1. Brian G. Booth. Diffusion MRI Analysis Techniques Inspired by the Preterm Infant Brain. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, November 2015.



2. Masoud Nosrati. Prior Knowledge for Targeted Object Segmentation in Medical Images. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, March 2015.

1. Alborz Amir-Khalili, Ghassan Hamarneh, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, and Rafeef Abugharbieh. Automatic Segmentation of Occluded Vasculature via Pulsatile Motion Analysis in Endoscopic Robot-Assisted Partial Nephrectomy Video. Medical Image Analysis (MedIA) (Special Issue: Invited best papers of the 2014 Conference on Medical Image Computing and Computer Assisted Intervention), 25(1):103-110, 2015. Keyword(s): Spatio-Temporal, Segmentation, Image-Guided Surgery, Anatomical Trees and Tubular Structures.



2. Shawn Andrews and Ghassan Hamarneh. The Generalized Log-Ratio Transformation: Learning Shape and Adjacency Priors for Simultaneous Thigh Muscle Segmentation. IEEE Transactions on Medical Imaging (IEEE TMI), 34(9):1773-1787, 2015. Keyword(s): Shape Modelling and Analysis, Segmentation, Uncertainty.



3. Brian G. Booth and Ghassan Hamarneh. Diffusion MRI for Brain Connectivity Mapping and Analysis (Chapter 7). MRI: Physics, Image Reconstruction, and Analysis, pp 137-171, 2015. ISBN: 9781482298871. Keyword(s): Diffusion MRI/Tensor-valued.



4. Brian G. Booth, Steven Miller, Colin J. Brown, Kenneth Poskitt, Vann Chau, Ruth Grunau, Anne Synnes, and Ghassan Hamarneh. STEAM - Statistical Template Estimation for Abnormality Mapping: a Personalized DTI Analysis Technique with Applications to the Screening of Preterm Infants. NeuroImage, 125:705-723, 2015. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Datasets, Synthesis/Simulation/Augmentation.



5. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Skin Lesion Tracking System using Structured Graphical Models. Medical Image Analysis (MedIA) (Special Issue on Discrete Graphical Models in Biomedical Image Analysis), 27:84-92, 2015. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology, Machine Learning.



6. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Streak-Detection in Dermoscopic Color Images using Localized Radial Flux of Principal Intensity Curvature (Chapter 7). Dermoscopy Image Analysis, pp 211-229, 2015. ISBN: 9781482253269. Keyword(s): Color/Multichannel/Vector-valued, Processing, Segmentation, Anatomical Trees and Tubular Structures, Dermatology.



7. Masoud Nosrati, Rafeef Abugharbieh, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, and Ghassan Hamarneh. Simultaneous Multi-Structure Segmentation and 3D Non-Rigid Pose Estimation in Image-Guided Robotic Surgery. IEEE Transactions on Medical Imaging (IEEE TMI), 35(1):1-12, 2015. Keyword(s): Segmentation, Registration and Matching, Tracking, Image-Guided Surgery.



8. Lisa Y. W. Tang, Beverly Hannah, Allard Jongman, Joan Sereno, Yue Wang, and Ghassan Hamarneh. Examining visible articulatory features in clear and plain speech. Speech Communications, 75:1-13, 2015. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



9. Ching-Wei Wang, Cheng-Ta Huang, Meng-Che Hsieh, Chung-Hsing Li, Sheng-Wei Chang, Wei-Cheng Li, Remy Vandaele, Raphael Maree, Sebastien Jodogne, Pierre Geurts, Cheng Chen, Guoyan Zheng, Chengwen Chu, Hengameh Mirzaalian, Ghassan Hamarneh, Tomaz Vrtovec, and Bulat Ibragimov. Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge. IEEE Transactions on Medical Imaging (IEEE TMI), 34(9):1890-900, 2015. Keyword(s): Challenge, Graph based, Optimization, Machine Learning, Registration and Matching.



10. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, and Ingrid Spadinger. Validation of non-rigid point-set registration methods using a porcine bladder pelvic phantom. Physics in Medicine and Biology (PMB), 61(2):825-854, 2015. Keyword(s): Registration and Matching, Brachytherapy.

1. Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Vessel Segmentation from Pulsatile Radial Motion. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9351, pages 403-410, 2015. Keyword(s): Anatomical Trees and Tubular Structures, Tracking.



