1. Reinhard Beichel, Brian Smith, Christian Bauer, Ethan Ulrich, Payam Ahmadvand, Mikalai Budzevich, Robert Gillies, Dmitry Goldgof, Milan Grkovski, Ghassan Hamarneh, Qiao Huang, Paul Kinahan, Charles Laymon, James Mountz, John Muzi, Mark Muzi, Sadek Nehmeh, Matthew Oborski, Yongqiang Tan, Binsheng Zhao, John Sunderland, and John Buatti. Multi-site Quality and Variability Analysis of 3D FDG PET Segmentations based on Phantom and Clinical Image Data. Medical Physics, 44(2):479-496, 2016. Keyword(s): Segmentation, Machine Learning, Functional/Molecular/Dynamic Imaging.



2. Aicha BenTaieb, Masoud Nosrati, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. Clinically-Inspired Automatic Classification of Ovarian Carcinoma Subtypes. Journal of Pathology Informatics, 7(1):1-28, 2016. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy.



3. Zhi Lu, Gustavo Carneiro, Andrew Bradley, Daniela Ushizima, Masoud Nosrati, Andrea Bianchi, Claudia Carneiro, and Ghassan Hamarneh. Evaluation of Three Algorithms for the Segmentation of Overlapping Cervical Cells. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), 21(2):441 - 450, 2016. Keyword(s): Challenge, Segmentation.



4. Masoud Nosrati, Alborz Amir-Khalili, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, Rafeef Abugharbieh, and Ghassan Hamarneh. Endoscopic Scene Labelling and Augmentation using Intraoperative Pulsatile Motion and Colour Appearance Cues with Preoperative Anatomical Priors. The International Journal for Computer Assisted Radiology and Surgery (IJCARS), 11(8):1409-1418, 2016. Keyword(s): Segmentation, Registration and Matching, Tracking, Image-Guided Surgery.



5. Urs Ribary, Alex L. Mackay, Alexander Rauscher, Christine M. Tipper, Debbie Giaschi, Todd S. Woodward, Vesna Sossi, Sam M. Doesburg, Lawrence M. Ward, Anthony Herdman, Ghassan Hamarneh, Brian G. Booth, and Alexander Moiseev. Emerging neuroimaging technologies: Towards future personalized diagnostics, prognosis, targeted intervention and ethical challenges. (Chapter 2). Neuroethics: Anticipating the Future, pp 15-53, 2016. ISBN: 9780198786832. Keyword(s): Diffusion MRI/Tensor-valued.



6. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Christina Aquino-Parsons, and Ingrid Spadinger. Bladder Accumulated Dose in Image-Guided High-Dose-Rate Brachytherapy for Locally Advanced Cervical Cancer and its Relation to Urinary Toxicity. Physics in Medicine and Biology (PMB), 1(24):8408-8424, 2016. Keyword(s): Registration and Matching, Brachytherapy.

1. Payam Ahmadvand, Noirin Duggan, Francois Benard, and Ghassan Hamarneh. Tumour Lesion Segmentation from 3D PET using a Machine Learning driven Active Surface. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 271-278, 2016. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging.



2. Payam Ahmadvand, Hillgan Ma, Jesse Tanguay, Anna Celler, Francois Benard, and Ghassan Hamarneh. A Level-Set based Segmentation of tumour lesions in PET images. In Quantitative Imaging Network (QIN) Annual Meeting, 2016. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging.



3. Aicha BenTaieb and Ghassan Hamarneh. Topology Aware Fully Convolutional Networks For Histology Gland Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9900, pages 460-468, 2016. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning.



4. Aicha BenTaieb, Jeremy Kawahara, and Ghassan Hamarneh. Multi-Loss Convolutional Networks for Gland Analysis in Microscopy. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 642-645, 2016. Keyword(s): Machine Learning, Microscopy, Deep Learning.



5. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9900, pages 175-183, 2016. Keyword(s): Neurodevelopment, Machine Learning.



6. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Neurodevelopment, Machine Learning.



7. Arafat Hussain, Ghassan Hamarneh, Tim O'Connell, Mohammed Mohammed, and Rafeef Abugharbieh. Segmentation-Free Estimation of Kidney Volumes in CT with Dual Regression Forests. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 156-163, 2016. Keyword(s): Machine Learning, Segmentation.



8. Jeremy Kawahara, Aicha BenTaieb, and Ghassan Hamarneh. Deep Features to Classify Skin Lesions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1397-1400, 2016. Keyword(s): Machine Learning, Dermatology, Deep Learning.



9. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Artificial Convolutional Neural Networks for Connectomes. In Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning.



10. Jeremy Kawahara and Ghassan Hamarneh. Multi-Resolution-Tract CNN with Hybrid Pretrained and Skin-Lesion Trained Layers. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 164-171, 2016. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning.



11. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Defining caveolae and scaffolds by computational network analysis of particle localization super-resolution microscopy. In American Society for Cell Biology (ASCB), San Francisco, California, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



12. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Discovering Biosignatures of Cav1 Domains: Computational Methods for Super-resolution Microscopy. In LSI Imaging Super-resolution Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



13. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Quantifying Caveolin-1 Molecular Domains via Machine Learning and Computational Network Analysis of Super-resolution Microscopy Data. In Bringing the ASCB to the LSI Imaging Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



14. Ismail M. Khater, David Scriven, Edwin Moore, and Ghassan Hamarneh. Sub-Cellular Network Analysis of Ryanodine Receptor Positioning in Control and Phosphorylated States. In IEEE Computing in Cardiology (IEEE CinC), pages 821-824, 2016. Keyword(s): Cardiology, Super Resolution Microscopy, Single Molecule Localization, Network Modelling and Analysis.



15. Lisa Y. W. Tang, Roger Tam, and Ghassan Hamarneh. Enhancing Accuracy of Symmetric Random Walker Image Registration Via a Novel Data-Consistency Measure. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 28-31, 2016. Keyword(s): Registration and Matching, Uncertainty.



16. Roja Zakariaee, Christina Aquino-Parsons, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Peter Lim, and Ingrid Spadinger. Can Bladder Late Complications be predicted in Cervical Cancer HDR Brachytherapy?. In World Congress of Brachytherapy (WCB), 2016. Keyword(s): Registration and Matching, Brachytherapy.

1. Shawn Andrews and Ghassan Hamarneh. Adaptable Precomputation for Random Walker Image Segmentation and Registration. Technical report arxiv:1607.04174, 7 2016. Keyword(s): Segmentation, Registration and Matching, Optimization, Uncertainty.



2. Colin J. Brown and Ghassan Hamarneh. Machine Learning on Human Connectome Data from MRI. Technical report arxiv:1611.08699, 11 2016. Keyword(s): Survey/Review, Machine Learning, Connectome, Diffusion MRI/Tensor-valued.



3. Masoud Nosrati and Ghassan Hamarneh. Incorporating prior knowledge in medical image segmentation: a survey. Technical report arxiv:1607.01092, 7 2016. Keyword(s): Survey/Review, Diffusion MRI/Tensor-valued, Segmentation, Optimization.

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