1. Li Wang, Yinghuan Shi, Heung-Il Suk, Alison Noble, and Ghassan Hamarneh, editors. Special Issue on Machine Learning in Medical Imaging (MLMI), volume 74. 2019. [bibtex-key = cmig2019mlmi]



2. Ghassan Hamarneh, Steven Pizer, and Hao (Richard) Zhang, editors. Proceedings of the Geometry for Anatomy (G4A), Banff International Research Station (BIRS) 5-day workshop. Banff, AB, Canada, 8 2011. [bibtex-key = g4a2011]



3. Ghassan Hamarneh and Rafeef Abugharbieh, editors. Proceedings of the First MICCAI Workshop on Analysis of Functional Medical Images, Workshop held in conjunction with the 2008 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). New York, NY, USA, 9 2008. Keyword(s): Functional/Molecular/Dynamic Imaging, Functional/Molecular/Dynamic Imaging, Spatio-Temporal. [bibtex-key = miccai_func2008_proc]



4. Ghassan Hamarneh and Rafeef Abugharbieh, editors. Proceedings of the Mathematical Methods for Medical Image Analysis (MMMIA), Banff International Research Station (BIRS) 5-day workshop. Banff, AB, Canada, 11 2007. [bibtex-key = mmmia2007]

1. Ghassan Hamarneh. Towards Intelligent Deformable Models for Medical Image Analysis. PhD thesis, Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, 2001. ISBN: 91-7291-082-8. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = phd2001]



2. Ghassan Hamarneh. Deformable Spatio-Temporal Shape Modeling. Licentiate thesis, Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, 1999. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = lic1999]



3. Ghassan Hamarneh. Implementation and Comparison of Four Different Boundary Detection Algorithms for Quantitative Ultrasonic Measurements of the Human Carotid Artery. Masters's thesis, Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, 1996. Keyword(s): Segmentation. [bibtex-key = msee1996]



4. Ghassan Hamarneh. PC-Based Digital Oscilloscope. Bachelor's thesis, Department of Electrical Engineering, University of Jordan, 1994. Keyword(s): Software and Tools. [bibtex-key = bsee1994]

1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample \(\zeta\)-mixup: Richer, More Realistic Synthetic Samples from a \(p\)-Series Interpolant. Journal of Big Data, 11(43):1-41, March 2024. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation, Classification, Dermatology. [bibtex-key = jbd2024]



2. Saeed Izadi, Isaac Shiri, Carlos Uribe, Parham Geramifar, Habib Zaidi, Arman Rahmim, and Ghassan Hamarneh. Enhanced Direct Joint Attenuation and Scatter Correction of Whole-Body PET Images via Context-Aware Deep Networks. Zeitschrift fuer Medizinische Physik, 000(000):000-000, 2024. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = zmedphys2024]



3. Ashish Sinha, Jeremy Kawahara, Arezou Pakzad, Kumar Abhishek, Matthieu Ruthven, Enjie Ghorbel, Anis Kacem, Djamila Aouada, and Ghassan Hamarneh. DermSynth3D: Synthesis of in-the-wild Annotated Dermatology Images (Sinha, Kawahara, Pakzad: Joint first authors). Medical Image Analysis (MedIA), 000(103145):000, 2024. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = media2024]



4. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Milene Ortiz-Silva, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts (Cardoen, Vandevoorde, Gao, and Ortiz: Joint first authors; Hamarneh and Nabi: Joint senior authors). The Journal Of Cell Biology (JCB), 1(jcb.202206109):000-000, 11 2023. Keyword(s): Super Resolution Microscopy, Object Detection, Restoration, Reconstruction, Interaction. [bibtex-key = jcb2023]



5. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. BioInformatics Advances, 3(1-5):000-000, 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility. [bibtex-key = bioinfadv2023]



6. Saurabh Garg, Haoyao Ruan, Ghassan Hamarneh, Dawn M. Behne, Allard Jongman, Joan Sereno, and Yue Wang. Mouth2Audio: Intelligible Audio Synthesis From Videos With Distinctive Vowel Articulation. International Journal of Speech Technology, 000(000):000-000, 2023. Keyword(s): Synthesis/Simulation/Augmentation, Tracking, Machine Learning, Deep Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = ijst2023b]



7. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. Frontiers in Communication - Language Sciences, 8(1148240):1-19, 2023. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = frontcomm2023]



8. Weina Jin, Mostafa Fatehi, Ru Guo, and Ghassan Hamarneh. Evaluating the Clinical Utility of Artificial Intelligence Assistance and its Explanation on the Glioma Grading Task. Artificial Intelligence In Medicine, 000(000):000-000, 2023. Keyword(s): Deep Learning, Explainable AI (XAI). [bibtex-key = aiim2023]



9. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Generating Post-Hoc Explanation from Deep Neural Networks for Multi-Modal Medical Image Analysis Tasks. MethodX, 10(102009):1-7, 2023. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal, Software and Tools. [bibtex-key = methodx2023]



10. Zahra Mirikharaji, Kumar Abhishek, Alceu Bissoto, Catarina Barata, Sandra Avila, Eduardo Valle, M. Emre Celebi, and Ghassan Hamarneh. A Survey on Deep Learning for Skin Lesion Segmentation (Mirikharaji and Abhishek: Joint first authors; Celebi and Hamarneh: Joint senior authors). Medical Image Analysis (MedIA), pp 1-55, 2023. Keyword(s): Machine Learning, Deep Learning, Segmentation, Survey/Review, Dermatology. [bibtex-key = media2023]



11. Shubam Sachdeva, Haoyao Ruan, Ghassan Hamarneh, Dawn Behne, Allard Jongman, Joan Sereno, and Yue Wang. Plain-to-clear speech video conversion for enhanced intelligibility. International Journal of Speech Technology (IJST), pp 1-22, 2023. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = ijst2023a]



12. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Cellular and Molecular Life Sciences (CMLS), 79(565):1-20, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = cmls2022]



13. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). PLOS ONE, 17(12):e0276726, 2022. Keyword(s): Super Resolution Microscopy, Machine Learning, Classification, Belief Theory, Biomarkers/Biosignatures, Generalizability. [bibtex-key = plosone2022]



14. Arafat Hussain, Zahra Mirikharaji, Mohammad Momeny, Mahmoud Marhamati, Ali Asghar Neshat, Rafeef Garbi, and Ghassan Hamarneh. Active Deep Learning from a Noisy Teacher for Semi-supervised 3D Image Segmentation: Application to COVID-19 Pneumonia Infection in CT. Computerized Medical Imaging and Graphics (CMIG), 102(102127):1-11, 2022. Keyword(s): Segmentation, Machine Learning, Deep Learning, COVID19, SARS-CoV-2. [bibtex-key = cmig2022]



15. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Denoising in the Deep Learning Era. Artificial Intelligence Review, 000(000):1-46, 2022. Keyword(s): Enhancement/Restoration/Denoising, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = aire2022]



16. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Guidelines and evaluation for clinical explainable AI in medical image analysis. Medical Image Analysis (MedIA), 102684:1-30, 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal. [bibtex-key = media2022b]



17. Ivan Klyuzhin, Yixi Xu, Anthony Ortiz, Juan Lavista Ferres, Ghassan Hamarneh, and Arman Rahmim. Testing the Ability of Convolutional Neural Networks to Learn Radiomic Features. Computer Methods and Programs in Biomedicine, 2019(106750):1-10, 2022. Keyword(s): Deep Learning, Functional/Molecular/Dynamic Imaging, Radiomics. [bibtex-key = cmpb2022]



18. M.Sadegh Saberian, Kathleen Moriarty, Andrea Olmstead, Christian Hallgrimson, François Jean, Ivan Robert Nabi, Maxwell Libbrecht, and Ghassan Hamarneh. DEEMD: Drug Efficacy Estimation against SARS-CoV-2 based on Cell Morphology with Deep Multiple Instance Learning. IEEE Transactions on Medical Imaging (IEEE TMI), 41(11):3128-3145, 2022. Keyword(s): Deep Learning, Machine Learning, COVID19, SARS-CoV-2. [bibtex-key = tmi2022]



19. Darren Sutton, Zamir K. Punja, and Ghassan Hamarneh. Characterization of Trichome Phenotypes to Assess Maturation and Flower Development in Cannabis sativa L. (Cannabis) by Automatic Trichome Gland Analysis. Smart Agricultural Technology (SAT), 3(100111):1-15, 2022. Keyword(s): Agritech, Precision Agriculture, Plant Phenotyping, Trichomes, Medicinal Cannabis. [bibtex-key = sat2022]



20. Mengliu Zhao, Jeremy Kawahara, Kumar Abhishek, Sajjad Shamanian, and Ghassan Hamarneh. Skin3D: Detection and Longitudinal Tracking of Pigmented Skin Lesions in 3D Total-Body Textured Meshes (Zhao and Kawahara: Joint first authors). Medical Image Analysis (MedIA), 77(102329):1-10, 2022. Keyword(s): Dermatology, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graph based, Tracking, Datasets. [bibtex-key = media2022]



21. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Predicting the Clinical Management of Skin Lesions using Deep Learning. Nature - Scientific Reports, 11(7769):1-14, 2021. Keyword(s): Dermatology, Machine Learning, Deep Learning, Clinical Management. [bibtex-key = nature_sr2021b]



22. Arafat Hussain, Ghassan Hamarneh, and Rafeef Garbi. Cascaded Localization Regression Neural Nets for Kidney Localization and Segmentation-free Volume Estimation. IEEE Transactions on Medical Imaging (IEEE TMI), 40(6):1555-1567, 2021. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization. [bibtex-key = tmi2021]



23. Arafat Hussain, Ghassan Hamarneh, and Rafeef Garbi. Learnable Image Histograms-based Deep Radiomics for Renal Cell Carcinoma Grading and Staging. Computerized Medical Imaging and Graphics (CMIG), 90(101924):1-10, 2021. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = cmig2021]



24. Saeed Izadi and Ghassan Hamarneh. AECNN: Adversarial and Enhanced Convolutional Neural Networks (Chapter 7). Computer-Aided Analysis of Gastrointestinal Videos, pp 59-62, 2021. ISBN: 978-3-030-64339-3. Keyword(s): Segmentation, Deep Learning, Generative Adversarial Network, Microscopy. [bibtex-key = caagv2021]



25. Ali Majd, Mohammed AlJasser, Hengameh Mirzaalian, Jerry Shapiro, Ghassan Hamarneh, Harvey Lui, Leopoldo Duailibe Nogueira Santos, Thomas Chu, and Tim K. Lee. A novel automated approach to rapid and precise in vivo measurement of hair morphometrics using a smartphone. Skin Research and Technology (SRT), 27:1128–1134, 2021. Keyword(s): Anatomical Trees and Tubular Structures, Dermatology, Color/Multichannel/Vector-valued, Software and Tools. [bibtex-key = srt2021]



26. Mohammad Momeny, Ali Asghar Neshat, Arafat Hussain, Solmaz Kia, Mahmoud Marhamati, Ahmad Jahanbakhshi, and Ghassan Hamarneh. Learning-to-Augment Strategy using Noisy and Denoised Data: Improving Generalizability of Deep CNN for the Detection of COVID-19 in X-ray Images. Computers in Biology and Medicine (CIBM), 136:104704, 2021. Keyword(s): Deep Learning, Classification, Augmentation, COVID19, SARS-CoV-2. [bibtex-key = cibm2021]



27. Saeid Asgari Taghanaki, Kumar Abhishek, Joseph Paul Cohen, Julien Cohen-Adad, and Ghassan Hamarneh. Deep Semantic Segmentation of Natural and Medical Images: A Review (Taghanaki and Abhishek: Joint first authors). Artificial Intelligence Review, 54(1):137-178, 2021. Keyword(s): Segmentation, Survey/Review, Machine Learning, Deep Learning. [bibtex-key = aire2020a]



28. Timothy H. Wong, Ismail M. Khater, Bharat Joshi, Mona Shahsavari, Ghassan Hamarneh, and Ivan Robert Nabi. Single molecule network analysis identifies structural changes to caveolae and scaffolds due to mutation of the caveolin-1 scaffolding domain (Wong and Khater: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific Reports, 11(7810):1-14, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = nature_sr2021]



29. Hanene Ben Yedder, Ben Cardoen, and Ghassan Hamarneh. Deep Learning for Biomedical Image Reconstruction: A Survey. Artificial Intelligence Review, 54(1):215-251, 2021. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = aire2020b]



30. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography. IEEE Transactions on Medical Imaging (IEEE TMI), 41(3):515-530, 2021. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = tmi2021b]



31. Ali Arab, Betty Chinda, George Medvedev, William Siu, Tao Gu, Hui Guo, Sylvain Moreno, Ghassan Hamarneh, Martin Ester, and Xiaowei Song. A Fast and Fully-Automated Deep-Learning Approach for Accurate Haemorrhage Segmentation and Volume Quantification in Non-Contrast Whole-Head CT (Arabi and Chinda: Joint first authors). Nature - Scientific reports, 10(19389):1-12, 2020. Keyword(s): Deep Learning, Segmentation. [bibtex-key = nature_sr2020b]



32. Ben Cardoen, Hanene Ben Yedder, Anmol Sharma, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE Transactions on Medical Imaging (IEEE TMI), 39(6):1942-1956, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = tmi2020]



33. Saurabh Garg, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. ADFAC: Automatic Detection of Facial Articulatory Features. MethodX, 7:101006, 2020. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal, Software and Tools. [bibtex-key = methodx2020]



34. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 148(4):2764-2764, 2020. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = jasa2020]



35. Weina Jin, Mostafa Fatehi, Kumar Abhishek, Mayur Mallya, Brian Toyota, and Ghassan Hamarneh. Artificial Intelligence in Glioma Imaging: Challenges and Advances. Journal of Neural Engineering, 17(2):021002, 2020. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = jne2020]



36. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. A Review of Super-resolution Single Molecule Localization Microscopy Cluster Analysis and Quantification Methods. Cell Patterns, 1(3):2666-3899, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures, Survey/Review. [bibtex-key = cellpatterns2020]



37. Chloe Lim, Hayyan Liaqat, William Siu, Ghassan Hamarneh, and George Medvedev. Future implementation of automated analysis tools for Multiple Sclerosis on conventional magnetic resonance imaging (Lim and Liaqat: Joint first authors; Hamarneh and Medvedev: Joint senior authors). Multiple Sclerosis. MSVirtual 2020 – Late Breaking News. Also appears in ACTRIMS-ECTRMS meeting, 1(3 SUPPL), 2020. Keyword(s): Segmentation, Software and Tools, Multiple Sclerosis, MRI. [bibtex-key = msj2020]



38. Rory Long, Kathleen Moriarty, Ben Cardoen, Guang Gao, A. Wayne Vogl, François Jean, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum (Long and Moriarty: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific reports, 10(20937):1-18, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning. [bibtex-key = nature_sr2020a]



39. Brian Smith, John Buatti, Christian Bauer, Ethan Ulrich, Payam Ahmadvand, Mikalai Budzevich, Robert Gillies, Dmitry Goldgof, Milan Grkovski, Ghassan Hamarneh, Paul Kinahan, John Muzi, Mark Muzi, Charles Laymon, James Mountz, Sadek Nehmeh, Matthew Oborski, Binsheng Zhao, John Sunderland, and Reinhard Beichel. Multi-Site Technical and Clinical Performance Evaluation of Quantitative Imaging Biomarkers from 3D FDG PET Segmentations of Head and Neck Cancer Images. Tomography, 6(2):65-76, 2020. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = tomography2020]



40. Saurabh Garg, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Computer-vision analysis reveals facial movements made during Mandarin tone production align with pitch trajectories. Speech Communications, 113:47-62, 2019. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = speechcomm2019]



41. Jeremy Kawahara, Sara Daneshvar, Giuseppe Argenziano, and Ghassan Hamarneh. Seven-Point Checklist and Skin Lesion Classification using Multi-Task Multi-Modal Neural Net. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI) (Special Issue on Skin Lesion Image Analysis for Melanoma Detection), 23(2):538-546, 2019. Keyword(s): Color/Multichannel/Vector-valued, Deep Learning, Dermatology, Classification, Multimodal, Datasets. [bibtex-key = jbhi2019a]



