National Science Foundation (NSF) Research Experience for

National Science Foundation (NSF) Research Experience for Undergraduates (REU) Program MedIX Site: Medical Informatics DePaul University & Northwestern University June 18th –August 24th, 2007 NSF REU MedIX Program MedIX: Medical Informatics eXperiences in undergraduate research Goals: – promote the possibility of graduate studies for bright, talented undergraduates – promote and encourage interdisciplinary studies in Computer Science and Medical Informatics to undergraduate students NSF REU Program - 2006 4/15/2009 2 NSF REUs & IGERT National Science Foundation (NSF): - Research Experience for Undergraduates (REU) Program: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5517&from=fund - 2002: 18 CISE REU sites - 2007: 43 CISE REU sites (21 states) IGERT: Integrative Graduate Education and Research Traineeship Program http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=12759 NSF REU Program - 2006 4/15/2009 3 CTI Graduate Assistantships Funding Opportunities for graduate students: @CTI, DePaul University: – GAANN fellowships: – Graduate Assistance in Areas of National Need – http://www.ed.gov/programs/gaann/index.html – CTI assistantships – http://www.cti.depaul.edu/programs/PHDinCS.asp NSF REU Program - 2006 4/15/2009 4 NSF REU MedIX Program Benefits of doing research at the undergraduate level: • participation as part of a team • teams of two undergraduate students and one faculty mentor • work performed in research labs: – CTI Intelligent Multimedia Processing (IMP) lab – CTI Medical Imaging (MI) lab – Northwestern Imaging Informatics Center • collaborations with graduate students working on the projects NSF REU Program - 2006 4/15/2009 5 Summer 2005 NSF REU Program - 2006 4/15/2009 6 Summer 2006 NSF REU Program - 2006 4/15/2009 7 NSF REU MedIX Program Benefits of doing research at the undergraduate level: • active involvement with faculty mentors - three computer science faculty mentors (two females) and one medical doctor mentor - weekly meetings with the mentor - mentor availabilities: Monday: Dr. Furst, Tuesday: Dr. Channin, Wednesday: Dr. Raicu, Thursday: Dr. Dettori, Friday: all mentors NSF REU Program - 2006 4/15/2009 8 NSF REU MedIX Program Benefits of doing research at the undergraduate level: • participation in current and interdisciplinary research Example of a MedIX project from Summer 2006: Original Image Initial Seed at 90% Split & Merge at 85% Split & Merge at 80% Liver Segmentation: M. Pham, R. Susomboon, T. Disney, D. Raicu, J. Furst, “A Comparison of Texture Models for Automatic Liver Segmentation”, SPIE Medical Imaging Conference, San Diego, CA, February 2007. NSF REU Program - 2006 4/15/2009 9 NSF REU MedIX Program Benefits of doing research at the undergraduate level: • presentation, dissemination of results, rewards of publishing and attending conferences – Internal presentations: • Presentations at the Visual Computing Seminar (each Friday) • Mid-Program and Final program Presentations (July 19th and August 23rd) – External presentations: - Conferences in the medical imaging field NSF REU Program - 2006 4/15/2009 10 NSF REU Program • Number of students (2005, 2006) – 17 students • Open Source – Texture-based Medical Image Retrieval code on Sourceforge: http://brisc.sourceforge.net/ • CRA Outstanding Undergraduate Research Awards – 1 Honorable Mention Award 2006 • Publications – 12 papers, 2 abstracts and 3 posters NSF REU Program - 2006 4/15/2009 11 Medical Informatics (MediX) Site - 2007 • S. I. Greenblum, M. O. Krucoff, J. Furst, D. Raicu, “An Automated Approach to Image Analysis of Noisy Microarrays”, VISAPP 2007, International Conference on Computer Vision Theory and Applications, Barcelona, Spain, March 8-11, 2007. T. Disney, M. Lam, D. Raicu, J. Furst, D. Channin, “A Lookup and Reference Tool for Pulmonary Computed Tomography Nodules”, The 2007 Annual Meeting of the Society for Imaging Informatics in Medicine (SIIM 2007), Rhode Island, June 2007 (to appear). S. J. Talbot, P. Mongkolwat, T. R. Amirtha, D. S. Channin, “Advancing Advanced Visualization in the Clinical Environment”, The 2007 Annual Meeting of the Society for Imaging Informatics in Medicine (SIIM 2007), Rhode Island, June 2007 (to appear) . L. Dettori, A. Bashir, J. Hasemann, “Texture Classification of Normal Tissues in Computed Tomography using Gabor filters”, SPIE Medical Imaging Conference, San Diego, CA, February 2007. M. Pham, R. Susomboon, T. Disney, D. Raicu, J. Furst, “A Comparison of Texture Models for Automatic Liver Segmentation”, SPIE Medical Imaging Conference, San Diego, CA, February 2007. M. Lam, T. Disney, M. Pham, D. Raicu, J. Furst, R. Susomboon, “Content-Based Image Retrieval for Pulmonary Computed Tomography Nodule Images”, SPIE Medical Imaging Conference, San Diego, CA, February 2007. 4/15/2009 12 • • • • • NSF REU Program - 2006 Medical Informatics (MediX) Site – 2006 (1) • • A. Bashir, J. Hasemann, L. Dettori, "Gabor-based Texture Classification of Tissues in Computed Tomography”, DePaul Science Day, November 10th 2006 (poster). S. I. Greenblum, M. O. Krucoff, J. Furst, “A Fully-Automated Method for Microarray Image Analysis” , The Seventeenth (17th ) Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, Argonne National Laboratory, IL, November 2006 (Poster). A. Bashir, J. Hasemann, L. Dettori, "Using Decision Trees for Gabor-based Texture Classification of Tissues in Computed Tomography” , Workshop for Women in Machine Learning (WIML) Co-located with the Grace Hopper Celebration of Women in Computing, San Diego, CA, October 2006 (Poster). L. Semler, L. Dettori. and W. Kerr, "Ridgelet-based Texture Classification in Computed Tomography", The 8th IASTED International Conference on Signal and Image Processing, Honolulu, HW, August 2006. W. Kerr, L. Dettori, and L. Semler, "A Methodology and Metric for Quantitative Analysis and Parameter Optimization of Unsupervised, Multi-Region Image Segmentation", The 8th IASTED International Conference on Signal and Image Processing, Honolulu, HW, August 2006. • • • NSF REU Program - 2006 4/15/2009 13 Medical Informatics (MediX) Site – 2006 (2) • Semler, L. & Dettori, L. "Curvelet-based Texture Classification of Tissues in Computed Tomography," IEEE International Conference on Image Processing (ICIP06) Atlanta, GA, USA. October, 2006. L. Semler, L. Dettori, “A Comparison of Wavelet-based and Ridgelet-based Texture Classification of Tissues in Computed Tomography”, International Conference on Computer Vision and Applications, Portugal, February 2006. N.J. Backman, B.W. Whitney, J.D. Furst, D.S. Raicu, “A prioritized and adaptive approach to volumetric seeded region growing using texture descriptors”, Proceedings of SPIE Electronic Imaging, San Jose, CA, January 2006. S. Handrick, B. Naimipour, J.D. Furst, D.S. Raicu, “Binning Strategies Evaluation for Tissue Classification in Computed Tomography Images”, Proceedings of SPIE Medical Imaging Conference, San Diego, CA, February 2006. B.W. Whitney, N.J. Backman, J.D. Furst, D.S. Raicu, “Single click volumetric segmentation of abdominal organs in Computed Tomography images” , Proceedings of SPIE Medical Imaging Conference, San Diego, CA, February 2006. R. Lerman, D.S. Raicu, J.D. Furst, “Contrast enhancement of soft-tissues in Computed Tomography images”, Proceedings of SPIE Medical Imaging Conference, San Diego, CA, February 2006 • • • • • NSF REU Program - 2006 4/15/2009 14 NSF REU MedIX Program Benefits of doing research at the undergraduate level: • great source of recommendation letters for graduate school • glimpse into the life of a graduate student Activities of the REU Program (Summer 2007): http://facweb.cs.depaul.edu/research/vc/medix/2007/index.htm NSF REU Program - 2006 4/15/2009 15 What REU MedIX Students Say About Research NSF REU Program - 2006 4/15/2009 16