CSE 554 Course Projects Fall 2012 CSE 554

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CSE 554 Course Projects Fall 2012 CSE 554 Course Project Slide 1

CSE 554 Course Projects Fall 2012 CSE 554 Course Project Slide 1

Basic Requirement • Using geometric algorithms to solve real-world problems in biomedicine – Not

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. , Image. J, Chimera) • Prototyping in Mathematica is recommended – A graphical user interface (GUI) may be required CSE 554 Course Project Slide 2

Algorithms that you will know… • Creating, processing, deforming, and analyzing geometry Segment Contour

Algorithms that you will know… • Creating, processing, deforming, and analyzing geometry Segment Contour Fair & Simplify Shape analysis Align (Before) CSE 554 Course Project (After) Slide 3

Finding a problem • Pick a problem mentioned by our guest speakers – Analysis

Finding a problem • Pick a problem mentioned by our guest speakers – Analysis of microtubule video – Registration of bone surface landmarks and/or regions • 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) CSE 554 Course Project Slide 4

Finding a problem • Example problems in the past DNA Gel Electrophoresis Analyzing Tool

Finding a problem • Example problems in the past DNA Gel Electrophoresis Analyzing Tool (Gabriel Stancu) CSE 554 Course Project Slide 5

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

Finding a problem • Example problems in the past Breast lesion segmentation (Noa Ben-Zvi) CSE 554 Course Project Slide 6

Finding a problem • Example problems in the past Measuring small bowel length (Billy

Finding a problem • Example problems in the past Measuring small bowel length (Billy Bennett) CSE 554 Course Project Slide 7

Finding a problem • Example problems in the past Analyzing 3 D cell shape

Finding a problem • Example problems in the past Analyzing 3 D cell shape in 2 -photon microscopy (Aron Lurie and Daniel Melzer) CSE 554 Course Project Slide 8

Finding a problem • Example problems in the past Registering deforming heart surfaces (Christopher

Finding a problem • Example problems in the past Registering deforming heart surfaces (Christopher Gloschat) CSE 554 Course Project Slide 9

Finding a problem • Avoid problems that are too simple – E. g. ,

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! CSE 554 Course Project Slide 10

Guidelines • Individual or in pairs – Requirements will be harder for team projects

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 CSE 554 Course Project Slide 11

Format • Project proposal – What is the problem, what are the required and

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 CSE 554 Course Project Slide 12

Timeline • Project proposal – Due by Thursday, Oct 25 (about three weeks away)

Timeline • Project proposal – Due by Thursday, Oct 25 (about three weeks away) – If you work on a new problem, discussion with Instructor prior to proposal submission is required. • Final presentations – Two dates: Tuesday, Dec 4 th and Thursday, 6 th – State your preference of these two dates in your proposal • Hand-ins – Due by midnight Tuesday, Dec 11 th CSE 554 Course Project Slide 13

Helpful Materials • 3 D programming – Open. GL: Industrial standard 3 D library

Helpful Materials • 3 D programming – Open. GL: Industrial standard 3 D library for C/C++ • The “red book”: Open. GL 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 Open. GL • Docs, samples, forums: http: //jogamp. org/jogl/www/ • GUI programming in C++ – Qt: http: //qt. nokia. com/products/ – FLTK: http: //www. fltk. org/ CSE 554 Course Project Slide 14