42. Jeremy Kawahara and Ghassan Hamarneh. Fully Convolutional Neural Networks to Detect Clinical Dermoscopic Features. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI) (Special Issue on Skin Lesion Image Analysis for Melanoma Detection), 23(2):578-585, 2019. Keyword(s): Color/Multichannel/Vector-valued, Deep Learning, Dermatology, Classification, Segmentation. [bibtex-key = jbhi2019b]



43. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PLOS ONE, 14(8):1-17, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures. [bibtex-key = plosone2019]



44. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Nature - Scientific reports, 9(9888):1-10, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2019]



45. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Caveolin-1 Domain Signatures via Graphlet Analysis of Single Molecule Super-Resolution Data. Bioinformatics, 35(18):3468-3475, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = bioinformatics2019]



46. Anmol Sharma and Ghassan Hamarneh. Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network. IEEE Transactions on Medical Imaging (IEEE TMI), 39(4):1170-1183, 2019. Keyword(s): Machine Learning, Deep Learning, Generative Adversarial Network, Synthesis/Simulation/Augmentation, Multimodal. [bibtex-key = tmi2019]



47. Saeid Asgari Taghanaki, Yefeng Zheng, S. Kevin Zhou, Bogdan Georgescu, Puneet Sharma, Daguang Xu, Dorin Comaniciu, and Ghassan Hamarneh. Combo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation. Computerized Medical Imaging and Graphics (CMIG), 75:24-33, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = cmig2019]



48. Saeedeh Afshari, Aicha BenTaieb, and Ghassan Hamarneh. Automatic Localization of Normal Active Organs in 3D PET Scans. Computerized Medical Imaging and Graphics (CMIG), 70:111-118, 2018. Keyword(s): Deep Learning, Machine Learning, Functional/Molecular/Dynamic Imaging, Localization. [bibtex-key = cmig2018c]



49. Aicha BenTaieb and Ghassan Hamarneh. Adversarial Stain Transfer for Histopathology Image Analysis. IEEE Transactions on Medical Imaging (IEEE TMI), 37(3):792-802, 2018. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Generative Adversarial Network. [bibtex-key = tmi2018]



50. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive connectome subnetwork extraction with anatomical and connectivity priors. Computerized Medical Imaging and Graphics (CMIG), 71(January):67-78, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = cmig2018b]



51. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Computer-vision analysis shows different facial movements for the production of different Mandarin tones. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 144(3):1720-1720, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = jasa2018b]



52. Peyman Gholami, Mohammad Ali Ahmadi-pajouh, Nabiollah Abolftahi, Ghassan Hamarneh, and Mohammad Kayvanrad. Segmentation and Measurement of Chronic Wounds for Bioprinting. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), 22(4):1269-1277, 2018. Keyword(s): Segmentation, Dermatology. [bibtex-key = jbhi2018c]



53. Ismail M. Khater, Fanrui Meng, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Nature - Scientific reports, 8(9009):1-15, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2018]



54. Joan Sereno, Allard Jongman, Yue Wang, Ghassan Hamarneh, Lisa Y. W. Tang, Saurabh Garg, Paul Tupper, Bob McMurray, Charles Redmon, Yuyu Zeng, Beverly Hannah, Keith Leung, and Sylvia Cho. Linking production and perception of clear speech. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 144(3):1725-1725, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = jasa2018a]



55. Saeid Asgari Taghanaki, Noirin Duggan, Hillgan Ma, Xinchi Hou, Anna Celler, Francois Benard, and Ghassan Hamarneh. Segmentation-Free Direct Tumor Volume and Metabolic Activity Estimation from PET Scans. Computerized Medical Imaging and Graphics (CMIG), 63(January):52-66, 2018. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = cmig2018a]



56. Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Modelling and Extraction of Pulsatile Radial Distension and Compression Motion for Automatic Vessel Segmentation from Video. Medical Image Analysis (MedIA), 40:184-198, 2017. Keyword(s): Spatio-Temporal, Segmentation, Image-Guided Surgery. [bibtex-key = media2017b]



57. Alborz Amir-Khalili, Ghassan Hamarneh, Roja Zakariaee, Ingrid Spadinger, and Rafeef Abugharbieh. Propagation of Registration Uncertainty During Multi-Fraction Cervical Cancer Brachytherapy. Physics in Medicine and Biology (PMB), 62(30):8116-81135, 2017. Keyword(s): Registration and Matching, Brachytherapy, Uncertainty. [bibtex-key = pmb2017]



58. Aicha BenTaieb, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. A Structured Latent Model for Ovarian Carcinoma Subtyping from Histopathology Slides. Medical Image Analysis (MedIA), 39:194-205, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Datasets. [bibtex-key = media2017]



59. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Convolutional Neural Networks for Brain Networks; Towards Predicting Neurodevelopment (Brown and Kawahara: Joint first authors). NeuroImage, 146(1):1038-1049, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning. [bibtex-key = neuroimage2017]



60. Saeid Asgari Taghanaki, Jeremy Kawahara, Brandon Miles, and Ghassan Hamarneh. Pareto-Optimal Multi-objective Dimensionality Reduction Deep Auto-Encoder for Mammography Classification. Computer Methods and Programs in Biomedicine, 145:85-93, 2017. Keyword(s): Machine Learning, Deep Learning, Optimization. [bibtex-key = cmpb2017]



61. Saeid Asgari Taghanaki, Yonghuai Liu, Brandon Miles, and Ghassan Hamarneh. Geometry Based Pectoral Muscle Segmentation from MLO Mammogram Views. IEEE Transactions on Biomedical Engineering (IEEE TBME), 64(1):2662-2671, 2017. Keyword(s): Segmentation. [bibtex-key = tbme2017]



62. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Christina Aquino-Parsons, and Ingrid Spadinger. Association of Bladder Dose with Late Urinary Side Effects in Cervical Cancer High-Dose-Rate Brachytherapy. Brachytherapy, 16(6):1175-1183, 2017. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = brachy2017]



63. 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. [bibtex-key = mp2017]



64. 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. [bibtex-key = jpi2016]



65. 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. [bibtex-key = jbhi2016]



66. 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. [bibtex-key = ijcars2016]



67. 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. [bibtex-key = neuroethics2016]



68. 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. [bibtex-key = pmb2016]



69. 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. [bibtex-key = media2015b]



70. 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. [bibtex-key = tmi2015a]



71. 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. [bibtex-key = crc2015b]



72. 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. [bibtex-key = neuroimage2015]



73. 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. [bibtex-key = media2015]



74. 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. [bibtex-key = crc2015a]



75. 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. [bibtex-key = tmi2015c]



76. 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. [bibtex-key = speechcomm2015]



77. 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. [bibtex-key = tmi2015b]



78. 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. [bibtex-key = pmb2015]



79. Shawn Andrews, Neda Changizi, and Ghassan Hamarneh. The Isometric Log-Ratio Transform for Probabilistic Multi-Label Anatomical Shape Representation. IEEE Transactions on Medical Imaging (IEEE TMI), 33(9):1890-1899, 2014. Keyword(s): Shape Modelling and Analysis, Segmentation, Uncertainty. [bibtex-key = tmi2014b]



80. Colin J. Brown, Steven Miller, Brian G. Booth, Shawn Andrews, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Structural Network Analysis of Brain Development in Young Preterm Neonates. NeuroImage, 101(0):667-680, 2014. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome. [bibtex-key = neuroimage2014]



81. Pablo Guzman, Ghassan Hamarneh, Rafael Ros, and Eduardo Ros. Arterial Mechanical Motion Estimation Based on a Semi-Rigid Body Deformation Approach. Sensors: Special Issue on Ultrasonic Sensors and Transducers for Applications in Biology, Medicine and NDT), 14(6):9429-9450, 2014. Keyword(s): Segmentation, Tracking, Deformable Models. [bibtex-key = sensors2014]



82. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Hair Enhancement in Dermoscopic Images using Dual-Channel Quaternion Tubularness Filters and MRF-based Multi-Label Optimization. IEEE Transactions on Image Processing (IEEE TIP), 23(12):5486-5496, 2014. Keyword(s): Anatomical Trees and Tubular Structures, Processing, Color/Multichannel/Vector-valued, Dermatology, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = tip2014]



83. Masoud Nosrati and Ghassan Hamarneh. Local optimization based Segmentation of Spatially-Recurring, Multi-Region Objects with Part Configuration Constraints. IEEE Transactions on Medical Imaging (IEEE TMI), 33(9):1845-1859, 2014. Keyword(s): Optimization, Segmentation. [bibtex-key = tmi2014a]



84. Manku Rana, Ghassan Hamarneh, and James Wakeling. 3D curvatures of muscle fascicles in triceps surae. Journal of Applied Physiology, 117(11):1388-1397, 2014. Keyword(s): Shape Modelling and Analysis. [bibtex-key = jappl2014]



85. Roja Zakariaee, Colin J. Brown, Ghassan Hamarneh, Christina Parsons, and Ingrid Spadinger. Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration. Medical Physics (also appeared in COMP 2014), 41(3):1, 2014. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = mp2014]



86. Brian G. Booth and Ghassan Hamarneh. Brain Connectivity Mapping and Analysis using Diffusion MRI (Chapter 19). Medical Imaging: Technology and Applications, pp 529-563, 2013. ISBN: 9781466582620. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = crc2013b]



87. Chris McIntosh and Ghassan Hamarneh. Medical Image Segmentation: Energy Minimization and Deformable Models (Chapter 23). Medical Imaging: Technology and Applications, pp 661-692, 2013. ISBN: 9781466582620. Keyword(s): Survey/Review, Segmentation, Deformable Models, Optimization. [bibtex-key = crc2013a]



88. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Spatial Normalization of Human Back Images for Dermatological Studies. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), 18(4):1494-1501, 2013. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = jbhi2013]



89. Manku Rana, Ghassan Hamarneh, and James Wakeling. 3D Fascicle Orientations in Triceps Surae. Journal of Applied Physiology, 115(1):116-125, 2013. Keyword(s): Shape Modelling and Analysis. [bibtex-key = jappl2013]



90. Lisa Y. W. Tang and Ghassan Hamarneh. Medical Image Registration: A Review (Chapter 22). Medical Imaging: Technology and Applications, pp 619-660, 2013. ISBN: 9781466582620. Keyword(s): Survey/Review, Optimization, Registration and Matching. [bibtex-key = crc2013c]



91. Oliver van Kaick, Hao (Richard) Zhang, and Ghassan Hamarneh. Bilateral Maps for Partial Matching. Computer Graphics Forum (CGF), 32(6):189-200, 2013. Keyword(s): Registration and Matching, Shape Modelling and Analysis. [bibtex-key = cgf2013]



92. Chris McIntosh and Ghassan Hamarneh. Medial-based Deformable Models in Non-convex Shape-spaces for Medical Image Segmentation using Genetic Algorithms. IEEE Transactions on Medical Imaging (IEEE TMI), 31(1):33-50, 2012. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Artificial Life, Optimization. [bibtex-key = tmi2012a]



93. Bernard Ng, Ghassan Hamarneh, and Rafeef Abugharbieh. Modeling Brain Activation in fMRI Using Group MRF. IEEE Transactions on Medical Imaging (IEEE TMI), 31(5):1113-1123, 2012. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = tmi2012b]



94. Peyman Rahmati, Andy Adler, and Ghassan Hamarneh. Mammography Segmentation with Maximum Likelihood Active Contours. Medical Image Analysis (MedIA), 16(6):1167-1186, 2012. Keyword(s): Segmentation, Deformable Models, Optimization. [bibtex-key = mia2012a]



95. Lisa Y. W. Tang, Tim Bressmann, and Ghassan Hamarneh. Tongue contour tracking in dynamic ultrasound via higher-order MRFs and efficient fusion moves. Medical Image Analysis (MedIA), 16(8):1503-1520, 2012. Keyword(s): Tracking, Registration and Matching, Graph based. [bibtex-key = mia2012b]



96. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based 3D shape analysis of thigh muscles: Patients with chronic obstructive pulmonary disease versus healthy adults. Academic Radiology, 18(2):155-166, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2011]



97. Ghassan Hamarneh, Chris McIntosh, and Mark S. Drew. Perception-based Visualization of Manifold-Valued Medical Images using Distance-Preserving Dimensionality Reduction. IEEE Transactions on Medical Imaging (IEEE TMI), 30(7):1314-1327, 2011. Keyword(s): Color/Multichannel/Vector-valued, Visualization, Diffusion MRI/Tensor-valued, Functional/Molecular/Dynamic Imaging. [bibtex-key = tmi2011b]



98. Preet Jassi and Ghassan Hamarneh. VascuSynth: Vascular Tree Synthesis Software. Insight Journal, January-June:1-12, 2011. Keyword(s): Segmentation, Validation, Shape Modelling and Analysis, Software and Tools, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = ij2011]



99. Boris Shabash, Zhi Feng Huang, and Ghassan Hamarneh. Medical Image Analysis with ITK on Apple iOS. Kitware Source - Software Developer's Quarterly, (16):3-5, 2011. Keyword(s): Software and Tools. [bibtex-key = source2011]



100. Andrea Tagliasacchi, Matt Olson, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. VASE: Volume-Aware Surface Evolution for Surface Reconstruction from Incomplete Point Clouds. Computer Graphics Forum (CGF) (Special Issue of Symposium on Geometry Processing 2011), 30(5):1563-1571, 2011. Keyword(s): Deformable Models, Shape Modelling and Analysis. [bibtex-key = cgf2011c]



101. Azadeh Yazdanpanah, Ghassan Hamarneh, Ben Smith, and Marinko Sarunic. Automated Segmentation of Intra-Retinal Layers from Optical Coherence Tomography Images using an Active Contour Approach. IEEE Transactions on Medical Imaging (IEEE TMI), 30(2):484-496, 2011. Keyword(s): Segmentation, Deformable Models. [bibtex-key = tmi2011a]



102. Oliver van Kaick, Andrea Tagliasacchi, Oana Sidi, Hao (Richard) Zhang, Daniel Cohen-Or, Lior Wolf, and Ghassan Hamarneh. Prior Knowledge for Part Correspondence. Computer Graphics Forum (CGF) (Special Issue of Eurographics 2011), 30(2):1-10, 2011. Keyword(s): Segmentation, Registration and Matching, Shape Modelling and Analysis. [bibtex-key = cgf2011b]



103. Oliver van Kaick, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. A Survey on Shape Correspondence. Computer Graphics Forum (CGF) (extended version of Eurographics 2010 STAR), 30(6):1681-1707, 2011. Keyword(s): Survey/Review, Registration and Matching, Shape Modelling and Analysis. [bibtex-key = cgf2011a]



104. Ghassan Hamarneh and Preet Jassi. VascuSynth: Simulating Vascular Trees for Generating Volumetric Image data with Ground Truth Segmentation and Tree Analysis. Computerized Medical Imaging and Graphics (CMIG), 34(8):605-616, 2010. Keyword(s): Segmentation, Validation, Shape Modelling and Analysis, Software and Tools, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = cmig2010]



105. Ahmed Saad, Ghassan Hamarneh, and Torsten Moeller. Exploration and Visualization of Segmentation Uncertainty using Shape and Appearance Prior Information. IEEE Transactions on Visualization and Computer Graphics (IEEE TVCG) (Special Issue of the IEEE Visualization Conference 2010), 16(6):1366-1375, 2010. Keyword(s): User Interaction, Segmentation, Uncertainty, Spatio-Temporal. [bibtex-key = tvcg2010]



106. Ahmed Saad, Torsten Moeller, and Ghassan Hamarneh. ProbExplorer: An Uncertainty-based Visual Analysis Tool for Medical Imaging. Computer Graphics Forum (CGF) (Special Issue of the proceedings of Eurographics/IEEE-VGTC Symposium on Visualization 2010), 29(3):1113-1122, 2010. Keyword(s): Software and Tools, Segmentation, Uncertainty, User Interaction, Visualization, Spatio-Temporal. [bibtex-key = cgf2010]



107. Boris Shabash, Ghassan Hamarneh, Zhi Feng Huang, and Luis Ibanez. ITK Image IO Interface with Apple iOS. Insight Journal, July-December:1-16, 2010. Keyword(s): Software and Tools. [bibtex-key = ij2010b]



