CS 4490z/4460z Project Topics Fall 2009

Robarts Institute Topics (taken)

contact: John Moore, jmoore@robarts.ca

Title: A software platform for augmented reality guidance of percutaneous medical procedures.
Background: State of the art clinical practice for percutaneous vascular access and peripheral nerve blocks involves the use of 2D ultrasound to guide a needle to its target. However, it is often difficult for the clinician to clearly identify both the target tissue and the needle tip simultaneously. This can lead to inaccurate and potentially dangerous delivery of medication. We have developed an augmented reality guidance system that integrates 2D ultrasound into a 3D virtual reality environment by using a magnetic tracking system to monitor the location of the ultrasound transducer and needle in 3D space. This system makes it possible to accurately monitor the needle tip location relative to the ultrasound fan at all times.
Project goals: Currently our augmented reality software system is built into a much broader software package (AtamaiViewer) that uses Python classes and wrapper classes with the Visualization Toolkit (VTK, a powerful, open source C++ graphics library). Our goal is to redevelop the needle guidance system into a stand-alone application.
The Student will be responsible for: Adapting the current software application (in python and VTK) into a stand-alone application in C++ (using VTK) Performing standard software engineering techniques for testing and debugging: this will involve using ultrasound, video capture utilities, as well as magnetic tracking technology in our laboratory at Robarts Research Institute modifying the application based on the recommendations of clinicians
Work space will be provided in our Image Guided Surgery Laboratory for software development and testing, as well as ample opportunities for consultation and exposure to a wide range of medical imaging and guidance technologies. The project offers a wonderful opportunity to apply object-oriented programming principles in a graphics-intensive medical application.

Prof. Mike Katchabaw's Topics

katchab@csd.uwo.ca

Area: gaming, multimedia, and such. A few things in particular:
- Porting some of our current music-generation software to other platforms. This could include Java Mobile Edition (it's standard edition now), C++ under Windows, and so on ...
- Character/story synthesis for video games. This would involve the extension of existing work and taking things in new directions.
- Looking into augmented reality applications. (Examples can be provided ...)

Prof. John Barron's Topics

barron@csd.uwo.ca

Matlab code for implementaing some optical flow techniques.
project1.pdf
project2.pdf

Prof. Lucian Ilie's Topics

ilie@csd.uwo.ca

C++ code for an industry internship project concerning DNA sequence analysis using mass spectrometry for a biotech company. If interested, please contact ilie@csd.uwo.ca for details.

Cross Canada projects (deadline passed)

contact: Prof. Greg Wilson, gvwilson@cs.utoronto.ca

more info at: http://ucosp.wordpress.com/

If you want to choose one of these, you must contact Greg Wilson BEFORE Labor Day (Sep.7)!
Also, you'll need a co-supervisor from Western and keep me informed about everything.

Dr. Peter Rogan's Topics

progan@uwo.ca

1. Implementation of algorithms for development of genomic probes for human genetic disease diagnosis
To identify unique, single copy sequences in human nucleic acid probes, confounding hybridization from interspersed repetitive sequences must be eliminated. This project involves development of distributed software (C++ or other high level language) to deduce single copy sequences which obviates the need to compare a genomic sequence with a comprehensive database of repetitive sequence family members. Parameter optimization will exploit biologically-defined, repeat sequence interspersion lengths. This would represent an improvement over current methods, since unrecognized repetitive sequences absent from the repeat sequence catalog can lead to a lack of genomic specificity. Successful development of a prototype will result in an offer of internship with a London genomics company.
2. Resource for in silico splicing mutation analysis
Candidate genes that contribute to complex disease phenotypes have revealed an abundance of genetic variants that may contribute to these disorders, many of which reside in non-coding regions and commonly alter mRNA splicing. Information theory-based models are related to splice site strength, changes in information can be used to predict mRNA splicing phenotypes (eg. benign polymorphisms can be distinguished mutations; determination of mutational severity.) We have developed software to detect genome-wide changes in splice site information. This project will enhance capabilities of our automated splice site information server by: adding SNP and exon information tables derived from recent human, mouse, and rat genome releases, developing additional models of splicing regulatory factors, adding exon naming and coordinate schema; and improving server performance by accelerating sequence retrieval and matrix computation procedures.

Prof. Bob Webber's topics

webber@csd.uwo.ca

In general, my interests are in software projects where execution speed is the primary focus and the task is either cpu-bound, memory-bound, or disk-bound. I am also interested in projects that explore the capabilities of existing publically available programs in the following areas (with associated wikipedia links): If you have other ideas, feel free to contact me at webber@csd.uwo.ca including 4490 in the subject line.

Prof. Mahmoud El-Sakka's topics

elsakka@csd.uwo.ca

Still-Image compression
It is widely believed that a picture is worth more than a thousand words. However, dealing with digital pictures (images) requires far more computer memory and transmission time than that needed for plain text. To be able to "efficiently" handle the huge amount of data associated with images, compression schemes are needed.
In this project, the details of few still-image compression schemes will be provided. The student will be asked to implement these schemes and compare their performance.
This project can accommodate more than one student, where each student will be given different set of still-image compression schemes to implement.

Prof. Jamie Andrews's topics

andrews@csd.uwo.ca

Johar is a package which lets programmers develop accessible applications -- that is, applications that can be accessed easily by people with disabilities (blind people, quadruplegics, etc.) as well as non-disabled people. After about 1 person-year of development, we are still just getting started. We need developers to further improve interface interpreters and to write more example applications. Any ideas are welcome.

Prof. Eric Schost's topics

eschost@csd.uwo.ca

Fast arithmetic on long integers The GNU Multiprecision Library (GMP) offers a variety of functions for long integers, mostly based on fast multiplication algorithms. The purpose of this project is to hack into this library and modify a few functions, to provide extra functionalities that are missing right now.