin
Green 565nm Myoglobin
Yellow 590nm Oxymyoglobin
Red 630nm RGB red, Metmyoglobin (weak)
Red 645nm Chlorophyll B
Red 660nm Oxidation, Chlorophyll A
Red 700nm Oxidation
NIR 850nm Baseline
NIR 870nm Baseline
NIR 890nm Fat shoulder (un-saturation)
NIR 910nm Protein (C-H)
NIR 920nm Carbohydrate (C-H)
NIR 940nm Fat
VideometerLab® NIR 950nm Valley (Carbohydrate, protein)
NIR 970nm Water
Very fast measurements of 18 channels

High spatial resolution
We cannot talk about spectral resolution  Only 18 specific wavelengths
Food Chemistry
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There might be many channels
Their combinations are analyzed
They are basically Hyperspectral Images, so they can be treated as such, with
several constraints in the spectral pre-processing
Common spectral indexes (Intensity at indicated nanometers)
Normalized difference vegetation (NDVI) = (800 - 640)/(800 + 640)
Green normalized difference vegetation (greenNDVI-I) = (550 - 640)/(550 + 640)

Green normalized difference vegetation (greenNDVI-II) = (800 - 550)/(800 + 550)
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Water band (WBI) = 950/900
Soil adjusted vegetation (SAVI) = ((800 – 649)*1.5)/(800 + 640 + 0.5)
Photochemical reflectance (PRI) = (531 - 570)/(531 + 570)
Red-edge vegetation stress (RVSI) = (714 + 752)/(2 – 733)
Modified chlorophyll absortion in reflectance

MCARI = [(700 - 670)-0.2*(700 - 550)]*(700/670)
Visible atmospherically resistant (VARI) = (550 - 640)/(550 + 640 - 4802)
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Hyperspectral Imaging
API
Lactose
Lubricants
Single spectrum for each x,y dimension
0.4
0.3
Absorbance
0.2
0.1
Types of radiations
0
-0.1
7000 6000 5000 4000
Wavenumber
y axis, N pixels
Single wavenumber image
Types of Measurements
x axis, M pixels
False color image
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Types of most common radiations in hyperspectral machinery
Visible region  400 – 750 nm Raman region  VIS-NIR
IR region  2500 - 50000nm / 4000 - 200 cm-1
NIR region  800 - 2500nm / 12500 - 4000 cm-1
Symmetrical Asymmetrical Bending

stretching stretching vibration
vibration vibration H-O-H
H-O-H H-O-H
Types of measurements: Pixel To Pixel (whisker-broom) scan
interferometer
interferometer
interferometer λ
lamp
Y
X
Difuse
Difuse
Difuse
reflectance
reflectance
reflectance
White light
sample
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Types of measurements: Line (push-broom) scan
y y y y
Dispersing
Dispersing Dispersing
Dispersing λ
filterfilterfilterfilter
λ λ λ λ lamp
Y
X
slit slit slit slit
White light
Difuse
reflectance
sample
Types of measurements: Plane scan. Global imaging
Focal plane Detector
Optics
lamp Y
x
Bandpass Filter (TF)
Difuse reflectance
White light
sample
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Types of measurements. The importance of illumination
Monochromator I
Sample
R
Source Detector I0
1 I ac
log  log 0 
R I s
Transmission Diffuse Reflection
I
T
I0
1 I
A  log  log 0  a  b  c
T I
Contrast
Dark Field Co-axial Difuse (I) Difuse (II)

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Some issues
Small pixel size

Big object size
Each pixel  mixed information
Penetration of the radiation
Illumination artifacts (shadows)
Depending on the slide*

Incident Diffusively
photons reflected
photons
Pixel size Pixel size
35% 28%
32% 42%
32% 28%
*Extracted from Image Analysis of Food Microstructure. John C. Russ. CRC PRESS. New York. 2005
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Some issues
It is mostly a SURFACE TECHNIQUE, Even though it penetrates a little
APPLICATIONS
(some)
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Some applications
MIR
Remote sensing
Forensics NIR NMR
Sorting Vis-NIR? Terahertz
Raman
Pharma Global Push-broom

Art Filters CCDs LEDs
Food
Quantitation
Resolution
Etc, etc, etc... Classification
Some applications
SPECTROSCOPY  LINE MAPPING – CONVEYOR BELT CONCEPT
An example  Detection of sugar ends in potatoes
EC3 Chemical system (http://www.chemical-imaging.com/index.html)
REAL-TIME
CONTROL
OF QUALITY
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Some applications
What are they doing here?
Fulfilled Quality parameters
GOO
D
Quality
BAD
Not fulfilled Quality parameters
Time or potatoe
Some applications
1) Data acquisition
2) Data pre-processing (handling of issues)
Calibration
3) Classification model (maybe PLS-DA) Internal validation
Prediction
4) Real time implementation + maintenance of the model
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Some applications
1) Data acquisition
2) Data pre-processing (handling of issues)
CHEMOMETRICS
3) Classification model (maybe PLS-DA)
Calibration
Internal validation
Prediction
4) Real time implementation + maintenance of the model
Some applications