108. Boris Shabash, Ghassan Hamarneh, Zhi Feng Huang, and Luis Ibanez. ITK on the iOS. Insight Journal, July-December:1-9, 2010. Keyword(s): Software and Tools. [bibtex-key = ij2010a]



109. Lisa Y. W. Tang, Ghassan Hamarneh, and Anna Celler. Dual-isotope Acquisition for CT-SPECT Registration of Infection Studies. Journal of Digital Imaging, 23(3):258-267, 2010. Keyword(s): Imaging, Registration and Matching, Validation, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = jdi2010]



110. Aaron Ward and Ghassan Hamarneh. GMAT: The Groupwise Medial Axis Transform for Fuzzy Skeletonization and Intelligent Pruning. IEEE Transactions Pattern Analysis and Machine Intelligence (IEEE TPAMI), 32(6):1084-1096, 2010. Keyword(s): Medial-based Shape Representation, Shape Modelling and Analysis, Registration and Matching. [bibtex-key = pami2010]



111. Lingshu Yin, Lisa Y. W. Tang, Ghassan Hamarneh, Brad Gill, Anna Celler, Sergey Shcherbinin, Tsien-Fei Fua, Anna Thompson, Mitchell Liu, Cheryl Duzenli, Finbar Sheehan, and Vitali Moiseenko. Complexity and accuracy of image registration methods in SPECT guided radiation therapy. Physics in Medicine and Biology (PMB), 55:237-246, 2010. Keyword(s): Registration and Matching, Color/Multichannel/Vector-valued, Functional/Molecular/Dynamic Imaging. [bibtex-key = pmb2010]



112. Eyal Zadicario, Shlomi Rudich, Ghassan Hamarneh, and Daniel Cohen-Or. Image-Based Motion Detection Using the Concept of Weighted Directional Descriptors. IEEE Engineering in Medicine and Biology Magazine (IEEE EMB), 20(2):87-94, 2010. Keyword(s): Registration and Matching, Tracking. [bibtex-key = emb2010]



113. Oliver van Kaick, Ghassan Hamarneh, Aaron Ward, Mark Schweitzer, and Hao (Richard) Zhang. Learning Fourier Descriptors for Computer-Aided Diagnosis of the Supraspinatus. Academic Radiology, 17(8):1040-1049, 2010. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2010a]



114. Warren Cheung and Ghassan Hamarneh. n-SIFT: n-dimensional Scale Invariant Feature Transform. IEEE Transactions on Image Processing (IEEE TIP), 18(9):2012-2021, 2009. Keyword(s): Registration and Matching. [bibtex-key = tip2009]



115. Ghassan Hamarneh and Xiaoxing Li. Watershed Segmentation using Prior Shape and Appearance Knowledge. Journal of Image and Vision Computing, 27(1-2):59-68, 2009. Keyword(s): Segmentation, Shape Modelling and Analysis. [bibtex-key = jivc2009]



116. Ghassan Hamarneh, Chris McIntosh, Tim McInerney, and Demetri Terzopoulos. Deformable Organisms: An Artificial Life Framework for Automated Medical Image Analysis (Chapter 15). Computational Intelligence In Medical Imaging: Techniques and Applications, pp 433-474, 2009. ISBN: 978-1420060591. Keyword(s): Processing, Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = crc2009]



117. Chris McIntosh and Ghassan Hamarneh. Evolutionary Deformable Models for Medical Image Segmentation: A Genetic Algorithm Approach to Optimizing Learned, Intuitive, and Localized Medial based Shape Deformation (Chapter 4.1). Genetic and Evolutionary Computation: Medical Applications, pp 47-67, 2009. ISBN: 978-0-470-74813-8. Keyword(s): Segmentation, Deformable Models, Artificial Life. [bibtex-key = gecma2009]



118. Manku Rana, Ghassan Hamarneh, and James Wakeling. Automated tracking of muscle fascicle orientation in B-mode ultrasound images. Journal of Biomechanics, 42(13):2068-2073, 2009. Keyword(s): Spatio-Temporal, Processing, Segmentation, Tracking. [bibtex-key = jbm2009]



119. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Efficient Interactive 3D Livewire Segmentation of Objects with Arbitrary Topologies. Computerized Medical Imaging and Graphics (CMIG), 32(8):639-650, 2008. Keyword(s): Segmentation, Software and Tools, User Interaction, Graph based. [bibtex-key = cmig2008]



120. Andy Rova, Anna Celler, and Ghassan Hamarneh. NMQC: A NEMA-Compliant Software Application for Gamma Camera Quality Control. Journal of Digital Imaging, 21(2):243-255, 2008. Keyword(s): Imaging, Software and Tools. [bibtex-key = jdi2008b]



121. Lisa Y. W. Tang, Ghassan Hamarneh, and Anna Celler. Validation of Mutual Information-Based Registration of CT and Bone SPECT Images in Dual-isotope Studies. Computer Methods and Programs in Biomedicine, 92(2):173-185, 2008. Keyword(s): Imaging, Registration and Matching, Validation, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = cmpb2008]



122. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Bicipital Groove Shape Analysis and Relationship to Tendopathy. Journal of Digital Imaging, 21(2):219-234, 2008. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = jdi2008a]



123. Warren Cheung and Ghassan Hamarneh. Scale Invariant Feature Transform for n-Dimensional Images (n-SIFT). Insight Journal, July-December:1-7, 2007. Keyword(s): Software and Tools, Registration and Matching. [bibtex-key = ij2007]



124. Ghassan Hamarneh and Judith Hradsky. Bilateral Filtering of Diffusion Tensor Magnetic Resonance Images. IEEE Transactions on Image Processing (IEEE TIP), 16(10):2463-2475, 2007. Keyword(s): Processing, Diffusion MRI/Tensor-valued. [bibtex-key = tip2007]



125. Ghassan Hamarneh and Chris McIntosh. Deformable Organisms for Medical Image Analysis (Chapter 12). Deformable Models: Biomedical and Clinical Applications, pp 387-443, 2007. ISBN: 978-0-387-31201-9. Keyword(s): Segmentation, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = dm2007b]



126. Ghassan Hamarneh and Chris McIntosh. Physically and Statistically based Deformable Models for Medical Image Analysis (Chapter 11). Deformable Models: Biomedical and Clinical Applications, pp 335-386, 2007. ISBN: 978-0-387-31201-9. Keyword(s): Segmentation, Deformable Models. [bibtex-key = dm2007a]



127. Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle: A Clinical Study of the Relationship between Shape and Pathology. Academic Radiology, 14(10):1229-1241, 2007. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2007]



128. Omer Ishaq, Ghassan Hamarneh, Roger Tam, Anthony Traboulsee, and David Li. Effects of mid sagittal plane selection on corpus callosal area. Multiple Sclerosis (special supplementary journal issue of all oral presentations in the 22nd Congress of the European Committee for Treatment and Research in Multiple Sclerosis (ECTRMS) 2006). Also appeared in ECTRMS 2006, 12(1):S173, 2006. Keyword(s): Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = msj2006]



129. Chris McIntosh and Ghassan Hamarneh. I-DO: A Deformable Organisms framework for ITK. Insight Journal, Special Issue: MICCAI 2006 Open Science Workshop:1-14, 2006. Keyword(s): Deformable Organisms, Software and Tools, Artificial Life. [bibtex-key = ij2006]



130. Vincent Chu and Ghassan Hamarneh. MATITK: Extending MATLAB with ITK. Insight Journal, Aug-Dec:1-8, 2005. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = ij2005]



131. Ghassan Hamarneh, Rafeef Abugharbieh, and Tim McInerney. Medial Profiles for Modeling Deformation and Statistical Analysis of Shape and their Use in Medical Image Segmentation.. International Journal of Shape Modeling (IJSM), 10(2):187-209, 2004. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Medial-based Shape Representation. [bibtex-key = ijsm2004]



132. Ghassan Hamarneh and Tomas Gustavsson. Deformable spatio-temporal shape models: extending active shape models to 2D+time.. Journal of Image Vision Computing, 22(6):461-470, 2004. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = jivc2004]



133. Tim McInerney, Ghassan Hamarneh, Martha Shenton, and Demetri Terzopoulos. Deformable Organisms for Automatic Medical Image Analysis. Yearbook of Medical Informatics 2004, Special Topic: Towards Clinical Bioinformatics, pp 466-481 (reprinted from Medical Image Analysis 6(3) 2002, pp.251-266), 2004. ISBN: 3-7945-2336-9. Keyword(s): Segmentation, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = ymi2004]



134. Ghassan Hamarneh. Towards Intelligent Deformable Models for Medical Image Analysis. In R Haux and C Kulikowski, editors, Summary of results from the VISIT (Visual Information Technology Program) 1997-2002, number 32, pages 144-147. Centre for Image Analysis, Uppsala University, 2004. ISSN: ISSN 1100-6641. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Deformable Organisms, Artificial Life. [bibtex-key = VISITsummary2004_97_02]



135. Rafeef Abugharbieh, Ghassan Hamarneh, Tomas Gustavsson, and Clemens Kaminski. Level Set Curve Matching and Particle Image Velocimetry for Resolving Chemistry and Turbulence Interactions in Propagating Flames. Journal of Mathematical Imaging and Vision, 19(3):199-218, 2003. Keyword(s): Registration and Matching. [bibtex-key = jmiv2003]



136. Tim McInerney, Ghassan Hamarneh, Martha Shenton, and Demetri Terzopoulos. Deformable organisms for automatic medical image analysis. Medical Image Analysis (MedIA), 6(3):251-266, 2002. Keyword(s): Segmentation, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = mia2002]



137. Rafeef Abugharbieh, Ghassan Hamarneh, Tomas Gustavsson, and Clemens Kaminski. Flame Front Tracking by Laser Induced Fluorescence Spectroscopy and Advanced Image Analysis. Journal of Optics Express, 8(5):278-287, 2001. Keyword(s): Segmentation, Registration and Matching. [bibtex-key = opex2001]

1. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. Continual-Zoo: Leveraging Zoo Models for Continual Classification of Medical Images. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) Workshop on Continual Learning (CLVision), pages 000-000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Continual Learning, Domain Generalization. [bibtex-key = cvpr_clvision2024]



2. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Milene Ortiz-Silva, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria–ER contacts (Cardoen, Vandevoorde, Gao, and Ortiz: Joint first authors; Hamarneh and Nabi: Joint senior authors). In Keystone Symposia on Molecular and Cellular Biology - Organelle Membrane Contact Sites in Health and Disease (Joint with: Mitochondria Signaling and Disease), pages 1, 2024. Keyword(s): Super Resolution Microscopy, Object Detection, Restoration, Reconstruction, Interaction. [bibtex-key = ksmcb2024a]



3. Tanya Gatsak, Kumar Abhishek, Hanene Ben Yedder, Saeid Asgari Taghanaki, and Ghassan Hamarneh. PET-Disentangler: PET Lesion Segmentation via Disentangled Healthy and Disease Feature Representations. In The Society of Nuclear Medicine and Molecular Imaging (SNMMI) Annual Meeting, pages 1, 2024. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = snmmi2024]



4. Aliasghar Khani, Saeid Asgari Taghanaki, Aditya Sanghi, Ali Mahdavi Amiri, and Ghassan Hamarneh. SLiMe: Segment Like Me. In International Conference on Learning Representations (ICLR), 2024. Keyword(s): Deep Learning, Machine Learning, One-/Few-Shot Learning, Segmentation, Diffusion Models, Foundational Models. [bibtex-key = iclr2024]



5. Jieyi Zheng, Ben Cardoen, Ghassan Hamarneh, and Ivan Robert Nabi. Comparison of Specificity of Confocal and Super-Resolution Approaches to Detecting Mitochondria-ER Contact Sites (Hamarneh and Nabi: Joint senior authors). In Keystone Symposia on Molecular and Cellular Biology - Organelle Membrane Contact Sites in Health and Disease (Joint with: Mitochondria Signaling and Disease), pages 1, 2024. Keyword(s): Super Resolution Microscopy, Object Detection. [bibtex-key = ksmcb2024b]



6. Elise Li Zheng, Weina Jin, Ghassan Hamarneh, and Sandra Soo-Jin Lee. What does “explainable” AI explain? Power dynamics and AI explainability in precision medicine. In Congress on Ethical, Legal, and Social Implications (ELSI): AI and machine learning | Equity and justice in genetics | Precision Medicine, 2024. Keyword(s): Explainable AI, Ethical AI, Societal Implications of AI. [bibtex-key = elsi2024]



7. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. $\zeta$-mixup: Richer, More Realistic Mixing of Multiple Images. In Medical Imaging with Deep Learning (MIDL), pages 1-5, 2023. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = midl2023]



8. Nourhan Bayasi, Siyi Du, Ghassan Hamarneh, and Rafeef Garbi. Continual-GEN: Continual Group Ensembling for Domain-agnostic Skin Lesion Classification. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Classification, Continual Learning. [bibtex-key = miccai_isic2023a]



9. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. Learning-to-Count by Learning-to-Rank. In Canadian Conference on Computer and Robot Vision (CRV), pages 1-8, 2023. Keyword(s): Deep Learning, Counting, Ranking. [bibtex-key = crv2023]



10. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. AViT: Adapting Vision Transformers for Small Skin Lesion Segmentation Datasets. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation, Transformers. [bibtex-key = miccai_isic2023b]



11. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. MDViT: Multi-domain Vision Transformer for Small Medical Image Segmentation Datasets Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), pages 000-000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Transformers, Classification. [bibtex-key = miccai2023]



12. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = ascb2022c]



13. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Goa, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS. In UBC SBME 2022, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = sbme2022]



14. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. BoosterNet: Improving Domain Generalization of Deep Neural Nets using Culpability-Ranked Features. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 528-538, 2022. Keyword(s): Machine Learning, Deep Learning, Classification, Continual Learning, Domain Generalization, Dermatology. [bibtex-key = cvpr2022]



15. Kayleigh Campbell, Colin J. Brown, Ghassan Hamarneh, Steven Miller, and Tim Oberlander. Disrupted structural network topology of the neonatal brain following prenatal SSRI antidepressant exposure, and its relationship with later infant neurodevelopment and behaviour at 2-years of age. In International Society for Developmental Psychobiology (ISDP), 2022. Keyword(s): Neurodevelopment, Diffusion MRI/Tensor-valued. [bibtex-key = isdp2022]



16. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. A novel sub-precision detection method (MCS-DETECT) identifies shape complexity of mitochondria-ER contacts (MERCs) in 3D STED super-resolution microscopy (Cardoen, Vandervoorde, and Gao: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Object Detection, Super Resolution Microscopy. [bibtex-key = ascb2022a]



17. Siyi Du, Ben Her, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. FairDisCo: Fairer AI in Dermatology via Disentanglement Contrastive Learning. In European Conference on Computer Vision (ECCV) ISIC Skin Image Analysis Workshop (ECCV ISIC), pages 185-202, 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = eccv_isic2022b]



18. Saeed Izadi, Isaac Shiri, Carlos Uribe, Parham Geramifar, Habib Zaidi, Arman Rahmim, and Ghassan Hamarneh. Context-Aware Filtering for Direct Joint Attenuation and Scatter Correction of Whole-Body PET Images. In The Society of Nuclear Medicine and Molecular Imaging (SNMMI) Annual Meeting, pages 1, 2022. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = snmmi2022]



19. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. Evaluating Explainable AI on Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?. In Association for the Advancement of Artificial Intelligence Conference (AAAI), volume 36, pages 11945-11953, 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Glioma Imaging, Machine Learning, MRI, Multimodal. [bibtex-key = aaai2022]



20. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. HDCluster: High-Degree Graph-Based Clustering Algorithm and its Application to Single Molecule Localization Microscopy. In Single Molecule Localization Microscopy Symposium, pages 1, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Clustering. [bibtex-key = smlms2022]



21. Ismail M. Khater, Timothy H. Wong, Christian Hallgrimson, Satish Moparthi, Stéphane Vassilopoulos, Ghassan Hamarneh, and Ivan Robert Nabi. Molecular architecture of clathrin plaques and pits defined by super-resolution network analysis (SuperResNET) (Khater and Wong: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2022b]



