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CSE 554 Course Projects

CSE 554 Course Projects. Fall 2013. Basic Requirement. Using geometric algorithms to solve real-world problems in biomedicine Not limited to algorithms in the Modules Not necessary to completely solve the problem, but need to show sufficient progress towards a solution Distributable tool

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CSE 554 Course Projects

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  1. CSE 554Course Projects Fall 2013

  2. Basic Requirement • Using geometric algorithms to solve real-world problems in biomedicine • Not limited to algorithms in the Modules • Not necessary to completely solve the problem, but need to show sufficient progress towards a solution • Distributable tool • Implemented in mainstream languages: C/C++, Java, Python, etc., or as plug-ins to existing software (e.g., ImageJ, Chimera) • Prototyping in Mathematica is recommended • A graphical user interface (GUI) may be required

  3. Algorithms that will be covered… • Creating, processing, deforming, and analyzing geometry Fair & Simplify Segment Contour Shape analysis Align (Before) (After)

  4. Finding a problem • Pick a problem mentioned by our guest speakers • Breast / lesion segmentation from mammograms • Measuring thickness of subchondral bone from CT • Counting osteoblast cells in histological images

  5. Finding a problem • Where to look for your own topic: • Your friends who work on image-related research • Faculty in Med School, BME, Biology, Chemistry, etc. • Many faculty working on imaging can be found through Imaging Science Pathway: http://imagingpathways.wustl.edu/ • Open problems of current interest • Check for research papers in imaging-related conferences (e.g. MICCAI) and journals (e.g., IEEE TMI)

  6. Finding a problem • Example problems in the past DNA Gel Electrophoresis Analyzing Tool (Gabriel Stancu)

  7. Finding a problem • Example problems in the past Breast lesion segmentation (Noa Ben-Zvi)

  8. Finding a problem • Example problems in the past Measuring small bowel length (Billy Bennett)

  9. Finding a problem • Example problems in the past Analyzing 3D cell shape in 2-photon microscopy (Aron Lurie and Daniel Melzer)

  10. Finding a problem • Example problems in the past Registering deforming heart surfaces (Christopher Gloschat)

  11. Finding a problem • Avoid problems that are too simple • E.g., edge detection, image blurring, or anything that can be solved by a few Matlab/Mathematica/Python commands. • … or too hard • E.g., automatic segmentation of X, a complete system for doing Y, etc. • Talk to Instructor before turning in the proposal!

  12. Guidelines • Individual or in pairs • Requirements will be harder for team projects • Choose any language you prefer • Discussion with the instructor or guest speaker is encouraged

  13. Format • Project proposal • What is the problem, what are the required and wish-list features, and timeline of development. • Final presentation (80%) • A 10-minute in-class live demo of what you have accomplished • Hand-in (20%) • Source code, executable tool (or plug-in), and test data • Project report • Description of the algorithms, features of your tool, and how to use them • Any known bugs and future work

  14. Timeline • Project proposal • Due by Thursday, Oct 24 (two weeks away) • If you work on a new problem, discussion with Instructor prior to proposal submission is required. • Final presentations • Two dates: Tuesday, Dec 3th and Thursday, 5th • State your preference of these two dates in your proposal • Hand-ins • Due by midnight Tuesday, Dec 10th

  15. Helpful Materials • 3D programming • OpenGL: Industrial standard 3D library for C/C++ • The “red book”: OpenGL Programming Guide • Online version with code: http://www.opengl.org/documentation/red_book/ • Great tutorial lessons: http://nehe.gamedev.net/lesson.asp?index=01 • Jogl: Java bindings for OpenGL • Docs, samples, forums: http://jogamp.org/jogl/www/ • GUI programming in C++ • Qt: http://qt.nokia.com/products/ • FLTK: http://www.fltk.org/

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