Biomedical Image Processing and Analysis

Fall 2014

original blurred low sampling edges

Resources page: For information on course resources for computer (matlab) assignments.
Engineering Information Technology: For information on computing resources in Engineering (circus, garage).
Yale Classes v2 server: For course information, under "Resources": slides, handouts, problem sets, etc.

Course Number BENG/EENG 445, ENAS 912
Course Title Biomedical Image Processing and Analysis
James Duncan (james dot duncan at yale dot edu)
Lawrence Staib (lawrence dot staib at yale dot edu)
Teaching Assistant
Gary Ho (gary dot ho at yale dot edu)
Contact for appointment.
Schedule TTh 4:00-5:15 at Becton 102


This course is an introduction to Biomedical Image Processing and Analysis covering image processing basics and techniques for image enhancement, compression, segmentation, registration and motion analysis. Students will learn the fundamentals behind image processing and analysis methods and algorithms with an emphasis on biomedical applications. This course is open to undergraduate and graduate students. We assume students have an understanding of linear systems (Eeng 310 or equivalent) and calculus up to differential equations. In addition, it is also helpful to have a familiarity with elementary probability theory. Please contact the instructors if you have questions regarding your preparation. There will be about ten homeworks and both a midterm and a final exam (during exam period). Homeworks will include Matlab programming assignments. Grading will be based approximately 1/3 on the homeworks, 1/3 on the midterm and 1/3 on the final. Undergraduates and graduates are graded separately; in addition, assignments may differ.


R. Gonzalez and R. Woods, Digital Image Processing, Prentice Hall (Book Website)

(On reserve in the Engineering Library.)

Chapters 1 and 2 online

Additional readings to be distributed during class.

Course Objectives:

Having successfully taken this course, you will be able to

Course Outline (dates/topics approximate), Fall 2010

Introduction (Read Gonzalez Ch. 1)
Sep 2 ls Intro/Organization
Fundamentals (Read Gonzalez Ch. 2)
Sep 7 ls Basics / Digitization (to be rescheduled)
Enhancement (Read Gonzalez Ch. 3)
Sep 9 ls Gray scale enhancement
Sep 14 ls Spatial Filtering
Sep 16 ls Spatial Filtering
Sep 21 ls Mathematical Morphology (Gonzalez Ch. 9.1-9.3)
Enhancement (Read Gonzalez Ch. 4)
Sep 23 jd Enhancement in the frequency domain
Sep 28 jd Enhancement in the frequency domain
Sep 30 jd Enhancement in the frequency domain
Compression (Read Gonzalez Ch. 8)
Oct 5 jd Compression
Oct 7 jd Compression
Rigid and Nonrigid Registration (Read handout)
Oct 12 ls Registration: Introduction and Transformations
Oct 14 ls Registration: Match Metrics
Oct 19 Registration: Match Metrics
Oct 21 Midterm Exam
Oct 26 ls Registration: Optimization and Interpolation
Oct 28 ls Registration: Robust
Motion (Read handout)
Nov 2 jd Motion
Nov 4 jd Motion
Segmentation (Read Gonzalez Ch. 10 and handout)
Nov 9 jd Segmentation
Nov 11 jd Segmentation
Nov 16 jd Segmentation
Nov 18 jd Segmentation
Nov 23 Thanksgiving Break
Nov 25 Thanksgiving Break
Nov 30 ls Diffusion Weighted Image Analysis
Dec 2 Review
Reading Period
Final Exam

Image Processing Links:

Gonzalez and Woods: Digital Image Processing
Image Database
Image Processing Tutorials

Tutorials on Image Analysis, Computer Vision
Image Processing (wikipedia)
Image Processing Tutorial
A-Z of Image Processing Concepts
efg 's Image Processing Page

One dimensional convolution demonstration: you can draw your own functions or select pre-defined ones.
Two dimensional filtering demonstration: first, Fourier transform, then view the magnitude log; apply gaussian smoothing or other filtering, then inverse transform.
Discrete Fourier Theory (1D)

Matlab Tutorials

Introduction to Image Compression

Image Motion Analysis Bibliography

Deformable Image Segmentation

Image Registration
Homogeneous Coordinates
Image Registration Bibliography

HIPR2: Image Processing Learning Resources with JAVA
Pilot European Image Proc. Archive

The Graphics File Format Page

Watermarking, steganography, information hiding
StirMark:Watermarking Robustness Test

Amara's Wavelet Page
Principles of Computerized Tomographic Imaging

Computer Vision Home Page
Computer Vision On-line Bibliography

Sep 2010