22. Mayur Mallya and Ghassan Hamarneh. Deep Multimodal Guidance for Medical Image Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 13437, pages 298–308, 2022. Keyword(s): Dermatology, Deep Learning, MRI, Microscopy, Multimodal. [bibtex-key = miccai2022]



23. Arezou Pakzad, Kumar Abhishek, and Ghassan Hamarneh. CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. In European Conference on Computer Vision (ECCV) ISIC Skin Image Analysis Workshop (ECCV ISIC), pages 203–219, 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = eccv_isic2022a]



24. Saeid Asgari Taghanaki, Aliasghar Khani, Fereshte Khani, Ali Gholami, Linh Tran, Ali Mahdavi-Amiri, and Ghassan Hamarneh. MaskTune: Mitigating Shortcut Learning by Tuning to Explore (Asgari, Khani, Khani, Gholami: Equal contribution). In Neural Information Processing Systems (NeurIPS), pages 1-13, 2022. Keyword(s): Classification, Deep Learning. [bibtex-key = neurips2022]



25. Kumar Abhishek and Ghassan Hamarneh. Matthews Correlation Coefficient Loss for Deep Convolutional Networks: Application to Skin Lesion Segmentation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 225-229, 2021. Keyword(s): Segmentation, Machine Learning, Deep Learning, Dermatology, Optimization. [bibtex-key = isbi2021]



26. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Direct AI-based Prediction of Clinical Management Bypassing Diagnosis: Application to Skin Lesions. In UBC Dermatology and Skin Science: Skin Research Day, 2021. Keyword(s): Deep Learning, Dermatology,. [bibtex-key = skin2021b]



27. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. Culprit-Prune-Net: Efficient Continual Sequential Multi-Domain Learning with Application to Skin Lesion Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 12907, pages 165-175, 2021. Keyword(s): Classification, Dermatology, Machine Learning, Deep Learning, Continual Learning, Domain Generalization. [bibtex-key = miccai2021]



28. Ben Cardoen and Ghassan Hamarneh. Learning to look beyond what we can see: Leveraging statistical learning to improve scientific discovery from fluorescence microscopy. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Processing, Belief Theory. [bibtex-key = bmiai2021a]



29. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Self-tuning Weakly Supervised Object Detection (SPECHT) of Sub-Diffraction Limited Caveolae and Scaffold and Amyloid-Beta Deposits. In American Society of Cell Biology -- Cell Bio 2021, 2021. Keyword(s): Object Detection, Super Resolution Microscopy, Belief Theory, Datasets. [bibtex-key = cellbio2021]



30. Ben Cardoen, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables detection of Caveolae in superresolution microscopy.. In Microscopy Societies Symposium - Advanced Imaging and Analysis at Nanoscale, November 2021. Keyword(s): Object Detection, Super Resolution Microscopy, Belief Theory. [bibtex-key = jsm2021]



31. Weina Jin and Ghassan Hamarneh. Physician-Centered Explainable AI. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Deep Learning, Explainable AI (XAI), Glioma Imaging. [bibtex-key = bmiai2021c]



32. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. One Map Does Not Fit All: Evaluating Saliency Map Explanation on Multi-Modal Medical Images. In International Conference on Machine Learning (ICML) workshop on Interpretable Machine Learning in Healthcare (IMLH), pages 1-13, 2021. Keyword(s): Deep Learning, Explainable AI (XAI), Glioma Imaging, Multimodal. [bibtex-key = icml_imlh2021]



33. Ismail M. Khater, Timothy H. Wong, Stéphane Vassilopoulos, Ivan Robert Nabi, and Ghassan Hamarneh. SuperResNET: a GUI software package for single molecule localization microscopy cluster analysis (Nabi and Hamarneh: Joint senior authors). In Single Molecule Localization Microscopy Symposium - Current Trends, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2021]



34. Mia McLean, Lynne Williams, Colin J. Brown, Ghassan Hamarneh, Cecil Chau, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Neonatal Pain-related Stress, Neonatal Structural Brain Subnetworks, Cortisol and Behavior at 4 years in Children Born Very Preterm. In 54th Annual Meeting of the International Society for Developmental Psychobiology, Chicago, USA, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = isdp2021]



35. Mia McLean, Lynne Williams, Jeremy Kawahara, Colin J. Brown, Ghassan Hamarneh, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Associations Between Neonatal Pain-Related Stress, Neonatal Brain Structural Connectome, and Behavior at School Age in Children Born Very Preterm. In 6th Annual Research Day Brain, Behaviour and Development (BB&D), Vancouver, Canada, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = bcbbd2021]



36. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = bmiai2021b]



37. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations - Application to Skin Lesion Segmentation. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) ISIC Skin Image Analysis Workshop (CVPR ISIC), pages 1837-1846, 2021. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = cvpr_isic2021]



38. Mengliu Zhao, Jeremy Kawahara, Sajjad Shamanian, Kumar Abhishek, and Ghassan Hamarneh. Computerized Localization and Tracking of Pigmented Skin Lesions on 3D Whole Body Textured Skin Meshes (Zhao and Kawahara: Joint first authors). In UBC Dermatology and Skin Science: Skin Research Day, 2021. Keyword(s): Deep Learning, Tracking, Dermatology. [bibtex-key = skin2021a]



39. Kumar Abhishek, Ghassan Hamarneh, and Mark S. Drew. Illumination-based Transformations Improve Skin Lesion Segmentation in Dermoscopic Images. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) ISIC Skin Image Analysis Workshop (CVPR ISIC), pages 728-729, 2020. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = cvpr_isic2020]



40. Ali Arab, Betty Chinda, William Siu, George Medvedev, Tao Gu, Hui Guo, Sylvain Moreno, Ghassan Hamarneh, Martin Ester, and Xiaowei Song. A fully-automated convolutional neural network with deep supervision approach for haemorrhage segmentation and volume quantification in CT scans. In American Society of Neuroradiology (ASNR), pages 1, 2020. Keyword(s): Deep Learning, Machine Learning, Segmentation. [bibtex-key = asnr2020]



41. Shahab Aslani, Vittorio Murino, Michael Dayan, Roger Tam, Diego Sona, and Ghassan Hamarneh. Scanner Invariant Multiple Sclerosis Lesion Segmentation from MRI. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 781-785, 2020. Keyword(s): Segmentation, Machine Learning, Deep Learning, Multiple Sclerosis, MRI. [bibtex-key = isbi2020]



42. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Automatic identification of protein complexes in multi-scale microscopy with applications tometastasis and Alzheimer disease. In The 2nd Annual Tri-Cluster Research Day, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = tricluster2020b]



43. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables identification of protein complexes in multi-scale microscopy with applications to metastasis and Alzheimer disease. In Centre for Artificial Intelligence Decision-making and Action (CAIDA), BC's AI Showcase, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = caida2020b]



44. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. In Acoustical Society of America Meeting (ASA), pages 1, 2020. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = asa2020]



45. Saeed Izadi and Ghassan Hamarneh. Patch-based Non-Local Bayesian Networks for Blind Confocal Microscopy Denoising. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 12265, pages 46–55, 2020. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = miccai2020]



46. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. SuperNet: Super-resolution Network Analysis and Quantification of Single Molecule Clusters. In Single Molecule Localization Microscopy Symposium - Showtime, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2020]



47. Chloe Lim, Hayyan Liaqat, William Siu, Ghassan Hamarneh, and George Medvedev. Future implementation of automated analysis tools for Multiple Sclerosis on conventional magnetic resonance imaging (Lim and Liaqat: Joint first authors; Hamarneh and Medvedev: Joint senior authors). In 8th joint Americas Committee for Treatment and Research in Multiple Sclerosis - European Committee for Treatment and Research in Multiple Sclerosis (joint ACTRIMS-ECTRMS), pages 1, 2020. Keyword(s): Segmentation, Software and Tools, Multiple Sclerosis, MRI. [bibtex-key = ectrms2020]



48. M.Sadegh Saberian, Kathleen Moriarty, Andrea Olmstead, François Jean, Ivan Robert Nabi, Maxwell Libbrecht, and Ghassan Hamarneh. Drug Repurposing Efficacy Estimation based on Morphological Analysis of SARS-CoV-2 Infected Cells within a Multiple Instance Learning Framework. In Machine learning for computational biology conference (MLCB), pages 1-13, 2020. Keyword(s): Deep Learning, Machine Learning, COVID19, SARS-CoV-2. [bibtex-key = mlcb2020]



49. Mengliu Zhao, Sajjad Shamanian, Priyanka Chandrashekar, Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Acquisition and Analysis of 3D Whole Body Skin Images for Dermatological Studies. In The 2nd Annual Tri-Cluster Research Day, Canada, pages 1, 2020. Keyword(s): Deep Learning, Dermatology. [bibtex-key = tricluster2020a]



50. Mengliu Zhao, Sajjad Shamanian, Priyanka Chandrashekar, Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Skin Lesion Localization and Tracking on 3D Whole Body Colored Surface Images. In Centre for Artificial Intelligence Decision-making and Action (CAIDA), BC's AI Showcase, Canada, pages 1, 2020. Keyword(s): Deep Learning, Dermatology. [bibtex-key = caida2020a]



51. Kumar Abhishek and Ghassan Hamarneh. Mask2Lesion: Mask-Constrained Adversarial Skin Lesion Image Synthesis. In Medical Image Computing and Computer-Assisted Intervention Workshop on Simulation and Synthesis in Medical Imaging (MICCAI SASHIMI), volume 11827, pages 71-80, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Generative Adversarial Network, Dermatology, Synthesis/Simulation/Augmentation. [bibtex-key = miccai_sashimi2019]



52. Saeedeh Afshari, Aicha BenTaieb, Zahra Mirikharaji, and Ghassan Hamarneh. Weakly Supervised Fully Convolutional Network for PET Lesion Segmentation. In SPIE Medical Imaging, volume 10949, pages 1-7, 2019. Keyword(s): Deep Learning, Machine Learning, Functional/Molecular/Dynamic Imaging, Localization. [bibtex-key = spiemi2019]



53. Ben Cardoen, Fiona Dickson, Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Interaction zone analysis of CAV1 - CAVIN1 in breast cancer cells. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = embo2019a]



54. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. ImHistNet: Learnable Image Histogram Based DNN with Application to Noninvasive Determination of Carcinoma Grades in CT Scans. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 130-138, 2019. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = miccai2019e]



55. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. Renal Cell Carcinoma Staging with Learnable Image Histogram-based Deep Neural Network. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 533-540, 2019. Keyword(s): Machine Learning, Deep Learning, Classification. [bibtex-key = miccai_mlmi2019c]



56. Saeed Izadi, Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. WhiteNNer - Blind Image Denoising via Noise Whiteness Priors. In International Conference on Computer Vision workshop on Visual Recognition for Medical Images (ICCV VRMI), pages 476-484, 2019. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = iccv_vrmi2019b]



57. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning for Medical Image Reconstruction (MICCAI MLMIR), volume 11905, pages 236-244, 2019. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = miccai_mlmir2019]



58. Weina Jin, Sheelagh Carpendale, Ghassan Hamarneh, and Diane Gromala. Bridging AI Developers and End Users: an End-User-Centred Explainable AI Taxonomy and Visual Vocabularies. In IEEE Visualization (IEEE Vis), 2019. Keyword(s): Explainable AI (XAI), Deep Learning, User Interaction, Visualization. [bibtex-key = vis2019]



59. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Cav1 Domains Using Super Resolution Microscopy and Machine Learning. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = embo2019b]



60. Zahra Mirikharaji, Yiqi Yan, and Ghassan Hamarneh. Learning to Segment Skin Lesions from Noisy Annotations. In Medical Image Computing and Computer-Assisted Intervention Workshop on Medical Image Learning with Less Labels and Imperfect Data (MICCAI MIL3ID), volume 11795, pages 207-215, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology. [bibtex-key = miccai_mil3id2019]



61. Saeid Asgari Taghanaki, Kumar Abhishek, Shekoofeh Azizi, and Ghassan Hamarneh. A Kernelized Manifold Mapping to Diminish the Effect of Adversarial Perturbations. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 11332-11341, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Classification. [bibtex-key = cvpr2019]



62. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Improved Inference via Deep Input Transfer. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 819-827, 2019. Keyword(s): Segmentation, Machine Learning, Deep Learning. [bibtex-key = miccai2019b]



63. Saeid Asgari Taghanaki, Aicha BenTaieb, Anmol Sharma, S. Kevin Zhou, Yefeng Zheng, Bogdan Georgescu, Puneet Sharma, Daguang Xu, Dorin Comaniciu, and Ghassan Hamarneh. SAT: Select, Attend, and Transfer: Light, Learnable Skip Connections. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 417-425, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = miccai_mlmi2019b]



64. Saeid Asgari Taghanaki, Mohammad Havaei, Tess Berthier, Francis Dutil, Lisa Di Jorio, Ghassan Hamarneh, and Yoshua Bengio. InfoMask: Masked Variational Latent Representation to Localize Chest Disease. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 739-747, 2019. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = miccai2019a]



65. Timothy H. Wong, Mona Shahsavari, Ismail M. Khater, Bharat Joshi, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy Identification of Focal Adhesion-Associated Caveolin-1 Domains (Wong and Shahsavari: Joint first authors). In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis. [bibtex-key = embo2019c]



66. Yiqi Yan, Jeremy Kawahara, and Ghassan Hamarneh. Melanoma Recognition via Visual Attention. In Information Processing in Medical Imaging (IPMI), volume 11492, pages 793–804, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology. [bibtex-key = ipmi2019]



67. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Limited-Angle Diffuse Optical Tomography Image Reconstruction using Deep Learning. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11764, pages 66-74, 2019. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = miccai2019c]



68. Chris Yoon, Ghassan Hamarneh, and Rafeef Abugharbieh. Generalizable Feature Learning in the Presence of Data Bias and Domain Class Imbalance with Application to Skin Lesion Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11767, pages 365-373, 2019. Keyword(s): Classification, Dermatology, Machine Learning, Deep Learning. [bibtex-key = miccai2019d]



69. Mengliu Zhao and Ghassan Hamarneh. Retinal Image Classification via Vasculature-guided Sequential Attention. In International Conference on Computer Vision workshop on Visual Recognition for Medical Images (ICCV VRMI), pages 381-387, 2019. Keyword(s): Anatomical Trees and Tubular Structures, Classification, Shape Modelling and Analysis, Machine Learning, Deep Learning. [bibtex-key = iccv_vrmi2019a]



70. Mengliu Zhao and Ghassan Hamarneh. Tree-LSTM: Using LSTM to Encode Memory in Anatomical Tree Prediction from 3D Images. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 637-645, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = miccai_mlmi2019a]



71. Aicha BenTaieb and Ghassan Hamarneh. Predicting Cancer with a Recurrent Visual Attention Model for Histopathology Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11071, pages 129-137, 2018. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning. [bibtex-key = miccai2018b]



72. Saurabh Garg, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Joint Gender-, Tone-, Vowel- Classification via Novel Hierarchical Classification for Annotation of Monosyllabic Mandarin Word Tokens. In IEEE International Conference on Acoustics, Speech, and Signal Processing (IEEE ICASSP), pages 5744-5748, 2018. Keyword(s): Tracking, Segmentation, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = icassp2018]



73. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Computer-vision analysis shows different facial movements for the production of different Mandarin tones. In Acoustical Society of America Meeting (ASA), pages 1, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = asa2018b]



74. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. Noninvasive Determination of Gene Mutations in Clear Cell Renal Cell Carcinoma using Multiple Instance Decisions Aggregated CNN. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11071, pages 657-665, 2018. Keyword(s): Super Resolution, Machine Learning, Deep Learning. [bibtex-key = miccai2018d]



75. Saeed Izadi, Zahra Mirikharaji, Jeremy Kawahara, and Ghassan Hamarneh. Generative Adversarial Networks to Segment Skin Lesions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 881-884, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Generative Adversarial Network, Segmentation. [bibtex-key = isbi2018b]



76. Saeed Izadi, Kathleen Moriarty, and Ghassan Hamarneh. Can Deep Learning Relax Endomicroscopy Hardware Miniaturization Requirements?. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11070, pages 57-64, 2018. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = miccai2018c]



