BME 404 | Course Introduction and Application Information - Department of Genetics and Bioengineering

Course Name

Biomedical Image Processing

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
BME 404	Fall/Spring	2	2	3	5

Prerequisites	None
Course Language	English
Course Type	Elective
Course Level	First Cycle
Mode of Delivery	-
Teaching Methods and Techniques of the Course	-
National Occupation Classification	-
Course Coordinator	Dr. Öğr. Üyesi Tannaz Akbarpour
Course Lecturer(s)	Dr. Öğr. Üyesi Tannaz Akbarpour
Assistant(s)	-

Course Objectives

The aim of this course is to provide students with a knowledge and understanding of fundamental principles of medical image enhancement, registration, classification, and segmentation.

Learning Outcomes

#	Content	PC Sub	* Contribution Level
#	Content	PC Sub	1	2	3	4	5
1	Define the principles and main technical aspects of medical imaging analysis
2	Explain the need for basic image processing techniques.
3	Describe fundamental approaches for enhancement of medical images
4	Describe fundamental approaches for segmentation of medical images.
5	Describe fundamental approaches for registration of medical images.

Course Description

Principles of acquisition, storage, visualization, and processing of medical image data. Sampling and quantization. Picture archiving and communication systems, Medical image formats. Basic and advanced image processing algorithms.

Course Category	Core Courses
	Major Area Courses
	Supportive Courses
	Media and Management Skills Courses
	Transferable Skill Courses

Week	Subjects	Related Preparation	Learning Outcome
1	Introduction and Overview	Lecture notes
2	Medical Imaging Technology	Chp 1, 6-8. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.1, SPIE Press
3	Medical Image Acquisition, Sampling, and Quantization	Lecture notes
4	Medical Image Storage, Archiving and Communication Systems and Formats	Chp 8-9. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.3, SPIE Press
5	Medical Image Processing, Enhancement, Filtering	Chp 4-5. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.2, SPIE Press
6	Medical Image Segmentation - I	Chp 2-3. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.2, SPIE Press
7	Medical Image Segmentation - II	Chp 2-3. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.2, SPIE Press
8	Review and Midterm Examination
9	Medical Image Registration - I	Chp 8. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.2, SPIE Press
10	Medical Image Registration - II	Chp 8. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.2, SPIE Press
11	Medical Image Visualization	Chp 1. "Handbook of Medical Imaging", Sonka and Fitzpatrick, Vol.3, SPIE Press
12	Medical Image Compression	Lecture notes
13	Medical Image Search and Retrieval	Lecture notes
14	Other Applications of Medical Image Analysis	Lecture notes
15	Evaluation of Term Projects
16	Final

Course Notes/Textbooks

Handbook of Medical Imaging, Medical Image Processing and Analysis (2009) by Milan Sonka and J. Michael Fitzpatrick, SPIE Press, ISBN: 0819477605.

Suggested Readings/Materials

Biomedical Signal and Image Processing (2005) by Kayvan Najarian and Robert Splinter, CRC Press, ISBN: 0849320992.\\nDigital Image Processing for Medical Applications (2009) by Geoff Dougherty, Cambridge Univ. Press, ISBN: 0521860857.\\nMedical Imaging Signals and Systems (2005) by Jerry L. Prince and Jonathan Links, Pearson, ISBN: 0130653535.\\nBiosignal and Medical Image Processing (2008) by John L. Semmlow, CRC Press, ISBN: 1420062301. Lecture slides will be distributed as softcopy.

Semester Activities	Number	Weigthing	LO 1	LO 2	LO 3	LO 4	LO 5
Participation
Laboratory / Application	4	20
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments
Presentation / Jury	1	5
Project	1	15
Seminar / Workshop
Oral Exams
Midterm	1	20
Final Exam	1	40
Total

Weighting of Semester Activities on the Final Grade		60
Weighting of End-of-Semester Activities on the Final Grade		40
Total

Semester Activities	Number	Duration (Hours)	Workload
Theoretical Course Hours (Including exam week: 16 x total hours)	16	2	32
Laboratory / Application Hours (Including exam week: '.16.' x total hours)	16	2	32
Study Hours Out of Class	16	2	32
Field Work			0
Quizzes / Studio Critiques			0
Portfolio			0
Homework / Assignments			0
Presentation / Jury	1	12	12
Project	1	12	12
Seminar / Workshop			0
Oral Exam			0
Midterms	1	12	12
Final Exam	1	18	18
		Total	150

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	To have adequate knowledge in Mathematics, Science and Genetics and Bioengineering; to be able to use theoretical and applied information in these areas on complex engineering problems.		-	-	-	-	-
2	To be able to identify, define, formulate, and solve complex Genetics and Bioengineering problems; to be able to select and apply proper analysis and modeling methods for this purpose.		-	-	-	-	-
3	To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose.		-	-	-	-	-
4	To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Genetics and Bioengineering applications; to be able to use information technologies effectively.		-	-	-	-	-
5	To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Genetics and Bioengineering research topics.		-	-	-	-	-
6	To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually.		-	-	-	-	-
7	To be able to communicate effectively in Turkish, both orally and in writing; to be able to author and comprehend written reports, to be able to prepare design and implementation reports, to present effectively, to be able to give and receive clear and comprehensible instructions.		-	-	-	-	-
8	To have knowledge about global and social impact of Genetics and Bioengineering practices on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Genetics and Bioengineering solutions.		-	-	-	-	-
9	To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in Genetics and Bioengineering applications.		-	-	-	-	-
10	To have knowledge about industrial practices such as project management, risk management, and change management; to have awareness of entrepreneurship and innovation; to have knowledge about sustainable development.		-	-	-	-	-
11	To be able to collect data in the area of Genetics and Bioengineering, and to be able to communicate with colleagues in a foreign language.		-	-	-	-	-
12	To be able to speak a second foreign language at a medium level of fluency efficiently.		-	-	-	-	-
13	To recognize the need for lifelong learning; to be able to access information, to be able to stay current with developments in science and technology; to be able to relate the knowledge accumulated throughout the human history to Genetics and Bioengineering.		-	-	-	-	-