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Zygmunt Wróbel
v
Preface
Modern methods of infrared, visible light or UV-light imaging are used in many
fields of science, starting with astronomy through biophysics, physics, geography
and ending with medicine. One such method allowing for imaging in a wide
wavelength spectrum is hyperspectral imaging. The use of this type of imaging
provides ample opportunities not only in terms of the qualitative assessment of
acquired images but also in their quantification. The possibility of quantitative
assessment is the result of analysis performed in the software provided with
hyperspectral cameras. However, due to the large amount of data, this software has
numerous limitations and is user-friendly in a limited way. On the other hand, there
are well-known methods of 2D image analysis and processing. Their implemen-
tation in hyperspectral imaging is not an easy task. Apart from the need to extend
2D images into the third dimension (in which respect there are known methods of
image analysis and processing, but in visible light), there remains the issue of
optimization. It concerns optimization of computational complexity, optimization
of analysis time and performance of preliminary calculations commonly used by
users. The tasks that need to be solved by the users analysing hyperspectral medical
images are also specific by their very nature. The specificity of these images stems
directly from the inter-individual variability in patients and thus the images anal-
ysed. For this reason, for almost any task in question, object segmentation,
comparison, calculation of characteristics, individual profiling of an algorithm are
extremely important. Dedicated algorithms enable to conduct automated, repeatable
measurements of, for example, a specific disease entity. However, profiled
(dedicated) algorithms also have drawbacks—data overfitting. Therefore, these
methods must be tested on images acquired under different conditions, with dif-
ferent hardware settings and for different operators, for example, a hyperspectral
camera. Only in this case, it is certain that the proposed new algorithm will meet the
requirements of universality when it comes to the data source and manner of
acquisition and will be profiled for a particular application. Therefore, the key
element is not only to propose new dedicated methods of hyperspectral image
analysis and processing but also to try to implement them in practice and test their
properties.
vii
viii Preface
First, I would like to thank Dr. Sławomir Wilczyński from the Medical University of
Silesia in Katowice for the inspiration and consultations in the area of dermatological
issues covered in the monograph. I would also like to thank Mr Raphael Stachiewicz
from Enformatic Sp. z. o. o., Poland, for providing the hyperspectral camera. It
allowed me to test the developed algorithms and perform measurements for objects
other than medical ones.
I also thank Prof. Zygmunt Wróbel from the University of Silesia in Katowice,
Poland, for his daily support and consultations.
ix
Contents
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Purpose and Scope of the Monograph . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 State of the Art . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 Basic Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4.1 Coordinate System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4.2 Evaluation of the Classifier Quality. . . . . . . . . . . . . . . . . . . 4
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2 Image Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3 Image Pre-Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.1 Affine Transformations of the Image . . . . . . . . . . . . . . . . . . . . . . . 23
3.2 Image Filtration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.2.1 Non-Adaptive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
3.2.2 Adaptive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.3 Image Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.4 Preliminary Version of the GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.5 Block Diagram of the Discussed Transformations . . . . . . . . . . . . . 35
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4 Image Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.1 Diagnostic Expectations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.2 Tracking Changes in the Shape of an Object . . . . . . . . . . . . . . . . . 40
4.3 Basic Analysis of Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.4 Block Diagram of the Discussed Transformations . . . . . . . . . . . . . 67
4.5 Measurement of Additional Features . . . . . . . . . . . . . . . . . . . . . . . 67
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
xi
xii Contents
5 Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
5.1 Decision Trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
5.2 Naive Bayes Classifier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.3 Discriminant Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.4 Support Vector Machine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.5 Receiver Operating Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.6 Pitfalls and Limitations of Classification . . . . . . . . . . . . . . . . . . . . . 98
5.7 Blok Diagram of the Discussed Transformations . . . . . . . . . . . . . . 105
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
6 Sensitivity to Parameter Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
6.1 Respositioning the ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
6.2 Resizing the ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
6.3 Rotation of the ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
6.4 The Other Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
7 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Selected Symbols
m,u Row
n,v Column
i Number of the image in a sequence—wavelength
L(m,n,i) Point of the matrix of the image L
L(C) Image resulting from conditional operations
L(D) Image which complements the image L
LBIN Binary image
LGRAY Image in grey levels
Erosion symbol
Dilation symbol
! Neighbourhood type
h Filter mask
pr Threshold
δg Measurement error
σ Standard deviation of the mean
θ Angle of inclination of the filter
A Amplitude
ACC Accuracy
B Number of bits of an image
FN False negative
FP False positive
I Number of images in a sequence
M Number of rows in a matrix
N Number of columns in a matrix
SE Structural element
SPC Specificity
TN True negative
TP True positive
TPR True positive rate
xiii
Chapter 1
Introduction
The purpose of this monograph is to present new and known modified methods of
hyperspectral image analysis and processing and profile them in terms of their
usefulness in medical diagnostics and research, as well as develop quantitative
diagnostic tools that can be used in everyday medical practice. The algorithms
proposed in this monograph have the following characteristics:
• they are fully automatic—they do not require operator intervention, if it is
necessary to provide additional parameters of the algorithm operation, they are
selected automatically,
• the results obtained on their basis are fully reproducible,
• their operation was tested on a group of several thousands of hyperspectral
images,
• they were implemented in Matlab,
• they have an open and tested source code attached to this monograph (in the
form of an external link),
• they can be freely extended and modified—owing to the open source code.