77. Jeremy Kawahara, Colin J. Brown, and Ghassan Hamarneh. Connectome Priors in Deep Neural Networks to Predict Autism (Kawahara and Brown: Joint first authors). In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 110-113, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Connectome, Machine Learning, Deep Learning, Classification. [bibtex-key = isbi2018c]



78. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Modular Structure of Caveolin-1 Scaffolds and Caveolae Identified by Single Molecule Localization Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1343 (Abstract P2707), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graph based. [bibtex-key = ascb2018b]



79. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolin-1 Domain Characterization Using Machine Learning and Graphlet Analysis of Single Molecule Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1342 (Abstract P2706), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = ascb2018a]



80. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Characterization of caveolin-1 domains via graphlet decomposition of SMLM super resolution data. In Genesis BME day, Vancouver, Canada, pages 1, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = bme2018]



81. Zahra Mirikharaji and Ghassan Hamarneh. Star Shape Prior in Fully Convolutional Networks for Skin Lesion Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11073, pages 737-745, 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology, Color/Multichannel/Vector-valued, Shape Modelling and Analysis. [bibtex-key = miccai2018a]



82. Zahra Mirikharaji, Saeed Izadi, Jeremy Kawahara, and Ghassan Hamarneh. Deep Auto-context Fully Convolutional Neural Network for Skin Lesion Segmentation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 877-880, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Segmentation. [bibtex-key = isbi2018a]



83. Adria Romero-Lopez, Tory Jarmain, Latif Abid, Jevin Maltais, Albert Jimenez, Jeremy Kawahara, Ghassan Hamarneh, Shuang Ao, Mohamed Akrout, Anirudh Challa, Michael Aristocrat, Katrina Cirone, Stephen Solis, and Andrew McCann. Q&A-informed image-based deep learning for skin disease recognition in the real world. In Self-Organizing Conference on Machine Learning (SOCML), pages 1, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Reinforcement Learning, Classification. [bibtex-key = socml2018]



84. Saeid Asgari Taghanaki, Arkadeep Das, and Ghassan Hamarneh. Vulnerability Analysis of Chest X-Ray Image Classification Against Adversarial Attacks. In Medical Image Computing and Computer-Assisted Intervention Workshop on Deep Learning Fails (MICCAI DLF), volume 11038, pages 87-94, 2018. Keyword(s): Machine Learning, Deep Learning, Adversarial Attacks. [bibtex-key = miccai_dlf2018]



85. Yue Wang, Beverly Hannah, Keith Leung, Sylvia Cho, Joan Sereno, Allard Jongman, Charles Redmon, Yuyu Zeng, Ghassan Hamarneh, Lisa Y. W. Tang, Saurabh Garg, Paul Tupper, and Bob McMurray. Linking production and perception of clear speech. In Acoustical Society of America Meeting (ASA), pages 1, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = asa2018a]



86. Hanene Ben Yedder, Aicha BenTaieb, Majid Shokoufi, Amir Zahiremami, Farid Golnaraghi, and Ghassan Hamarneh. Deep Learning based Image Reconstruction for Diffuse Optical Tomography. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning for Medical Image Reconstruction (MICCAI MLMIR), volume 11074, pages 112-119, 2018. Keyword(s): Image Reconstruction, Diffuse Optical Tomography, Machine Learning, Deep Learning. [bibtex-key = miccai_mlmir2018]



87. Mengliu Zhao and Ghassan Hamarneh. TreeNet: Multi-Loss Deep Learning Network to Predict Branch Direction for Extracting 3D Anatomical Trees. In Medical Image Computing and Computer-Assisted Intervention Workshop on Deep Learning in Medical Image Analysis (MICCAI DLMIA), volume 11045, pages 47-55, 2018. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Machine Learning, Deep Learning, Bifurcation/Junction. [bibtex-key = miccai_dlmia2018]



88. Payam Ahmadvand, Noirin Duggan, Francois Benard, and Ghassan Hamarneh. Tumour Lesion Segmentation from 3D PET using a Machine Learning driven Active Surface. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = healthtech2017b]



89. Aicha BenTaieb and Ghassan Hamarneh. Artificial Pathologists: Machine Learning Models for Histopathology. In Annual SFU Health Research Day - Women's Health Research Symposium, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning. [bibtex-key = sfu_health2017]



90. Aicha BenTaieb and Ghassan Hamarneh. Topology Aware Fully Convolutional Networks For Histology Gland Segmentation. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning. [bibtex-key = healthtech2017a]



91. Aicha BenTaieb and Ghassan Hamarneh. Uncertainty Driven Multi-Loss Fully Convolutional Networks for Histopathology. In Medical Image Computing and Computer-Assisted Intervention Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis (MICCAI LABELS), volume 10552, pages 155-163, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning. [bibtex-key = miccai_labels2017a]



92. Colin J. Brown, Kathleen Moriarty, Steven Miller, Brian G. Booth, Vann Chau, Anne Synnes, Ruth Grunau, and Ghassan Hamarneh. Prediction of Brain Network Age and Factors of Delayed Maturation in Very Preterm Infants. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10433, pages 84-91, 2017. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = miccai2017b]



93. Mian Huang and Ghassan Hamarneh. SwifTree: Interactive Extraction of 3D Trees Supporting Gaming and Crowdsourcing. In Medical Image Computing and Computer-Assisted Intervention Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis (MICCAI LABELS), volume 10552, pages 116-125, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Gaming, Crowdsourcing. [bibtex-key = miccai_labels2017b]



94. Arafat Hussain, Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Collage CNN for Renal Cell Carcinoma Detection from CT. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10541, pages 229-237, 2017. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization. [bibtex-key = miccai_mlmi2017]



95. Arafat Hussain, Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Segmentation-Free Kidney Localization and Volume Estimation Using Aggregated Orthogonal Decision CNNs. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10435, pages 612-620, 2017. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization. [bibtex-key = miccai2017c]



96. Bebart Janbek, Brian G. Booth, and Ghassan Hamarneh. A Tensor Field Mumford-Shah Segmentation of Neural Pathways in DW-MRI. In Society for Industrial and Applied Mathematics (SIAM) Annual Meeting, Pittsburgh, Pennsylvania, USA, pages 1, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Segmentation, Optimization. [bibtex-key = siam2017b]



97. 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 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning, Classification. [bibtex-key = healthtech2017c]



98. Jeremy Kawahara, Kathleen Moriarty, and Ghassan Hamarneh. Graph Geodesics to Find Progressively Similar Skin Lesion Images. In Medical Image Computing and Computer-Assisted Intervention Workshop on Graphs in Biomedical Image Analysis (MICCAI GRAIL), pages 1-11, 2017. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Graph based. [bibtex-key = miccai_grail2017]



99. Ismail M. Khater, Youtao Liu, Qian Liu, Fanrui Meng, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. Distinguishing Biological and Non-Biological Networks in Single Molecule Localization Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), Philadelphia, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2017]



100. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = healthtech2017d]



101. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In SIAM-IMAGING Manitoba Workshop on Mathematical Imaging Science, Winnipeg, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = siam2017a]



102. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In Gordon Research Conference, Andover, NH, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = gordon2017a]



103. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Molecular Level Quantification of Cav1 Clusters in Super-Resolution Imaging Data. In Frontiers in Biophysics, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = frontiers_biophysics2017]



104. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction. [bibtex-key = healthtech2017e]



105. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths (Mirikharaji and Zhao: Joint first authors). In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10434, pages 242-250, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction. [bibtex-key = miccai2017a]



106. Saeid Asgari Taghanaki, Noirin Duggan, Hillgan Ma, Anna Celler, Francois Benard, and Ghassan Hamarneh. Lesion volume Estimation from PET without Requiring Segmentation. In Quantitative Imaging Network (QIN) Annual Meeting, 2017. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = qin2017]



107. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Localization in 3D Images via Evolutionary Geometric Deformable Templates. In Canadian Conference on Computer and Robot Vision (CRV), pages 124-130, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Deformable Models, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = crv2017a]



108. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Leveraging Tree Statistics for Extracting Anatomical Trees from 3D Medical Images. In Canadian Conference on Computer and Robot Vision (CRV), pages 131-138, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = crv2017b]



109. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Tree Structure Analysis in 3D Medical Images. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = healthtech2017f]



110. 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. [bibtex-key = miccai_mlmi2016b]



111. 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. [bibtex-key = qin2016]



112. 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. [bibtex-key = miccai2016a]



113. 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. [bibtex-key = isbi2016a]



114. 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. [bibtex-key = neuroscix2016b]



115. 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. [bibtex-key = miccai2016b]



116. 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. [bibtex-key = miccai_mlmi2016c]



117. 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. [bibtex-key = isbi2016b]



118. 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. [bibtex-key = neuroscix2016a]



119. 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. [bibtex-key = miccai_mlmi2016a]



120. 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. [bibtex-key = ascb2016]



121. 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. [bibtex-key = superres2016]



122. 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. [bibtex-key = ascblsi2016]



123. 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. [bibtex-key = cinc2016]



124. 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. [bibtex-key = isbi2016c]



125. 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. [bibtex-key = wcb2016]



126. 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. [bibtex-key = miccai2015d]



127. 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. [bibtex-key = miccai2015b]



128. 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. [bibtex-key = miccai2015a]



129. 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. [bibtex-key = wcd2015a]



130. 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. [bibtex-key = nanolytica2015]



131. 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. [bibtex-key = asci2015]



132. 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. [bibtex-key = wcd2015c]



133. 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. [bibtex-key = ccma2015]



134. 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. [bibtex-key = wcd2015b]



135. 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. [bibtex-key = isbs2015]



136. 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. [bibtex-key = isbi2015c]



137. 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. [bibtex-key = isbi2015a]



138. 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. [bibtex-key = can-acn2015]



139. 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. [bibtex-key = isbi2015b]



140. 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. [bibtex-key = miccai2015c]



141. 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. [bibtex-key = icphs2015]



142. 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. [bibtex-key = wcmpbe2015]



143. Alborz Amir-Khalili, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, Ghassan Hamarneh, and Rafeef Abugharbieh. Auto Localization and Segmentation of Occluded Vessels in Robot-Assisted Partial Nephrectomy. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8673, pages 407-414, 2014. Keyword(s): Spatio-Temporal, Segmentation, Image-Guided Surgery. [bibtex-key = miccai2014d]



144. Shawn Andrews, Lisa Y. W. Tang, and Ghassan Hamarneh. Fast Random Walker Image Registration using Precomputation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 189-192, 2014. Keyword(s): Registration and Matching, Fast MIA. [bibtex-key = isbi2014d]



145. Shawn Andrews, Lisa Y. W. Tang, and Ghassan Hamarneh. Topology Preservation and Anatomical Feasibility in Random Walker Image Registration. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8673, pages 210-217, 2014. Keyword(s): Registration and Matching. [bibtex-key = miccai2014a]



146. Brian G. Booth and Ghassan Hamarneh. DTI-DeformIt: Generating Ground-Truth Validation Data for Diffusion Tensor Image Analysis Tasks. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 730-733, 2014. Keyword(s): Diffusion MRI/Tensor-valued, Synthesis/Simulation/Augmentation, Software and Tools, Validation, Physical Modelling. [bibtex-key = isbi2014b]



147. Colin J. Brown, Steven Miller, Brian G. Booth, Shawn Andrews, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Analysis of Structural Connectome Development in Healthy Preterm Neonates. In Annual Neuroscience Extravaganza, Brain Research Centre, UBC, 2014. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment. [bibtex-key = neuroscix2014]



148. Ivan Figueroa, Jean-Marc Peyrat, Ghassan Hamarneh, and Rafeef Abugharbieh. Biomechanical Kidney Model for Predicting Tumor Displacement in the Presence of External Pressure Load. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 810-813, 2014. Keyword(s): Physical Modelling. [bibtex-key = isbi2014e]



149. Ghassan Hamarneh, Alborz Amir-Khalili, Masoud Nosrati, Ivan Figueroa, Jeremy Kawahara, Osama Al-Alao, Jean-Marc Peyrat, Julien Abi-Nahed, Abdulla Al-Ansari, and Rafeef Abugharbieh. Towards Multi-Modal Image-Guided Tumour Identification in Robot-Assisted Partial Nephrectomy. In IEEE Middle East Conference on Biomedical Engineering (IEEE MECBME), pages 159-162, 2014. Keyword(s): Image-Guided Surgery, Segmentation, Registration and Matching, Physical Modelling, Multimodal. [bibtex-key = mecbme2014]



150. Jeremy Kawahara, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, Rafeef Abugharbieh, and Ghassan Hamarneh. Automatic Labelling of Tumourous vs Tumour-Free Frames in Free-Hand Laparoscopic Ultrasound Video. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8674, pages 677-684, 2014. Keyword(s): Spatio-Temporal, Machine Learning, Segmentation, Image-Guided Surgery. [bibtex-key = miccai2014c]



151. Hengameh Mirzaalian and Ghassan Hamarneh. Automatic Globally-Optimal Pictorial Structures with Random Decision Forest Based Likelihoods For Cephalometric X-Ray Landmark Detection. In Automatic Cephalometric X-Ray Landmark Detection Challenge 2014, in conjunction with IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1-12, 2014. Keyword(s): Challenge, Machine Learning, Optimization. [bibtex-key = isbi2014_chlg_ceph]



152. Masoud Nosrati and Ghassan Hamarneh. A Variational Approach for Overlapping Cell Segmentation. In Overlapping Cervical Cytology Image Segmentation Challenge, in conjunction with IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1-2, 2014. Keyword(s): Challenge, Segmentation. [bibtex-key = isbi2014_chlg_cell]



153. Masoud Nosrati, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, Rafeef Abugharbieh, and Ghassan Hamarneh. Efficient Multi-Organ Segmentation in Multi-View Endoscopic Videos using Pre-Op Priors. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8674, pages 324-331, 2014. Keyword(s): Fast MIA, Registration and Matching, Segmentation, Optimization, Image-Guided Surgery. [bibtex-key = miccai2014b]



154. Lisa Y. W. Tang and Ghassan Hamarneh. Random Walk Image Registration via Cost Aggregation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 576-579, 2014. Keyword(s): Registration and Matching, Fast MIA. [bibtex-key = isbi2014c]



155. Roja Zakariaee, Colin J. Brown, Ghassan Hamarneh, Christina Parsons, and Ingrid Spadinger. Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration. In Canadian Organization of Medical Physicists 60th Annual Scientific Meeting (COMP), 2014. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = comp2014]



156. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Detection in 3D Vascular Images Using Novel Features and Random Forest. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 421-424, 2014. Keyword(s): Anatomical Trees and Tubular Structures, Machine Learning, Bifurcation/Junction. [bibtex-key = isbi2014a]



157. Alborz Amir-Khalili, Masoud Nosrati, Jean-Marc Peyrat, Ghassan Hamarneh, and Rafeef Abugharbieh. Uncertainty-Encoded Augmented Reality for Robot-Assisted Partial Nephrectomy: A Phantom Study. In Medical Image Computing and Computer-Assisted Intervention Workshop on Medical Imaging and Augmented Reality (MICCAI MIAR), volume 8090, pages 182-191, 2013. Keyword(s): Uncertainty, Image-Guided Surgery, Stereo/Multi-View Reconstruction. [bibtex-key = miccai_miar2013]



158. Alborz Amir-Khalili, Jean-Marc Peyrat, Ghassan Hamarneh, and Rafeef Abugharbieh. 3D Surface Reconstruction of Organs using Patient-Specific Shape Priors in Robot-Assisted Laparoscopic Surgery. In Medical Image Computing and Computer-Assisted Intervention Workshop on on Abdominal Imaging: Computational and Clinical Applications (MICCAI ABDI), volume 8198, pages 184-193, 2013. Keyword(s): Image-Guided Surgery, Stereo/Multi-View Reconstruction. [bibtex-key = miccai_abdi2013]



159. Brian G. Booth and Ghassan Hamarneh. A Cross-sectional Piecewise Constant Model for Segmenting Highly Curved Fiber Tracts in Diffusion MR Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8151, pages 469-476, 2013. Keyword(s): Diffusion MRI/Tensor-valued, Segmentation. [bibtex-key = miccai2013b]



160. Brian G. Booth, Steven Miller, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Modelling the Healthy Premature Infant Brain. In Annual Neuroscience Extravaganza, Brain Research Centre, UBC, 2013. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment. [bibtex-key = neuroscix2013]



