ANNOUNCEMENTS |
MIDTERM: Scheduled for 10/28/2014 during normal class period. Open books and open notes. Bring calculators.
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 |
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 |
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:
Grade | Minimum percentage | Grade | Minimum percentage | Grade | Minimum percentage |
A | 95% | A- | 90% | ||
B+ | 85% | B | 80% | B- | 75% |
C+ | 70% | C | 65% | C- | 60% |
D+ | 50% | D | 45% |
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 |
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 | HW3 discussion |
4 | Fundamentals of Ultrasound Imaging | 10/21/2014 | 10/28/2014 | 35 | HW4 discussion |
5 | Image Filtering and Enhancement | 11/06/2014 | 11/18/2014 | 40 | HW5 discussion |
6 | A Complete Image Analysis Chain | 11/18/2014 | 12/02/2014 | 45 | HW6 discussion |
LINKS |
Here is a collection of some links I found interesting: