Applications in image-based tracking

Intra-procedure image tracking is an essential component when developing systems to perform many image-guided interventions. Electromagnetic, optical and mechanical devices are typically used to track real-time imaging devices during the procedures. Pure image-based tracking is an alternative method that can be used to determine the position and the orientation of the imaging device via image registration. Low cost and compact design are the major advantages of this approach by eliminating the need for hardware tracking devices in the system. In the experiments described in this thesis, we used the transformation given by the mechanical tracking device to initialize the registrations. If the registration is performed without this initialization, it has to simultaneously

compensate for motion of the prostate as well as the motion of the TRUS probe. This would be a very challenging correspondence problem considering the limited information available in a single plane 2D TRUS image. If the prior knowledge of the prostate

anatomy and the prostate motion can be used to provide a reasonable initialization to the registration algorithm, that could help to make the registration problem more tractable

162

when only using the image information. Technical advancements in methodology for incorporating prior domain knowledge into the registration framework might help to achieve accurate and robust results that would benefit the development of software-based solutions and their widespread use for tracking purposes.

163

References

1. J. Bax, D. Cool, L. Gardi, K. Knight, D. Smith, J. Montreuil, S. Sherebrin, C. Romagnoli and A. Fenster, "Mechanically assisted 3D ultrasound guided prostate biopsy system," Med Phys 35, 5397-5410 (2008).

2. V. V. Karnik, A. Fenster, J. Bax, D. W. Cool, L. Gardi, I. Gyacskov, C. Romagnoli and A. D. Ward, "Assessment of image registration accuracy in three-dimensional transrectal ultrasound guided prostate biopsy," Med Phys 37, 802-813 (2010).

3. A. Peltier, F. Aoun, F. El-Khoury, E. Hawaux, K. Limani, K. Narahari, N. Sirtaine and R. van Velthoven, "3D versus 2D Systematic Transrectal Ultrasound-Guided Prostate Biopsy: Higher Cancer Detection Rate in Clinical Practice," Prostate Cancer 2013, 783243 (2013).

4. G. A. Sonn, S. Natarajan, D. J. A. Margolis, M. MacAiran, P. Lieu, J. T. Huang, F. J. Dorey and L. S. Marks, "Targeted Biopsy in the Detection of Prostate Cancer Using an Office Based Magnetic Resonance Ultrasound Fusion Device," Journal of Urology

189, 86-91 (2013).

5. D. G. Engehausen, K. Engelhard, S. A. Schwab, M. Uder, S. Wach, B. Wullich and F. S. Krause, "Magnetic Resonance Image-Guided Biopsies with a High Detection Rate of Prostate Cancer," Sci World J (2012).

6. J. Cepek, B. A. Chronik, U. Lindner, J. Trachtenberg, S. R. Davidson, J. Bax and A. Fenster, "A system for MRI-guided transperineal delivery of needles to the prostate for focal therapy," Med Phys 40, 012304 (2013).

7. S. Crouzet, J. Y. Chapelon, O. Rouviere, F. Mege-Lechevallier, M. Colombel, H. Tonoli-Catez, X. Martin and A. Gelet, "Whole-gland ablation of localized prostate cancer with high-intensity focused ultrasound: oncologic outcomes and morbidity in 1002 patients," Eur Urol 65, 907-914 (2014).

8. A. J. Hung, Y. Ma, P. Zehnder, M. Nakamoto, I. S. Gill and O. Ukimura,

"Percutaneous radiofrequency ablation of virtual tumours in canine kidney using Global Positioning System-like technology," BJU Int 109, 1398-1403 (2012). 9. H. Neshat, D. W. Cool, K. Barker, L. Gardi, N. Kakani and A. Fenster, "A 3D

ultrasound scanning system for image guided liver interventions," Med Phys 40, 112903 (2013).

164

Appendix A

A.1 Permission to reproduce previously published material in

Chapters 2, 3 and 4

165

A.2 Permission to reproduce previously published material in

Chapters 5

169

Curriculum Vitae

EDUCATION

 The University of Western Ontario, Canada 2009-present

PhD Candidate in Biomedical Engineering

Thesis title: Image-based registration methods for quantification and compensation of prostate motion during trans-rectal ultrasound (TRUS)-guided biopsy

 University of Moratuwa, Sri Lanka 2004-2008

B. Sc. in Engineering (First Class Honors) – 98th _{percentile overall GPA (3.99 / 4.2)}

Major: Electronics and Telecommunication Engineering Thesis title: Centralized traffic controlling system for railways

SCHOLARSHIPS, HONORS AND AWARDS

2013: Third prize award, Imaging Network Ontario (ImNO) Consortium poster competition.

2012: Third prize award, Imaging Network Ontario (ImNO) Consortium poster competition.

2011: First prize award, Imaging Network Ontario (ImNO) Consortium poster competition.

2010-2012: Natural Sciences and Engineering Council (NSERC) in Computer-Assisted Medical Interventions (CAMI) graduate scholarship ($15,000/yr).

2009-2014: Western Graduate Research Scholarship, The University of Western Ontario – Biomedical Engineering Graduate Program ($16,000/yr).

2004-2008: Academic merit scholarship sponsored by Dialog Telekom PLC, Sri Lanka; provided funding during undergraduate study ($2000). This is a competitive scholarship awarded to the top 25 students in the physical science stream in Sri Lanka.

2004-2008: Dean's List, University of Moratuwa (For achieving grade point average higher than 3.8 out of 4.2 in every semester of attendance).

2007: Awarded University Colors for tennis for being a member of the champion-team in Sri Lanka University Games (SLUG).

PUBLICATIONS

PEER-REVIEWED JOURNALS (Published, accepted or under review)

1. T. De Silva, A. Fenster, D. W. Cool, L. Gardi, C. Romagnoli, J. Samarabandu, A. D. Ward, “2D-3D rigid registration to compensate for prostate motion during 3D TRUS- guided biopsy”, Medical Physics, 40(2), 022904, 2013.

170

2. T. De Silva, A. Fenster, J. Bax, C. Romagnoli, J. Izawa, J. Samarabandu, A. D. Ward, “Quantification of prostate deformation due to needle insertion during TRUS-guided biopsy: Comparison of hand-held and mechanically stabilized systems”, Medical Physics,

38(3): 1718-32, 2011.

3. T. De Silva, D. W. Cool, L. Gardi, C. Romagnoli, A. Fenster, A. D. Ward, “Evaluating the

utility of intra-procedure 3D TRUS image information in guiding registration for motion compensation during prostate biopsy”, submitted to Medical Physics, submittedJanuary, 2014. (under review)

PEER-REVIEWED JOURNALS (Work in progress with greater than 80% work completed)

4. T. De Silva, D. W. Cool, J. Yuan, C. Romagnoli, A. Fenster, A. D. Ward, “Robust 2D-3D

registration optimization using learned prostate motion data”, in preparation for IEEE

Transactions on Medical Imaging.

PEER-REVIEWED CONFERENCE PROCEEDINGS

1. T. De Silva, D. W. Cool, C. Romagnoli, A. Fenster, A. D. Ward, "Evaluating the utility of 3D TRUS image information in guiding intra-procedure registration for motion compensation", Proceedings of the SPIE International Symposium on Medical Imaging 2014, San Diego, CA: February 15-20, 2014 (accepted for podium presentation). 2. T. De Silva, D. Cool, J. Yuan, C. Romagnoli, A. Fenster, A. D. Ward. “Improving 2D-3D

registration optimization using learned prostate motion data” Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 6363, 124-131, Nagoya, Japan, 2013 (8 pages; poster presentation; 32% acceptance rate). 3. T. De Silva, A. Fenster, J. Bax, L. Gardi, C. Romagnoli, J. Samarabandu, A. D. Ward.

"2D-3D rigid registration to compensate for prostate motion during 3D TRUS-guided biopsy", Proceedings of the SPIE International Symposium on Medical Imaging 2012, paper # 63160O, San Diego, CA: February 4-9, 2011 (podium presentation).

4. T. De Silva, A. Fenster, C. Romagnoli, J. Samarabandu, A. D. Ward, “Evaluating image-

similarity metrics to detect prostate motion during 3D TRUS-guided prostate biopsy”,

AAPM/COMP, Vancouver, Canada, 2011 (podium presentation).

5. T. De Silva, J. Bax, A. Fenster, J. Samarabandu, A. D. Ward, “Quantification of prostate

deformation due to needle insertion during TRUS-guided biopsy: Comparison of hand- held and mechanically stabilized systems”, Proceedings of the SPIE International

Symposium on Medical Imaging 2011, paper # 79680U, Orlando, FL: February 13-17,

2011 (podium presentation).

6. T. De Silva, A. Fenster, J. Samarabandu, A. D. Ward, “Quantification of prostate

deformation due to needle insertion during TRUS-guided biopsy”, Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention

(MICCAI), 6363, 213-220, Beijing, China, 2010 (8 pages; poster presentation; 32%

171

7. T. Ambegoda, T. De Silva, K.T. Hemachandra, T.N. Samarasinghe, K. Samarasinghe Centralized Traffic Controlling System for Sri Lanka Railways. IEEE 4th International

Conference on Information and Automation for Sustainability, 145-149, 2008 (podium

presentation).

INVITED TALKS

 “Image-based registration for prostate motion compensation during 3D TRUS-guided biopsy”. Techna Institute, Toronto, ON, Canada. November 18, 2013. Host: Dr. Vladimir Pekar.

 “Quantification of prostate deformation due to needle insertion during TRUS-guided biopsy: Comparison of hand-held and mechanically stabilized systems”, Huazhong University of Science and Technology, Wuhan, Hubei, China. September 27, 2010. Host: Dr. Mingyue Ding.

 “Quantification of prostate deformation due to needle insertion during TRUS-guided biopsy”, University of Moratuwa, Sri Lanka. June 10, 2010. Host: Dr. I. Dayawansa.

PROFESSIONAL EXPERIENCE

2011 Participated in Google Summer of Code project (GSOC) for Kitware Inc.

Oversight: Dr. Marcus D. Hanwell and Dr. Jeff Baumes

Implemented and integrated two selected algorithms from IEEE VisWeek 2010 to VTK ((1) vtkAxisExtended and (2) vtkCellTreeLocator). This work was featured in a Kitware blog post at http://www.kitware.com/source/home/post/44.

2008-2009 Assistant Research Engineer for computer vision related embedded-design projects at Zone24x7 Research Laboratory, Sri Lanka.

2006-2007 Telecommunication Engineering Intern at Dialog Telekom PLC, Sri Lanka, which is the largest telecommunication service provider in Sri Lanka.

2009-2014 Teaching Assistant at the University of Western Ontario for the following courses.

2009 SE2250a Software Construction. Oversight: Dr. Jagath Samarabandu.

2010 ENGSCI1036b Programming Fundamentals for Engineers. Oversight: Dr. Quazi Rahman.

2011 SE3350 Software Engineering Design. Oversight: Dr. Keivan Kian-Mehr.

2012 ECE4455 Engineering Analysis of Physiological Systems. Oversight: Dr. James Lacefield.

2013 ECE4438 Advanced Image Processing and Analysis. Oversight: Dr. Aaron D. Ward.