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Some applications
EC3 Chemical system (http://www.chemical-imaging.com/index.html)
REAL-TIME
CONTROL OF
QUALITY
Some applications
Plastic sorting
- automated / robotic sorting units
- new hyperspectral sensor systems
- waste management systems
- generic tool for product designers to optimize the
end-of-life product.
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Some applications
Plastic sorting
Global model
Flame retardants
Some applications
Plastic sorting
False color image of the samples Identification of the samples
ABS PA6 PP PP
0.15 REF 2.02 2.02
100
PBT PBT ABS PBT
0.10 REF 0.2 0.1
200
ABS PS PP PS
0.15 0.9 REF REF
300
ABS ABS PS PA6
REF REF 0.9 REF
400
PA6 PS PP ABS
0.10 0.0 REF 0.10
500
PS PBT PS PS
0.7 REF 0.7 REF
600
50 100 150 200
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Some applications
Plastic sorting
Some applications
Plastic sorting - Pellets are individuals 
INTEGRATION SURFACE RESOLUTION WITH

SPECTRAL RESOLUTION
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Some applications
Plastic sorting - Pellets are individuals 
INTEGRATION SURFACE RESOLUTION WITH

SPECTRAL RESOLUTION
Some applications
Pharmaceutical production
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Some applications
Some applications
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Some applications
Some applications
Forensics
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Some applications
Forensics
Some applications
Forensics
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Some applications
Food production
Some applications
Food production  Bread
50
2
100
150
1
200
250 0
300
-1
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Some applications
Food production  Blue berries
CLASS 3 – CLASS 4
19 diffuse wavelengths 365-970 nm LED’s
Some applications
Food production  Blue berries
CALIBRATION VALIDATION
error rate = 0.01 error rate = 0.00
explained variance = 98% accuracy = 1
class 1: Specificity = 0.99; Sensitivity = 0.99; Precision = 0.99 class 1: Specificity = 1; Sensitivity = 1; Precision = 1
class 2: Specificity = 0.99; Sensitivity = 0.99; Precision = 0.99 class 2: Specificity = 1; Sensitivity = 1; Precision = 1
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Some applications
Food production  Coffee
Arabica Robusta
AS tr. set
RS tr. set
Some applications
Confocal microscopy
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Some applications
Confocal microscopy
Some applications
Remote sensing, precission agriculture
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Some applications
Post-harvesting
Some applications
MIR
Remote sensing
Forensics NIR NMR
It is extremely difficult to define a general Vis-NIR?
frameworkTerahertz
on
Sorting
hyperspectral image analysis.
Raman
It is strongly dependent on the application:
DOING WHAT in WHERE

Food
Quantitation
Resolution
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Some applications
MIR
Remote sensing
Forensics NIR NMR
Raman

Food
Quantitation
Resolution
Some applications
MIR
Remote sensing
Forensics NIR NMR
BUY MY BOOK! Raman

Food
Quantitation
Resolution
37

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19/11/2017

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Chemical Image Definition

A chemical image is any image that gives chemical information

Medical Image Definition

A medical image is any image that gives medical information

An image is a representation of the external form of an object

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

The spatial dimensions are sub-divided by pixels

Every pixel is an entity (individual) that is influence:

Where does that value come from?

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

The spatial dimensions are sub-divided by pixels

Every pixel is an entity (individual) that is influence:

It is the length of the pixel IN BOTH SPATIAL DIRECTIONS

It is also important to consider the relative spatial resolution (area or length)

Values on the pixels. Scientific information

Every pixel contains only one value

Usually ranged between limits

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Values on the pixels. Scientific information

Every pixel contains three values

Ranged between limits depending on the storage

The three values are combined to form real colors

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Values on the pixels. Scientific information

Every pixel contains a discrete number of values usually higher than 4

The values come from different types of sources

The sources are usually discrete wavelengths

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Values on the pixels. Scientific information

Every pixel contains a important number of values. Usually a spectrum

The values usually come from the same spectral source

Spectral resolution: Separation between wavelengths

Multiband images are also hyperspectral images

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

The visible radiation (400 – 750 nm)

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

The visible radiation (400 – 750 nm)

Day vision (cone sensors) Night vision (rod sensors)

BLUE GREEN RED GREEN

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

Red, Green and Blue channels

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

Red, Green and Blue channels Blue

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

Red, Green and Blue channels Blue

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

Red, Green and Blue channels

It depends on the precision of the numbers and the storage capability

Pure red = [255 0 0]

There are many other precisions. This is known as color depth

FOOD, U. Copenhagen, Denmark. www.models.life.ku.dk www.hypertools.org jmar@life.ku.dk

Red Green Blue images

Other color spaces