Teaching in Fall 2014
Biomedical Imaging & Analysis (BIA)
Offered at: SYSU-CMU Joint Institute of Engineering
Instructor: Prahlad G Menon, PhD
Course Description:
The goals of this course are to familiarize students with biological and medical imaging data from various imaging modalities (eg: Magnetic Resonance Imaging (MRI), X-ray Computed Tomography (CT), Fluoroscopy, Ultrasound and Optical Systems for Microscopy), how these data are acquired as well as how to process 2D, 3D and 4D (3D + time) data for quantification and visualization purposes using contemporary software tools and open-source libraries (including, SimpleITK, ITK, VTK). Additionally, this course integrates these image-processing concepts their real-world applications from the fields of mechanical and biomedical engineering, including computational simulation of mechanics or flow for improved medical diagnosis, treatment & image-guided surgery.
Students will build a strong fundamental mathematical and programming background in regard to formulating and implementing complex image processing pipelines, while appreciating the nuances of the basic mathematical principles such as linear algebra, Fourier theory, statistics, machine learning etc. in the context of advanced signal processing settings. Major image-processing topics covered will include basic image filtering and de-noising, feature detection, medical and biological image segmentation, registration, shape characterization as well as biomarker extraction and validation. Finally, the tools and techniques learned during this course will be applied by students at a systems level with the goal of building image-processing pipelines to solve a practical bioimaging problem through an independent project. At the end of the course, students will be equipped with theoretical and practical skills in medical image analysis and visualization, including skills relevant to general image processing such as quantification of data and classification.
Faculty Course Evaluation (Fall 2014)
J1-791, SYSU-CMU JIE (click image below to download PDF)
ANNOUNCEMENTS:
Final Projects Conference
Thursday, 4 Dec 2014, Image Processing Algorithms & Pipelines
On Thursday, 4 December 2014, J1-791 will culminate with a conference where each of the 13 project teams in the class will present their class projects on biomedical image / signal processing algorithms and image / signal processing pipelines, which cumulatively represent applications of a subset of topics covered during the course of the semester. These projects which are based on image / signal processing algorithms are all strongly related to their real-world applications from the fields of biomedical engineering and computer vision, and cover a range of interesting topics ranging from tumor detection in magnetic resonance images and segmentation of computed tomography images to characterization / classification of disease from medical data and development of mobile applications to demonstrate feasibility of complex image processing pipelines. We look forward to seeing you at the conference on 4 December.
Conference Agenda:
1) Poster Session (Noon to 1:00 pm) Thursday, 4 Dec. :
VENUE: Main lobby, SYSU-CMU JIE building, SYSU East Campus, Guangzhou, China.
2) Oral presentation session (1:00 pm to 3:00 pm) Thursday, 4 Dec. :
VENUE: Lecture Hall(Rm 102), First Floor, SYSU-CMU JIE building, SYSU East Campus, Guangzhou, China.
Seven presentations, each 12 minutes long with 3 minutes for Q&A, starting at 1:15 pm.
Join us Online, using the following BlueJeans link:
www.bluejeans.com/174356879
Just want to dial in? (all numbers)
1) Direct-dial with my iPhone or
+1 408 740 7256+1 408 740 7256
+1 888 240 2560+1 888 240 2560 (US Toll Free)
+1 408 317 9253+1 408 317 9253 (Alternate Number)
2) Enter Meeting ID: 174356879
Conference Agenda:
1) Poster Session (Noon to 1:00 pm) Thursday, 4 Dec. :
VENUE: Main lobby, SYSU-CMU JIE building, SYSU East Campus, Guangzhou, China.
2) Oral presentation session (1:00 pm to 3:00 pm) Thursday, 4 Dec. :
VENUE: Lecture Hall(Rm 102), First Floor, SYSU-CMU JIE building, SYSU East Campus, Guangzhou, China.
Seven presentations, each 12 minutes long with 3 minutes for Q&A, starting at 1:15 pm.
Join us Online, using the following BlueJeans link:
www.bluejeans.com/174356879
Just want to dial in? (all numbers)
1) Direct-dial with my iPhone or
+1 408 740 7256+1 408 740 7256
+1 888 240 2560+1 888 240 2560 (US Toll Free)
+1 408 317 9253+1 408 317 9253 (Alternate Number)
2) Enter Meeting ID: 174356879
Learning Objectives
Image Processing, Biomodeling and Visualization
The learning objectives of this course are:
• To introduce students the fundamentals of medical imaging, image processing, computational geometry, visualization and numerical methods for analysis of medical image data, as well as
• To expose students novel and advanced applications in computational biomedicine and other engineering fields.
Prerequisites: Basic vector calculus and linear algebra (or permission of the instructor), as well as a working knowledge of Matlab as well as either C++ or Python.
Text books:
1) Machine Vision, by Wesley E. Snyder & Hairong Qi, © 2004, ISBN 978-0-521-16981-3 (paperback) or 978-0-521-83046-1 (hardback)
2) Insight into Images: Principles and Practice for Segmentation, Registration and Image Analysis, edited by Terry S. Yoo, © 2004, ISBN 1-56881-217-5
• To introduce students the fundamentals of medical imaging, image processing, computational geometry, visualization and numerical methods for analysis of medical image data, as well as
• To expose students novel and advanced applications in computational biomedicine and other engineering fields.
Prerequisites: Basic vector calculus and linear algebra (or permission of the instructor), as well as a working knowledge of Matlab as well as either C++ or Python.
Text books:
1) Machine Vision, by Wesley E. Snyder & Hairong Qi, © 2004, ISBN 978-0-521-16981-3 (paperback) or 978-0-521-83046-1 (hardback)
2) Insight into Images: Principles and Practice for Segmentation, Registration and Image Analysis, edited by Terry S. Yoo, © 2004, ISBN 1-56881-217-5
Lab visits - Image Guided Surgical Navigation
Multiple lab visits will be scheduled during the semester to provide students with hands-on experience using image-guidance technology in the context of cardiovascular interventions. In one example, a mannequin heart will be accessed minimally invasively using a pericardial access needle introduced by sub-xyphoid access, under magnetic field image guidance.
Syllabus & Course Material, Fall 2014
Available upon request via email; write to: pgmenon@andrew.cmu.edu
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