161. Colin J. Brown, Brian G. Booth, and Ghassan Hamarneh. K-Confidence: Assessing Uncertainty in Tractography using k Optimal Paths. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 250-253, 2013. Keyword(s): Diffusion MRI/Tensor-valued, Optimization, Uncertainty. [bibtex-key = isbi2013a]



162. Colin J. Brown, Brian G. Booth, and Ghassan Hamarneh. Uncertainty in Tractography via Tract Confidence Regions. In Medical Image Computing and Computer-Assisted Intervention Workshop on Computational Diffusion MRI (MICCAI CDMRI), pages 13-22, 2013. Keyword(s): Uncertainty, Diffusion MRI/Tensor-valued. [bibtex-key = miccai_cdmri2013]



163. Ghassan Hamarneh, Alborz Amir-Khalili, Masoud Nosrati, Ivan Figueroa, Osama Al-Alao, Abdulla Al-Ansari, Julien Abi-Nahed, Jean-Marc Peyrat, and Rafeef Abugharbieh. Towards Image-Guided Minimally Invasive Robotic Surgery for Partial Nephrectomy. In The Qatar Foundation Annual Research Conference (QF-ARC), 2013. Keyword(s): Image-Guided Surgery, Stereo/Multi-View Reconstruction. [bibtex-key = qfarc2013]



164. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Augmenting Auto-context with Global Geometric Features for Spinal Cord Segmentation. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 212-219, 2013. Keyword(s): Segmentation, Machine Learning, Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = miccai_mlmi2013a]



165. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Globally Optimal Spinal Cord Segmentation using A Minimal Path in High Dimensions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 836-839, 2013. Keyword(s): Segmentation, Optimization, Anatomical Trees and Tubular Structures, Graph based, Multiple Sclerosis, MRI. [bibtex-key = isbi2013b]



166. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Novel Morphological and Appearance Features for Predicting Physical Disability from MR Images in Multiple Sclerosis Patients. In Medical Image Computing and Computer-Assisted Intervention Workshop on Computational Methods and Clinical Applications for Spine Imaging (MICCAI CSI), pages 1-13, 2013. Keyword(s): Machine Learning, Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = miccai_csi2013]



167. Tayebeh Lotfi, Lisa Y. W. Tang, Shawn Andrews, and Ghassan Hamarneh. Improving probabilistic image registration via reinforcement learning and uncertainty evaluation. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 188-195, 2013. Keyword(s): Uncertainty, Registration and Matching, Machine Learning. [bibtex-key = miccai_mlmi2013b]



168. Hamidreza Mirzaei, Lisa Y. W. Tang, Rene Werner, and Ghassan Hamarneh. Decision Forests with Spatio-temporal Features for Graph-based Tumour Segmentation in 4D Lung CT. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 179-186, 2013. Keyword(s): Segmentation, Machine Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = miccai_mlmi2013c]



169. Masoud Nosrati, Shawn Andrews, and Ghassan Hamarneh. Bounded Labeling Function for Global Segmentation of Multi-Part Objects with Geometric Constraints. In IEEE International Conference on Computer Vision (IEEE ICCV), pages 2032-2039, 2013. Keyword(s): Optimization, Segmentation. [bibtex-key = iccv2013]



170. Masoud Nosrati and Ghassan Hamarneh. Segmentation of Cells with Partial Occlusion and Part Configuration Constraint using Evolutionary Computation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8149, pages 461-468, 2013. Keyword(s): Optimization, Segmentation. [bibtex-key = miccai2013c]



171. Manku Rana, Ghassan Hamarneh, and James Wakeling. Changes to 3D muscle fascicle geometry during contraction. In American Society of Biomechanics (ASB), 2013. Keyword(s): Shape Modelling and Analysis, Tracking. [bibtex-key = asb2013]



172. Lisa Y. W. Tang and Ghassan Hamarneh. Random walks with efficient search and contextually adapted image similarity for deformable registration. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8150, pages 43-50, 2013. Keyword(s): Optimization, Registration and Matching, Uncertainty. [bibtex-key = miccai2013a]



173. Shawn Andrews, Brian G. Booth, Steven Miller, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Towards highly-automated detection of white matter injury in prematurely born babies from diffusion tensor MRI. In NeuroDevNet Brain Development Conference, pages 99, 2012. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment. [bibtex-key = neurodevnet2012]



174. Daniel Baboiu and Ghassan Hamarneh. Vascular Bifurcation Detection in Scale-Space. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 41-46, 2012. Keyword(s): Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = mmbia2012b]



175. Brian G. Booth and Ghassan Hamarneh. Competitive Tractography for Extracting Brain Connectivity from Diffusion MRI. In The 6th Annual Canadian Neuroscience Meeting (CAN-ACN), 2012. Keyword(s): Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = can-acn2012]



176. Brian G. Booth and Ghassan Hamarneh. Global Multi-Region Competitive Tractography. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 73-78, 2012. Keyword(s): Diffusion MRI/Tensor-valued, Uncertainty. [bibtex-key = mmbia2012a]



177. Brian G. Booth, Steven Miller, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Modelling the Healthy Premature Infant Brain. In Child and Family Research Imaging Facility Grand Opening Event, 2012. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment. [bibtex-key = cfri2012]



178. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Learning Features for Streak Detection in Dermoscopic Color Images using Localized Radial Flux of Principal Intensity Curvature. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 97-101, 2012. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Anatomical Trees and Tubular Structures, Dermatology. [bibtex-key = mmbia2012d]



179. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Uncertainty-based Feature Learning for Skin Lesion Matching using a High Order MRF Optimization Framework. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 7511, pages 98-105, 2012. Keyword(s): Machine Learning, Uncertainty, Optimization, Dermatology. [bibtex-key = miccai2012]



180. Hengameh Mirzaalian, Ahmed Saad, and Ghassan Hamarneh. Iterative Segmentation and Motion Correction for Dynamic PET Images based on Radioactive Tracer Kinetics. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 265-270, 2012. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Registration and Matching, Tracking. [bibtex-key = mmbia2012c]



181. Krishna Nand, Ghassan Hamarneh, and Rafeef Abugharbieh. Diffusion Tensor Image Processing using Biquaternions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 538-541, 2012. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = isbi2012b]



182. Fahime Sheikhzadeh, Roger Tam, and Ghassan Hamarneh. Spatial Distribution of Lesions as a Surrogate Biomarker for Disability in Multiple Sclerosis. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 273-278, 2012. Keyword(s): Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = mmbia2012e]



183. Lisa Y. W. Tang, Alfred O Hero, and Ghassan Hamarneh. Locally-Adaptive Similarity Metric for Deformable Medical Image Registration. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 728-731, 2012. Keyword(s): Machine Learning, Registration and Matching. [bibtex-key = isbi2012a]



184. Shawn Andrews, Ghassan Hamarneh, Azadeh Yazdanpanah, Bahareh HajGhanbari, and W. Darlene Reid. Probabilistic Multi-Shape Segmentation of Knee Extensor and Flexor Muscles. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6893, pages 651-658, 2011. Keyword(s): Segmentation, Uncertainty, Optimization. [bibtex-key = miccai2011a]



185. Shawn Andrews, Chris McIntosh, and Ghassan Hamarneh. Convex Multi-Region Probabilistic Segmentation with Shape Prior in the Isometric Logratio Transformation Space. In IEEE International Conference on Computer Vision (IEEE ICCV), pages 2096-2103, 2011. Keyword(s): Optimization, Segmentation, Uncertainty. [bibtex-key = iccv2011]



186. Brian G. Booth and Ghassan Hamarneh. Consistent Information Content Estimation for Diffusion Tensor MR Images. In IEEE Conference on Healthcare Informatics, Imaging and Systems Biology (IEEE HISB), pages 166-173, 2011. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = hisb2011a]



187. Brian G. Booth and Ghassan Hamarneh. Exact Integration of Diffusion Orientation Distribution Functions for Graph-Based Diffusion MRI Analysis. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 935-938, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = isbi2011]



188. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. 3D shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Canadian Physiotherapy Association Congress, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = cpa2011]



189. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based Three dimensional shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Heart+Lung Health Fest, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = hlf2011]



190. Chris McIntosh, Ghassan Hamarneh, Matt Toom, and Roger Tam. Spinal Cord Segmentation for Volume Estimation in Healthy and Multiple Sclerosis Subjects using Crawlers and Minimal Paths. In IEEE Conference on Healthcare Informatics, Imaging and Systems Biology (IEEE HISB), pages 25-31, 2011. Keyword(s): Artificial Life, Deformable Organisms, Segmentation, Anatomical Trees and Tubular Structures, Multiple Sclerosis, MRI. [bibtex-key = hisb2011b]



191. Hengameh Mirzaalian, Ghassan Hamarneh, Bahareh HajGhanbari, and W. Darlene Reid. 3D Shape Analysis of the Knee Extensor and Flexor Muscles in Patients with COPD using Mesh Projection-based Features. In Medical Image Computing and Computer-Assisted Intervention Workshop on Mesh Processing in Medical Image Analysis (MICCAI MeshMed), pages 1-8, 2011. Keyword(s): Medial-based Shape Representation, Shape Modelling and Analysis. [bibtex-key = miccai_meshmed2011]



192. Krishna Nand, Rafeef Abugharbieh, Brian G. Booth, and Ghassan Hamarneh. Detecting Structure in Diffusion Tensor MR Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6892, pages 90-97, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Processing, Anatomical Trees and Tubular Structures. [bibtex-key = miccai2011c]



193. Manku Rana, Ghassan Hamarneh, and James Wakeling. Automated methods for determination of 3D muscle fascicle orientation in human muscle using free hand ultrasound. In American Society of Biomechanics (ASB), 2011. Keyword(s): Shape Modelling and Analysis, Tracking. [bibtex-key = asb2011]



194. Andrea Tagliasacchi, Matt Olson, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. VASE: Volume-Aware Surface Evolution for Surface Reconstruction from Incomplete Point Clouds. In Symposium on Geometry Processing (SGP) (also appears in the Special Issue of the Journal Computer Graphics Forum), pages 1563-1571, 2011. Keyword(s): Deformable Models, Shape Modelling and Analysis. [bibtex-key = sgp2011]



195. Lisa Y. W. Tang, Ghassan Hamarneh, and Tim Bressmann. A Machine Learning Approach to Tongue Motion Analysis in 2D Ultrasound Image Sequences. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 7009, pages 151-158, 2011. Keyword(s): Tracking, Machine Learning. [bibtex-key = miccai_mlmi2011]



196. Andrew Top, Ghassan Hamarneh, and Rafeef Abugharbieh. Active Learning for Interactive 3D Image Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6893, pages 603-610, 2011. Keyword(s): Uncertainty, User Interaction, Segmentation. [bibtex-key = miccai2011b]



197. Oliver van Kaick, Andrea Tagliasacchi, Oana Sidi, Hao (Richard) Zhang, Daniel Cohen-Or, Lior Wolf, and Ghassan Hamarneh. Prior Knowledge for Part Correspondence. In Eurographics (also appears in the Special Issue of the Journal Computer Graphics Forum), pages 1-10, 2011. Keyword(s): Segmentation, Registration and Matching, Shape Modelling and Analysis. [bibtex-key = eg2011]



198. Shawn Andrews, Ghassan Hamarneh, and Ahmed Saad. Fast Random Walker with Priors using Precomputation for Interactive Medical Image Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6363, pages 9-16, 2010. Keyword(s): Segmentation, Graph based. [bibtex-key = miccai2010b]



199. Neda Changizi and Ghassan Hamarneh. Probabilistic Multi-Shape Representation using an Isometric Log-Ratio Mapping. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6363, pages 563-570, 2010. Keyword(s): Shape Modelling and Analysis, Uncertainty. [bibtex-key = miccai2010a]



200. Neda Changizi and Ghassan Hamarneh. Probabilistic multi-label representation for anatomical statistical shape analysis. In SFU Exchange, 2010. Keyword(s): Shape Modelling and Analysis, Uncertainty. [bibtex-key = sfu_exchange2010b]



201. Neda Changizi, Ghassan Hamarneh, Omer Ishaq, Aaron Ward, and Roger Tam. Extraction of the Plane of Minimal Cross-Sectional Area of the Corpus Callosum using Template-Driven Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6363, pages 17-24, 2010. Keyword(s): Registration and Matching, Segmentation, Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = miccai2010c]



202. Hengameh Mirzaalian and Ghassan Hamarneh. Vessel Scale Selection using MRF Optimization. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 3273-3278, 2010. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Graph based. [bibtex-key = cvpr2010a]



203. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Back Atlas for Tracking Pigmented Skin Lesions. In Annual UBC and CIHR Skin Research Day, 2010. Keyword(s): Registration and Matching, Tracking, Dermatology. [bibtex-key = skin2010]



204. Shane Mottishaw, Sergey Zhuravlev, Lisa Y. W. Tang, Alexandra Fedorova, and Ghassan Hamarneh. An Evaluation of Parallelization Techniques for MRF Image Segmentation. In International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making (MICCAI HP), pages 10 pages, 2010. Keyword(s): Segmentation, Software, Fast MIA. [bibtex-key = miccai_hp2010b]



205. Bernard Ng, Rafeef Abugharbieh, and Ghassan Hamarneh. Group MRF for fMRI Activation Detection. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 2887-2894, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = cvpr2010b]



206. Bernard Ng, Ghassan Hamarneh, and Rafeef Abugharbieh. Detecting Brain Activation in fMRI Using Group Random Walker. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6362, pages 331-338, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = miccai2010d]



207. Bernard Ng, Arash Vahdat, Ghassan Hamarneh, and Rafeef Abugharbieh. Generalized Sparse Classifiers for Decoding Cognitive States in fMRI. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 6357, pages 108-115, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = miccai_mlmi2010]



208. Peyman Rahmati, Ghassan Hamarneh, Doron Nussbaum, and Andy Adler. A New Preprocessing Filter for Digital Mammograms. In International Conference on Image and Signal Processing (ICISP), pages 585-592, 2010. Keyword(s): Processing. [bibtex-key = icisp2010]



209. Manku Rana, Ghassan Hamarneh, and James Wakeling. In- vivo determination of 3D muscle architecture of the human triceps muscle using free hand ultrasound. In Society of Integrative and Comparative Biology (SICB), 2010. Keyword(s): Shape Modelling and Analysis, Tracking. [bibtex-key = sicb2010]



210. Josna Rao, Rafeef Abugharbieh, and Ghassan Hamarneh. Adaptive Regularization for Image Segmentation Using Local Image Curvature Cues. In European Conference on Computer Vision (ECCV), pages 651-665, 2010. Keyword(s): Segmentation, Optimization, Graph based. [bibtex-key = eccv2010]



211. Ahmed Saad, Ghassan Hamarneh, and Torsten Moeller. Exploration and Visualization of Segmentation Uncertainty using Shape and Appearance Prior Information. In IEEE Visualization (IEEE Vis) (also appears in the Special Issue of the Journal IEEE Transactions on Visualization and Computer Graphics), pages 1366-1375, 2010. Keyword(s): User Interaction, Segmentation, Uncertainty, Spatio-Temporal. [bibtex-key = vis2010]



212. Ahmed Saad, Torsten Moeller, and Ghassan Hamarneh. ProbExplorer: An Uncertainty-based Visual Analysis Tool for Medical Imaging. In Eurographics/IEEE-VGTC Symposium on Visualization (IEEE EuroVis) (also appears in the Special Issue of the Journal Computer Graphics Forum)., volume 29, pages 1113-1122, 2010. Keyword(s): Software and Tools, Segmentation, Uncertainty, User Interaction, Visualization, Spatio-Temporal. [bibtex-key = eurovis2010]



213. Ahmed Saad, Torsten Moeller, and Ghassan Hamarneh. ProbExplorer: Uncertainty-guided Exploration and Editing of Probabilistic Medical Image Segmentation. In SFU Exchange, 2010. Keyword(s): Software and Tools, Segmentation, Uncertainty, User Interaction, Visualization, Spatio-Temporal. [bibtex-key = sfu_exchange2010a]



214. Ben Smith, Ghassan Hamarneh, and Ahmed Saad. Fast GPU Fitting of Kinetic Models for Dynamic PET. In International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making (MICCAI HP), pages 10 pages, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Software and Tools, Fast MIA. [bibtex-key = miccai_hp2010a]



