ENGG 4620/6620: Biomedical Imaging

ANNOUNCEMENTS

SUMMARY

Biomedical Imaging (3): Fundamental principles and applications of noninvasive imaging modalities in medicine (X-rays, tomography, magnetic resonance, ultrasound); computer methods and algorithms for image processing, enhancement and analysis.

Class schedule:
Fall Semester, Tue/Thu 5:00 to 6:15 pm in 213 Driftmier
Computer lab: 310 Driftmier

CONTENTS

INTRODUCTION

Hardly any development in Medical Sciences has revolutionized medicine as much as the discovery that it was possible to look into the body without cutting. A hundred years ago, Conrad Wilhelm Röntgen discovered the X-rays. Since then, noninvasive imaging of the body literally got a new dimension with the invention of 3D tomography. CT and MRI allow to acquire cross-sectional images and to obtain three-dimensional reconstructions of structures. Two additional modalities will be covered, positron emission tomography (PET), which allows the imaging of tissue function. Particularly in conjunction with MRI, it allows new insights in the function of the brain. Ultrasound is a different modality. It is based on sound wave reflection, and its advantages are the relatively inexpensive equipment, and the radiation-free principle.

These fascinating techniques are the topic of this class. We will look at the physical principles of X-rays and magnetic resonance, as well as ultrasound imaging. The goal of this class is to understand physics and technology of those imaging modalities. The second half of the semester is dedicated to image processing and analysis. Most modern modalities rely heavily on computer processing of the measured data. Some image processing methods are inherent to the modality, such as the filtered backprojection in computed tomography or the Fourier transform of the k-space matrix in MRI. Of course, the computer can do more than provide the reconstructed images. Spatial measurements (e.g. the size of an embryo in ultrasound) and density (e.g. bone mineral density in osteoporosis) can easily be performed. The computer can also aid in enhancing image quality, suppression of noise and other artifacts, or in segmenting an object of interest - the separation of that object from surrounding image regions. The class will cover the four important steps of image enhancement, segmentation, quantification, and visualization.

SYLLABUS

Lecture block Topic
1 Introduction to Biomedical Imaging
History and development of Biomedical Imaging
2 X-rays: Physics and instrumentation
X-ray tubes, detectors, X-ray attenuation in tissue
Film, image intensifiers, detectors
3 Quantitative X-ray imaging
4 The Fourier transform
5 Computed Tomography: Principles
Reconstruction algorithms
Instruments and aplications
6 MRI: Physical foundations
Precession and spin echo
Gradient encoding
image reconstruction
7 Image processing: Fundamentals
Image representations:
from matrices to false-coloring
8 Filtering concepts (1) The convolution operation
9 Filtering concepts (1) Convolution filters
Convolutions. Smoothing, sharpening, background removal
Laplacian, Robert's Cross, Kirsch, Sobel, Canny edge, Frey and Chen
10 Filtering concepts (3) Fourier filters
Fourier transformation; spectrum interpretation
Lowpass and highpass filters
11 Filtering concepts (4) Morphological operators
Rank filter; erosion, dilation, opening, closing; skeletonization
12 Statistical representation of images
Histogram manipulation
13 Segmentation methods
Basic thresholding
14 Segmentation methods
Automated thresholding, hysteresis thresholding,
Region growing & Watershed segmentation
15 Image quantification
Density and size quantification
Shape quantification

BOOKS

Medical Imaging Technology by M.A. Haidekker, SpringerBriefs in Physics (2013)
Disclaimer: The author does not get royalty payments from the sale of this book

In addition, you need to obtain Chapters 2 and 3 of the book
Advanced Biomedical Image Analysis (M. Haidekker),
John Wiley & Sons, 2011
Follow this link to access the chapters on-line through our library


Recommended further reading:

Geoff Dougerty: "Digital Image Processing for Medical Applications",
Cambridge 2009, ISBN 978-0-521-86085-7
Excellent book that combines both the physics of imaging modalities and the computer processing steps needed for image formation and for further image processing. This book is a great complement for the class notes and strongly recommended.

Essential Physics of Medical Imaging
by G. Bushberg et al.
Lippincott Williams & Wilkins
This textbook covers all aspects of medical image acquisition. Presents an understanding of the theory and applications of the science including basic concepts, X-ray imaging, ultrasound, MRI, nuclear medicine, radiation protection, radiation dosimetry, and radiation biology. Abundant illustrations. This book is directed at students with a medical background.

The Image Processing Handbook
by John C. Russ
CRC Press
A very comprehensive and extensive book covering all aspects of image processing in Engineering and Science. Unfortunately, this comes at a relatively high price.

Digital Image Processing Algorithms and Applications
by Ioannis Pitas
Wiley-Interscience
This book is a good reference for those of you who are interested in actually programming those algorithms. It provides lots of C source code. However, algorithms are limited to entry-level image processing methods.

Magnetic Resonance Imaging: Physical Principles and Sequence Design
by E. Mark Haacke, Robert W. Brown, Michael R. Thompson, Ramesh Venkatesan
John Wiley & Sons
For those of you who really want to get into MRI, this book provides even more in-depth MRI knowledge, covering the special area of sequence design for specific medical and research applications

COMPUTER LAB

If you have a Linux computer, please let me know and we'll install Crystal Image on your computer. If not, you will get access to a computer in Lab 310 which runs Crystal Image (cimage).

GRADING

The grade will be based about equally on the homeworks, the midterm exam, and the final exam. You will receive score points based on the fill-the-bucket principle, i.e. for each homework assignment and for each test, you accrue score points. Your final grade will be determined from the score you achieved relative to the maximum score achievable. Typically, you receive a maximum of 20 points per homework, and 100 points per test, resulting in a maximum score of around 300 points.

We use a fixed grading system. There will be no adjustment based on the overall class performance. To earn a passing grade, you will have to achieve an overall score of at least 45%. The following table shows the percentage of your score you need to reach for a specific grade:

GradeMinimum percentage GradeMinimum percentage GradeMinimum percentage
A95% A-90%   
B+85% B80% B-75%
C+70% C65% C-60%
D+50% D45%   

If you reach a cumulative score of 90% or more through homeworks and Midterm by the last day of classes, you may opt out of the Final. Your grade will then be based on your cumulative score in percent of the achievable score up to that point. To opt out of the Final, you need to let me know before the last day of class.

RESOURCES

Click here to enter the resources page. On this page, you will find items for download, such as the Scion Image program and photocopied texts. You will have to obtain the password for CSEE 4620 in order to access this page.

OFFICE HOURS

Office hours TBD or by individual appointment in my office 404 Driftmier.
The best way to ask questions is to join the discussion thread for each homework (see link under
Homeworks)

HOMEWORKS

Fall 2014 homework assignments

No. Homework Date assigned Date due Maximum Score Discussion thread
1 X-ray principles 9/02/14 9/09/14 25 HW1 discussion
2 Playing with the discrete Fourier transform 9/11/14 9/18/14 20 HW2 discussion
3 Computed Tomography Reconstruction 9/30/14 10/07/14 30 HW2 discussion

LINKS

Here is a collection of some links I found interesting:

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