The scope of the monograph includes medical images and, in particular, der-
matological ones. However, they are only used to test the discussed methods. The
scope of the monograph is divided into acquisition, image pre-processing, image
processing and their classification presented in the following chapters.
1.2 Material
The subject of hyperspectral image analysis and the imaging method itself has been
known for many years. On the day of writing this monograph, the end of 2016, the
PubMed database contained 1922 publications containing the word “hyperspectral”
in the title or description. Slightly different numbers (the number of articles) were
given by the AuthorMapper database, namely 1825 publications, 18,643 authors
from 6105 institutions. A breakdown by countries, institutions, authors, journals
and subjects (the first 5 are listed) is presented in Table 1.1.
As shown above, the leaders in terms of publications on hyperspectral imaging
are the United States, author Chang Chein-I and the area of Computer Science with
1420, 56, 1299 publications respectively. Image Processing and Computer Vision is
a particularly exploited subject, which is extremely important from the point of
view of this monograph. This subject includes such areas as (the number of pub-
lications is given in parentheses): Signal, Image and Video Processing (39); Journal
of Real-Time Image Processing (37); Reference Recognition and Image Analysis
(27); Hyperspectral Imaging (26); Real-Time Progressive Hyperspectral Image
Processing (26); Neural Computing and Applications (25); Advances in Visual
Computing (22) Image Analysis and Recognition (22); Image and Signal
Processing (22); Multiple Classifier Systems (20); Machine Vision and
Applications (19); Hyperspectral Data Compression (17); Advanced Concepts for
1.3 State of the Art 3
Table 1.1 The first 5 countries, 5 institutions, 5 authors, 5 journals, 5 subjects related to the word
“hyperspectral”
Country United China Germany India France
States
Number of 1420 [1–5] 995 [6–10] 455 [11–15] 347 [16–20] 311 [21–25]
publications
Institution Chinese Zhejiang University of University of Wuhan
Academy of University California Maryland University
Sciences
Number of 162 [26–30] 67 [31–34] 64 [35–40] 47 [41–44] 43 [44–50]
publications
Author Chang, Graña, Manuel Sun, Da-Wen Goodacre, Wang, Liguo
Chein-I [51, [53, 54] [55–58] Royston [59, [61, 62]
52] 60]
Number of 56 29 21 18 18
publications
Journal Precision Journal of the Environmental Analytical Environmental
Agriculture Indian Society of Monitoring and and Earth Sciences
Remote Sensing Assessment Bioanalytical
Chemistry
Number of 144 [63, 64] 140 [65, 66] 100 [67, 68 91 [69, 70] 77 [71, 72]
publications
Subject Computer Life Sciences Artificial Earth Image
Science Intelligence Sciences Processing and
(incl. Robotics) Computer
Vision
Number of 1299 [73, 960 [75, 76] 908 [77, 78] 859 [79, 80] 830 [81, 82]
publications 74]
Classifiers were usually induced by using the training data representing 2/3 of the
total number of data. The remaining 1/3 of the data was used to test the classifier
quality [96]. The training and test data were divided randomly. In the cases pre-
sented in this monograph, the division can be distorted. This is due to the fact that
1.4 Basic Definitions 5
1-R
2-G
3-B
both the training and test vectors result from calculations for a sequence of images.
The number of images in the sequence to be analysed is affected by the operator.
Therefore, it does not have to be a strict division into 1/3 and 2/3. In each case,
evaluation of the classifier quality was based on determination of four values:
• False Positive (FP)—cases incorrectly classified as positive,
• False Negative (FN)—cases incorrectly classified as negative,
• True Positive (TP)—positive cases classified correctly,
• True Negative (FN)—negative cases classified correctly.
On their basis, sensitivity TPR and specificity SPC were defined as [97, 98]:
6 1 Introduction
TP
TPR ¼ 100% ð1:1Þ
TP þ FN
TN
SPC ¼ 100% ð1:2Þ
TN þ FP
TP þ TN
ACC ¼ 100% ð1:3Þ
TP þ TN þ FP þ FN
The parameters SPC and TPR will be the basis for creating the receiver operating
characteristic curves (ROC), which are graphs of changes in TPR as a function of
100-SPC [99]. Additionally, the area under the curve (AUC) will be calculated
[100].
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