215. Lisa Y. W. Tang and Ghassan Hamarneh. Graph-based tracking of the tongue contour in ultrasound sequences with adaptive temporal regularization. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA) in conjunction with the IEEE Conference on Computer Vision and Pattern Recognition (IEEE CVPR), pages 154-161, 2010. Keyword(s): Tracking, Registration and Matching, Graph based. [bibtex-key = mmbia2010]



216. Lisa Y. W. Tang, Ghassan Hamarneh, and Rafeef Abugharbieh. Reliability-Driven, Spatially-Adaptive Regularization for Deformable Registration. In Workshop on Biomedical Image Registration (WBIR), pages 173-185, 2010. Keyword(s): Registration and Matching. [bibtex-key = wbir2010]



217. Andrew Top, Ghassan Hamarneh, and Rafeef Abugharbieh. Spotlight: Automated Confidence-based User Guidance for Increasing Efficiency in Interactive 3D Image Segmentation. In Medical Image Computing and Computer-Assisted Intervention Workshop on Medical Computer Vision (MICCAI MCV), volume 6533, pages 204-213, 2010. Keyword(s): Uncertainty, User Interaction, Segmentation. [bibtex-key = miccai_mcv2010]



218. Oliver van Kaick, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. A Survey on Shape Correspondence. In EuroGraphics: State-of-the-Art Report, pages 61-82, 2010. Keyword(s): Survey/Review, Registration and Matching, Shape Modelling and Analysis. [bibtex-key = eg2010]



219. Ghassan Hamarneh. Airway Segmentation using Crawlers and Optimal Paths. In First International Workshop on Dynamic Modeling of the Oral, Pharyngeal and Laryngeal Complex for Biomedical Applications (OPAL), pages 43, 2009. Keyword(s): Deformable Organisms, Segmentation, Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = opal2009]



220. Ghassan Hamarneh. Multi-Label MRF Optimization via a Least Squares s-t Cut. In International Symposium on Visual Computing: Special Track on Optimization for Vision, Graphics and Medical Imaging: Theory and Applications (ISVC OVGMI), volume 5875-I, pages 1055-1066, 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = isvc2009a]



221. Ghassan Hamarneh and Neda Changizi. Barycentric Label Space. In Medical Image Computing and Computer-Assisted Intervention Workshop on Probabilistic Models for Medical Image Analysis (MICCAI PMMIA), pages 162-173, 2009. Keyword(s): Shape Modelling and Analysis, Uncertainty. [bibtex-key = miccai_pmmia2009]



222. Thomas Humphries, Ahmed Saad, Anna Celler, Ghassan Hamarneh, Torsten Moeller, and Manfred Trummer. Segmentation-Based Regularization of Dynamic SPECT Reconstructions. In IEEE Medical Imaging / Nuclear Science Conference (IEEE MIC/NSS), pages 2849-2852, 2009. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = mic2009]



223. Chris McIntosh and Ghassan Hamarneh. Optimal Weights for Convex Functionals in Medical Image Segmentation. In International Symposium on Visual Computing: Special Track on Optimization for Vision, Graphics and Medical Imaging: Theory and Applications (ISVC OVGMI), volume 5875-I, pages 1079-1088, 2009. Keyword(s): Optimization, Segmentation, Machine Learning. [bibtex-key = isvc2009b]



224. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Graph-based Approach to Skin Mole Matching Incorporating Template-Normalized Coordinates. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 2152-2159, 2009. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = cvpr2009]



225. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Skin Mole Matching Incorporating Template-Normalized Coordinates. In Annual UBC and CIHR Skin Research Day, 2009. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = skin2009]



226. Bernard Ng, Rafeef Abugharbieh, Ghassan Hamarneh, and Martin McKeown. Random Walker Based Estimation and Spatial Analysis of Probabilistic fMRI Activation Maps. In Medical Image Computing and Computer-Assisted Intervention Workshop on Statistical modeling and detection issues in intra- and inter-subject functional MRI data analysis (MICCAI fMRI), pages 37-44, 2009. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = miccai_fmri2009]



227. Manku Rana, Ghassan Hamarneh, and James Wakeling. In- vivo determination of 3D muscle architecture of the human triceps surfae using free hand ultrasound. In Canadian Student Conference in Biomedical Computing (CSCBC), 2009. Keyword(s): Shape Modelling and Analysis, Tracking. [bibtex-key = cscbc2010]



228. Josna Rao, Ghassan Hamarneh, and Rafeef Abugharbieh. Adaptive Contextual Energy Parameterization for Automated Image Segmentation. In Lecture Notes in Computer Science, International Symposium on Visual Computing: Special Track on Optimization for Vision, Graphics and Medical Imaging: Theory and Applications (ISVC OVGMI), volume 5875-I, pages 1089-1100, 2009. Keyword(s): Optimization, Segmentation. [bibtex-key = isvc2009c]



229. Maryam Sadeghi, Geoff Tien, Ghassan Hamarneh, and Stella Atkins. Hands-free Interactive Image Segmentation Using Eyegaze. In SPIE Medical Imaging, volume 72601H, pages 1-10, 2009. Keyword(s): Segmentation, User Interaction, Graph based. [bibtex-key = spiemi2009]



230. Yonas Weldeselassie, Ghassan Hamarneh, Faisal Beg, and Stella Atkins. Novel Decomposition of Tensor Distance into Shape and Orientation Distances. In Medical Image Computing and Computer-Assisted Intervention Workshop on Diffusion Modelling and the Fibre Cup (MICCAI DMFB), pages 173-180, 2009. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = miccai_dmfc2009]



231. Yonas Weldeselassie, Ghassan Hamarneh, Samantha Palmer, Martin McKeown, and Stella Atkins. Diffusion Properties of Cortico-Striatal White Matter Tractography As Sensistive Markers of Parkinson's Disease. In The 17th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), 2009. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = ismrm2009]



232. Azadeh Yazdanpanah, Ghassan Hamarneh, Ben Smith, and Marinko Sarunic. Intra-retinal Layer Segmentation in Optical Coherence Tomography using an Active Contour Approach. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 5762, pages 649-656, 2009. Keyword(s): Deformable Models, Segmentation. [bibtex-key = miccai2009]



233. Lingshu Yin, Lisa Y. W. Tang, Ghassan Hamarneh, Anna Celler, Sergey Shcherbinin, Tsien-Fei Fua, Hannah Carolan, Anna Thompson, Mitchell Liu, Cheryl Duzenli, Brad Gill, Finbar Sheehan, John Powe, Daniel Worsley, and Vitali Moiseenko. Evaluating geometrical accuracy of image registration methods in SPECT guided radiation therapy. In Medical Image Computing and Computer-Assisted Intervention Workshop on Geometric accuracy in image guided intervention (MICCAI GAIGI), pages 63-70, 2009. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = miccai_gaigi2009]



234. Lingshu Yin, Lisa Y. W. Tang, Ghassan Hamarneh, Vitali Moiseenko, Anna Celler, Sergey Shcherbinin, Tsien-Fei Fua, Anna Thompson, Mitchell Liu, Cheryl Duzenli, Brad Gill, Finbar Sheehan, John Powe, and Daniel Worsley. Quantitative evaluation on the accuracy of image registration methods in SPECT guided radiation therapy for lung cancer patients. In Canadian Organization of Medical Physicists 55th Annual Scientific Meeting (COMP), 2009. Keyword(s): Functional/Molecular/Dynamic Imaging, Registration and Matching, Multimodal. [bibtex-key = comp2009]



235. Ghassan Hamarneh, Preet Jassi, and Lisa Y. W. Tang. Simulation of Ground-Truth Validation Data via Physically- and Statistically-based Warps. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 5241, pages 459-467, 2008. Keyword(s): Registration and Matching, Segmentation, Shape Modelling and Analysis, Software and Tools, Validation, Synthesis/Simulation/Augmentation, Physical Modelling. [bibtex-key = miccai2008b]



236. William Ma, Ghassan Hamarneh, Greg Mori, Katie Dinelle, and Vesna Sossi. Motion Estimation for Functional Medical Imaging Studies using a Stereo Video Head Pose Tracking System. In IEEE Medical Imaging / Nuclear Science Conference (IEEE MIC/NSS), pages 4086-4090, 2008. Keyword(s): Tracking, Registration and Matching. [bibtex-key = mic2008]



237. Manku Rana, Ghassan Hamarneh, and James Wakeling. Automated tracking of muscle fascicle orientation in B-mode ultrasound images. In North American Congress on Biomechanics (NACB), 2008. Keyword(s): Shape Modelling and Analysis, Tracking. [bibtex-key = nacb2008]



238. Ahmed Saad, Ghassan Hamarneh, Torsten Moeller, and Ben Smith. Kinetic Modeling based Probabilistic Segmentation for Molecular Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 5241, pages 244-252, 2008. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Uncertainty, Graph based. [bibtex-key = miccai2008a]



239. Lilong Shi, Brian Funt, and Ghassan Hamarneh. Quaternion Color Curvature. In Color Imaging (IS&T/SID CI), pages 338-341, 2008. Keyword(s): Processing, Color/Multichannel/Vector-valued, Anatomical Trees and Tubular Structures. [bibtex-key = ci2008]



240. Ben Smith, Ahmed Saad, Ghassan Hamarneh, and Torsten Moeller. Recovery of Dynamic PET Regions via Simultaneous Segmentation and Deconvolution. In Ghassan Hamarneh and Rafeef Abugharbieh, editors, Medical Image Computing and Computer-Assisted Intervention Workshop on Analysis of Functional Medical Image Data (MICCAI functional), pages 33-40, 2008. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = miccai_func2008]



241. Lisa Y. W. Tang and Ghassan Hamarneh. SMRFI: Shape Matching via Registration of Vector-Valued Feature Images. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 1-8, 2008. Keyword(s): Registration and Matching. [bibtex-key = cvpr2008]



242. Lisa Y. W. Tang, Ghassan Hamarneh, and Anna Celler. Increasing Accuracy of Mutual Information-Based Registration of Tumor SPECT and CT Images with Dual-isotope Studies. In Society for Imaging Informatics in Medicine Annual Meeting (SIIM), pages 59-61, 2008. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = siim2008]



243. Warren Cheung and Ghassan Hamarneh. n-SIFT: n-dimensional Scale Invariant Feature Transform for Matching Medical Images. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 720-723, 2007. Keyword(s): Registration and Matching. [bibtex-key = isbi2007b]



244. Mark S. Drew and Ghassan Hamarneh. Visualizing Diffusion Tensor Dissimilarity using an ICA Based Perceptual Color Metric. In Color Imaging (IS&T/SID CI), pages 42-47, 2007. Keyword(s): Visualization, Diffusion MRI/Tensor-valued, Color. [bibtex-key = ci2007]



245. Zhe Fang, Torsten Moeller, Ghassan Hamarneh, and Anna Celler. Visualization and Exploration of Time-Varying Medical Image Data Sets. In Graphics Interface (GI), pages 281-288, 2007. Keyword(s): Visualization, User Interaction, Spatio-Temporal, Segmentation. [bibtex-key = gi2007]



246. Ghassan Hamarneh, Aaron Ward, and Richard Frank. Quantification and Visualization of Localized and Intuitive Shape Variability using a Novel Medial-Based Shape Representation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1232-1235, 2007. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation. [bibtex-key = isbi2007a]



247. Ghassan Hamarneh, Aaron Ward, Chris McIntosh, Ben Smith, Lisa Y. W. Tang, Ahmed Saad, Yonas Weldeselassie, and Omer Ishaq. Medical Image Analysis. In TechMed, Vancouver, May 16, 2007. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Deformable Organisms, Artificial Life, Imaging, Software and Tools. [bibtex-key = techmed2007]



248. Omer Ishaq, Ghassan Hamarneh, Roger Tam, and Anthony Traboulsee. Longitudinal, Regional and Deformation-Specific Corpus Callosum Shape Analysis for Multiple Sclerosis. In IEEE Engineering in Medicine and Biology (IEEE EMBC), pages 2110-2113, 2007. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation, Multiple Sclerosis, MRI. [bibtex-key = embc2007]



249. Chris McIntosh and Ghassan Hamarneh. Is a Single Energy Functional Sufficient? Adaptive Energy Functionals and Automatic Initialization. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 503-510, 2007. Keyword(s): Deformable Models, Segmentation, Optimization, Machine Learning. [bibtex-key = miccai2007c]



250. Chris McIntosh, Ghassan Hamarneh, and Greg Mori. Human Limb Delineation and Joint Position Recovery Using Localized Boundary Models. In IEEE Workshop on Motion and Video Computing (IEEE WMVC), pages 31-38, 2007. Keyword(s): Segmentation, Deformable Models, Deformable Organisms, Tracking. [bibtex-key = wmvc2007]



251. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-Vessel: Extending Livewire for Simultaneous Extraction of Optimal Medial and Boundary Paths in Vascular Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 444-451, 2007. Keyword(s): Deformable Models, Segmentation, Anatomical Trees and Tubular Structures, Graph based. [bibtex-key = miccai2007a]



252. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Segmentation of Complex Objects with Non-Spherical Topologies from Volumetric Medical Images using 3D Livewire. In SPIE Medical Imaging, volume 6512-31, pages 1-10, 2007. Keyword(s): Segmentation, User Interaction, Graph based. [bibtex-key = spiemi2007a]



253. Ahmed Saad, Ben Smith, Ghassan Hamarneh, and Torsten Moeller. Simultaneous Segmentation, Kinetic Parameter Estimation, and Uncertainty Visualization of Dynamic PET Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 726-733, 2007. Keyword(s): Segmentation, Functional/Molecular/Dynamic Imaging, Uncertainty, Graph based. [bibtex-key = miccai2007b]



254. Aaron Ward and Ghassan Hamarneh. 3D Surface Parameterization Using Manifold Learning for Medial Shape Representation. In SPIE Medical Imaging, volume 6512-0X, pages 1-8, 2007. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation. [bibtex-key = spiemi2007d]



255. Aaron Ward and Ghassan Hamarneh. Statistical Shape Modeling using MDL Incorporating Shape, Appearance, and Expert Knowledge. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4791, pages 278-285, 2007. Keyword(s): Shape Modelling and Analysis, Registration and Matching. [bibtex-key = miccai2007d]



256. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. Anatomical Shape Analysis: Exploring the Relationship between Shape and Pathology. In CIHR National Research Poster Competition, Canadian Student Health Research Forum (CSHRF), Winnipeg, June 6-7, 2007. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = cshrf2007]



257. Yonas Weldeselassie and Ghassan Hamarneh. DT-MRI Segmentation Using Graph Cuts. In SPIE Medical Imaging, volume 6512-1K, pages 1-9, 2007. Keyword(s): Segmentation, Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = spiemi2007b]



258. Yonas Weldeselassie, Ghassan Hamarneh, and Daniel Weiskopf. Tensor Distance Based Adaptive Seeding Algorithm for DT-MRI Visualization. In SPIE Medical Imaging, volume 65092M, pages 1-9, 2007. Keyword(s): Visualization, Diffusion MRI/Tensor-valued. [bibtex-key = spiemi2007c]



259. Oliver van Kaick, Ghassan Hamarneh, Hao (Richard) Zhang, and Paul Wighton. Contour Correspondence via Ant Colony Optimization. In Pacific Graphics (PG), pages 271-280, 2007. Keyword(s): Registration and Matching, Optimization. [bibtex-key = pg2007]



260. Anna Celler, Andy Rova, and Ghassan Hamarneh. NMQC: A NEMA-compliant software application for gamma camera quality control. In Annual meeting of the Canadian Society of Nuclear Medicine (CSNM), 2006. Keyword(s): Imaging, Software and Tools. [bibtex-key = csnm2006a]



261. Anna Celler, Lisa Y. W. Tang, Ghassan Hamarneh, and Philip Cohen. Co-registration of CT-SPECT images for tumor localization and dosimetry. In European Association of Nuclear Medicine Annual Congress (EANM), pages 260, 2006. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = eanm2006]



262. Vincent Chu and Ghassan Hamarneh. MATLAB-ITK interface for medical image filtering, segmentation, and registration. In SPIE Medical Imaging, volume 61443T, pages 1-8, 2006. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = spiemi2006a]