2. Aicha BenTaieb, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. Automatic Diagnosis of Ovarian Carcinomas via Sparse Multiresolution Tissue Representation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 629-636, 2015. Keyword(s): Machine Learning, Microscopy, Deep Learning.



3. Colin J. Brown, Steven Miller, Brian G. Booth, Ken Poskitt, Vann Chau, Anne Synnes, Jill Zwicker, Ruth Grunau, and Ghassan Hamarneh. Prediction of Motor Function in Very Preterm Infants using Connectome Features and Local Synthetic Instances. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 69-76, 2015. Keyword(s): Neurodevelopment, Machine Learning, Synthesis/Simulation/Augmentation.



4. Jeremy Kawahara and Ghassan Hamarneh. Image Content-Based Navigation of Skin Conditions. In World Congress of Dermatology (WCD), 2015. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Visualization, User Interaction.



5. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identifying Sub-Cellular Domains in PC3 cells by Analysing Caveolin-1 Proteins from Nanoscopy Super-Resolution Data. In NanoLytica, Burnaby, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



6. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Advanced Structural and Chemical Imaging (ASCI) Symposium, Pullman, Washington, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



7. Ali Majd, Mohammed AlJasser, Hengameh Mirzaalian, Jerry Shapiro, Ghassan Hamarneh, and Tim K. Lee. Automated Counting of Hair Using an iPhone. In World Congress of Dermatology (WCD), 2015. Keyword(s): Anatomical Trees and Tubular Structures, Dermatology, Color/Multichannel/Vector-valued, Software and Tools.



8. Fanrui Meng, Ismail M. Khater, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Canadian Cytometry and Microscopy Association (CCMA), Toronto, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



9. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. A computer vision tracking system for pigmented skin lesions. In World Congress of Dermatology (WCD), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Optimization, Registration and Matching, Tracking, Graph based, Dermatology.



10. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Detecting Streaks from Dermoscopic Images of Pigmented Skin Lesions. In The International Society for Biophysics and Imaging of the Skin (ISBS), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Dermatology.



11. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Skin Lesion Matching using Jacobian Based Descriptors for Topology Preservation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1407-1410, 2015. Keyword(s): Dermatology, Registration and Matching.



12. Masoud Nosrati and Ghassan Hamarneh. Segmentation of Overlapping Cervical Cells: A Variational Method with Star-Shape Prior. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 186-189, 2015. Keyword(s): Segmentation.



13. Jenna Smith-Forrester, Naama Rotem-Kohavi, Colin J. Brown, Ghassan Hamarneh, and Naznin Virji-Babul. Changes in Structural Brain Connectivity Following Concussion. In The 9th Annual Canadian Neuroscience Meeting (CAN-ACN). Symposium: Vision and Movement Order and Disorder: From Bench to Bedside, 2015. Keyword(s): Diffusion MRI/Tensor-valued.



14. Lisa Y. W. Tang, Shawn Andrews, and Ghassan Hamarneh. Random Walker Image Registration with Inverse Consistency. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 837-840, 2015. Keyword(s): Registration and Matching, Uncertainty.



15. Lisa Y. W. Tang, Ghassan Hamarneh, Anthony Traboulsee, and Roger Tam. Corpus callosum segmentation in MS studies using normal atlases and optimal hybridization of extrinsic and intrinsic image cues. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9351, pages 123-131, 2015. Keyword(s): Registration and Matching, Segmentation, Multiple Sclerosis, MRI.



16. Lisa Y. W. Tang, Beverly Hannah, Allard Jongman, Joan Sereno, Yue Wang, and Ghassan Hamarneh. Examining Visible Articulatory Features in Clear and Conversational Speech. In The International Congress of Phonetic Sciences (ICPhS), pages 1-4, 2015. Keyword(s): Tracking, Segmentation, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



17. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, and Ingrid Spadinger. Phantom Validation of a Point-Set Deformable Registration Method using Pig Bladder. In World Congress on Medical Physics and Biomedical Engineering (WCMPBE), 2015. Keyword(s): Registration and Matching, Brachytherapy.

1. Shawn Andrews and Ghassan Hamarneh. Multi-Region Probabilistic Dice Similarity Coefficient using the Aitchison Distance and Bipartite Graph Matching. Technical report arxiv:1509.07244, 9 2015. Keyword(s): Segmentation, Validation, Graph based, Registration and Matching.

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