263. Ghassan Hamarneh and Judith Hradsky. Bilateral Filtering of Diffusion Tensor MR Images. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 508-512, 2006. Keyword(s): Processing, Diffusion MRI/Tensor-valued. [bibtex-key = isspit2006a]



264. Ghassan Hamarneh and Judith Hradsky. DTMRI Segmentation using DT-Snakes and DT-Livewire. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 513-518, 2006. Keyword(s): Segmentation, Deformable Models, Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = isspit2006b]



265. Omer Ishaq, Ghassan Hamarneh, Roger Tam, and Anthony Traboulsee. Effects of Mid Sagittal Plane Perturbation and Image Interpolation on Corpus Callosum Area Calculation. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 197-202, 2006. Keyword(s): Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = isspit2006c]



266. Omer Ishaq, Ghassan Hamarneh, Roger Tam, Anthony Traboulsee, and David Li. Effects of mid sagittal plane selection on corpus callosal area. In 22nd Congress of the European Committee for Treatment and Research in Multiple Sclerosis (ECTRMS) (Also appeared in Multiple Sclerosis Journal 12(1):S173, 2006), pages 616, 2006. Keyword(s): Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = ectrms2006]



267. Chris McIntosh and Ghassan Hamarneh. Genetic algorithm driven statistically deformed models for medical image segmentation. In ACM Workshop on Medical Applications of Genetic and Evolutionary Computation Workshop, in conjunction with the Genetic and Evolutionary Computation Conference (ACM GECCO MedGEC), pages 8 pages, 2006. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models, Artificial Life. [bibtex-key = medgec2006]



268. Chris McIntosh and Ghassan Hamarneh. I-DO: A Deformable Organisms framework for ITK. In Medical Image Computing and Computer-Assisted Intervention Open Science Workshop (also appears in the Insight Journal) (MICCAI OS), pages 1-14, 2006. Keyword(s): Deformable Organisms, Software and Tools, Artificial Life. [bibtex-key = miccai_os2006]



269. Chris McIntosh and Ghassan Hamarneh. Spinal Crawlers: Deformable Organisms for Spinal Cord Segmentation and Analysis. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4190, pages 808-815, 2006. Keyword(s): Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Anatomical Trees and Tubular Structures. [bibtex-key = miccai2006]



270. Chris McIntosh and Ghassan Hamarneh. Vessel Crawlers: 3D Physically-based Deformable Organisms for Vasculature Segmentation and Analysis. In IEEE Conference on Computer Vision and Pattern Recognition (IEEE CVPR), pages 1084-1091, 2006. Keyword(s): Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = cvpr2006]



271. Andy Rova, Anna Celler, and Ghassan Hamarneh. NMQC: A NEMA-compliant software application for gamma camera quality control. In Annual meeting of the Society for Computer Applications in Radiology (SCAR), pages 91-93, 2006. Keyword(s): Imaging, Software and Tools. [bibtex-key = scar2006b]



272. Andy Rova, Anna Celler, and Ghassan Hamarneh. NMQC: A NEMA-compliant software for gamma camera quality control. In Vancouver Coastal Health Research Institute (VCHRI), 2006. Keyword(s): Imaging, Software and Tools. [bibtex-key = vchri2006a]



273. Kevin Stevenson, Mark Schweitzer, and Ghassan Hamarneh. Multi-angle deformation analysis of Hoffa's fat pad. In SPIE Medical Imaging, volume 6143-29, pages 1-9, 2006. Keyword(s): Segmentation, Registration and Matching. [bibtex-key = spiemi2006c]



274. Lisa Y. W. Tang, Anna Celler, and Ghassan Hamarneh. Co-registration and fusion of CT and SPECT images. In Annual meeting of the Canadian Society of Nuclear Medicine (CSNM), 2006. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = csnm2006b]



275. Lisa Y. W. Tang, Ghassan Hamarneh, and Anna Celler. Co-registration and fusion of CT and SPECT images using mutual information. In Vancouver Coastal Health Research Institute (VCHRI), 2006. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = vchri2006b]



276. Lisa Y. W. Tang, Ghassan Hamarneh, and Anna Celler. Co-registration of Bone CT and SPECT Images Using Mutual Information. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 116-121, 2006. Keyword(s): Registration and Matching, Multimodal, Functional/Molecular/Dynamic Imaging. [bibtex-key = isspit2006d]



277. Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle. In Medical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 96-103, 2006. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = miccai_jd2006b]



278. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Shape Description of the Bicipital Groove: Correlation to Pathology. In Medical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 80-87, 2006. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = miccai_jd2006a]



279. Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. 3D shape description of the bicipital groove of the proximal humerus. In SPIE Medical Imaging, volume 6143-27, pages 1-9, 2006. Keyword(s): Shape Modelling and Analysis. [bibtex-key = spiemi2006b]



280. Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. Computational and Visualization Techniques for Understanding the Shape Variations of the Bicipital Groove of the Proximal Humerus. In Annual meeting of the Society for Computer Applications in Radiology (SCAR), pages 47-49, 2006. Keyword(s): Visualization, Shape Modelling and Analysis. [bibtex-key = scar2006a]



281. Artur Chodorowski, Ulf Mattsson, Morgan Langille, and Ghassan Hamarneh. Color lesion boundary detection using live wire. In SPIE Medical Imaging, volume 5747, pages 1589-1596, 2005. Keyword(s): Segmentation, Deformable Models, Color/Multichannel/Vector-valued, Graph based. [bibtex-key = spiemi2005d]



282. Vincent Chu and Ghassan Hamarneh. MATITK: MATLAB-ITK Interface for Medical Image Processing. In 1st Annual Medical Technology Research Showcase, Vancouver, BC, 2005. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = medical_showcase2005a]



283. Ghassan Hamarneh, Vincent Chu, Marcelo Bordalo-Rodrigues, and Mark Schweitzer. Deformation analysis of Hoffa's fat pad from CT images of knee flexion and extension. In SPIE Medical Imaging, volume 5746, pages 527-534, 2005. Keyword(s): Segmentation, Registration and Matching, Shape Modelling and Analysis. [bibtex-key = spiemi2005b]



284. Ghassan Hamarneh and Chris McIntosh. Physics-based deformable organisms for medical image analysis. In SPIE Medical Imaging, volume 5747, pages 326-335, 2005. Keyword(s): Segmentation, Shape Modelling and Analysis, Medial-based Shape Representation, Deformable Organisms, Artificial Life. [bibtex-key = spiemi2005a]



285. Ghassan Hamarneh, Johnson Yang, Chris McIntosh, and Morgan Langille. 3D live-wire-based semi-automatic segmentation of medical images. In SPIE Medical Imaging, volume 5747, pages 1597-1603, 2005. Keyword(s): Segmentation, Deformable Models. [bibtex-key = spiemi2005c]



286. Xiaoxing Li and Ghassan Hamarneh. Modeling Prior Shape and Appearance Knowledge in Watershed Segmentation. In Canadian Conference on Computer and Robot Vision (CRV), pages 27-33, 2005. Keyword(s): Segmentation, Shape Modelling and Analysis. [bibtex-key = crv2005]



287. Chris McIntosh and Ghassan Hamarneh. Artificial Life Models for Medical Image Analysis - 2D and 3D ITK-Based Deformable Organisms. In 1st Annual Medical Technology Research Showcase, Vancouver, BC, 2005. Keyword(s): Segmentation, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = medical_showcase2005c]



288. Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. Shape Description of the Bicipital Groove of the Proximal Humerus. In 1st Annual Medical Technology Research Showcase, Vancouver, BC, 2005. Keyword(s): Shape Modelling and Analysis. [bibtex-key = medical_showcase2005b]



289. Ghassan Hamarneh and Chris McIntosh. Corpus Callosum Segmentation in Magnetic Resonance Images Using Artificial Organisms. In The MSHRF/CIHR Strategic Training Program in Neurobiology and Behaviour. Neuroscience Research Colloquia, Annual Neuroscience Extravaganza, Brain Research Centre, UBC, 11 2004. Keyword(s): Segmentation, Deformable Organisms, Artificial Life. [bibtex-key = neuroscix2004]



290. Josette Chen, Lee Adamson, Leila Baghdadi, Jonathan Bishop, Nick Bock, John Cargill, Lori Davidson, Jun Dazai, Stuart Foster, Ghassan Hamarneh, Natasha Kovacevic, Nir Lifshitz, Brian Nieman, Janet Rossant, John Sled, Yuqing Zhou, and Mark Henkelman. Current Progress of Imaging Screens at the Mouse Imaging Centre. In Integrated Functional Genomics of the Mouse (IFGM), 10 2003. Keyword(s): Imaging, Processing, Segmentation, Registration and Matching. [bibtex-key = ifgm2003]



291. Ghassan Hamarneh, Josette Chen, Nir Lifshitz, and Mark Henkelman. Local volume changes of the corpus callosum from 3D MR images of wildtype and knockout mouse brains. In 11th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), 2003. Keyword(s): Registration and Matching, Shape Modelling and Analysis. [bibtex-key = ismrm2003b]



292. Ghassan Hamarneh, Josette Chen, Brian Nieman, Jeff Henderson, and Mark Henkelman. Processing, Segmentation, Registration, and Deformation Analysis of 3D MR Images of Mice.. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 2879, pages 878-885, 2003. Keyword(s): Processing, Segmentation, Registration and Matching, Deformable Models. [bibtex-key = miccai2003a]



293. Ghassan Hamarneh, Herve Delingette, and Mark Henkelman. 3D segmentation of mouse organs from MR images using deformable simplex mesh models. In 11th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), 2003. Keyword(s): Segmentation, Deformable Models. [bibtex-key = ismrm2003a]



294. Ghassan Hamarneh and Tim McInerney. Physics-based shape deformations for medical image analysis. In SPIE Electronic Imaging, volume 5014, pages 354-362, 2003. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation, Deformable Models. [bibtex-key = spieei2003]



295. Mark Henkelman, Josette Chen, John Sled, John Cargill, Ghassan Hamarneh, Natasha Kovacevic, Leila Baghdadi, Stuart Foster, Yuqing Zhou, Jonathan Bishop, Nick Bock, Brian Nieman, Johnathon Walls, Lori Davidson, Jun Dazai, Nir Lifshitz, Colin McKerlie, Lee Adamson, and Janet Rossant. Imaging for Mouse Phenotyping. In 17th International Mouse Genome Conference (IMGC), 11 2003. Keyword(s): Imaging. [bibtex-key = imgc2003]



296. Natasha Kovacevic, Ghassan Hamarneh, and Mark Henkelman. Anatomically Guided Registration of Whole Body Mouse MR Images.. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 2879, pages 870-877, 2003. Keyword(s): Registration and Matching. [bibtex-key = miccai2003b]



297. Ghassan Hamarneh. [Time Varying Shape, Spatio-Temporal Models] Deformable Spatio-Temporal Shape Models. In R Fisher, editor, In CVonline: On-Line Compendium of Computer Vision [Online], 2002. Note: Available: http://www.dai.ed.ac.uk/CVonline/. [2002, January, 22nd]. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = cvonline2002]



298. Ghassan Hamarneh, Natasha Kovacevic, John Sled, and Mark Henkelman. Deformable Surface Models for Segmenting 3D MR Images of Mice. In Imaging Network Ontario's 2nd Annual Imaging Symposium (INO), 2002. Keyword(s): Segmentation, Deformable Models. [bibtex-key = ino2002a]



299. Mark Henkelman, Nick Bock, Josette Chen, Ghassan Hamarneh, Natasha Kovacevic, and Stuart Foster. Parallel MR Imaging for Mouse Phenotyping. In XXth International Conference on Magnetic Resonance in Biological Systems (MRBS), pages 90, 2002. Keyword(s): Imaging. [bibtex-key = icmrbs2002]



300. Mark Henkelman, Josette Chen, John Cargill, Nick Bock, Brian Nieman, Nir Lifshitz, Stuart Foster, Allison Duckett, John Sled, Jun Dazai, Natasha Kovacevic, Ghassan Hamarneh, Colin McKerlie, Janet Rossant, and Johnathon Walls. An Imaging Centre for Mouse Phenotyping. In 16th International Mouse Genome Conference (IMGC), 2002. Keyword(s): Imaging, Processing, Segmentation, Registration and Matching. [bibtex-key = imgc2002]



301. Natasha Kovacevic, Ghassan Hamarneh, John Sled, and Mark Henkelman. 3D Registration of MR Mouse Images. In Imaging Network Ontario's 2nd Annual Imaging Symposium (INO), 2002. Keyword(s): Registration and Matching. [bibtex-key = ino2002b]



302. Rafeef Abugharbieh, Tomas Gustavsson, Clemens Kaminski, and Ghassan Hamarneh. Flame Front Matching and Tracking in PLIF Images using Geodesic Paths and Level Sets. In IEEE International Conference on Computer Vision workshop on Variational and Level Set Methods in Computer Vision (IEEE ICCV VLSM), pages 112-118, 2001. Keyword(s): Segmentation, Registration and Matching. [bibtex-key = iccv_vlsm2001]



303. Ghassan Hamarneh and Tomas Gustavsson. Deformable Spatio-Temporal Shape Models: Extending ASM to 2D+Time. In British Machine Vision Conference (BMVC), volume 1, pages 13-22, 2001. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = bmvc2001]



304. Ghassan Hamarneh and Tim McInerney. Controlled Shape Deformations via Medial Profiles. In Vision Interface (VI), pages 252-258, 2001. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation. [bibtex-key = vi2001]



305. Ghassan Hamarneh, Tim McInerney, and Demetri Terzopoulos. Deformable Organisms for Automatic Medical Image Analysis.. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 2208, pages 66-75, 2001. Keyword(s): Segmentation, Deformable Organisms, Artificial Life. [bibtex-key = miccai2001]



306. Karin Althoff, Ghassan Hamarneh, and Tomas Gustavsson. Tracking Contrast in Echocardiography by a Combined Snake and Optical Flow Technique. In IEEE Computers in Cardiology (IEEE CinC), volume 27, pages 29-32, 2000. Keyword(s): Segmentation, Deformable Models. [bibtex-key = cinc2000a]



307. Ghassan Hamarneh. Image Segmentation with Constrained Snakes. In Swedish Image Analysis Society Newsletter SSABlaskan, number 8, pages 5-6, 2000. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = ssablaskan2000]



308. Ghassan Hamarneh, Karin Althoff, and Tomas Gustavsson. Snake Deformations Based on Optical Flow Forces for Contrast Agent Tracking in Echocardiography. In Swedish Symposium on Image Analysis (SSIA), pages 45-48, 2000. Keyword(s): Segmentation, Deformable Models. [bibtex-key = ssab2000b]



309. Ghassan Hamarneh, Artur Chodorowski, and Tomas Gustavsson. Active Contour Models: Application to Oral Lesion Detection in Color Images. In IEEE International Conference on Systems, Man, and Cybernetics (IEEE SMC), volume 4, pages 2458 -2463, 2000. Keyword(s): Segmentation, Deformable Models, Color. [bibtex-key = smc2000a]



310. Ghassan Hamarneh and Tomas Gustavsson. Combining Snakes and Active Shape Models for Segmenting the Human Left Ventricle in Echocardiographic Images. In IEEE Computers in Cardiology (IEEE CinC), volume 27, pages 115-118, 2000. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = cinc2000b]



311. Ghassan Hamarneh and Tomas Gustavsson. Constraining Contour Deformations Using Statistical a Priori Knowledge of Shape without Requiring Point-to-Point Correspondence. In Swedish Symposium on Image Analysis (SSIA), pages 33-36, 2000. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = ssab2000a]



312. Ghassan Hamarneh and Tomas Gustavsson. Statistically Constrained Snake Deformations. In IEEE International Conference on Systems, Man, and Cybernetics (IEEE SMC), volume 3, pages 1610-1615, 2000. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = smc2000b]



313. Ghassan Hamarneh and Tomas Gustavsson. A Method for Modeling and Segmentation of Spatio-Temporal Shapes. In Swedish Symposium on Image Analysis (SSIA), pages 49-52, 1999. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = ssab1999]



314. Rafeef Abugharbieh, Ghassan Hamarneh, and Tomas Gustavsson. Review - Active Shape Models - Part II: Image Search and Classification. In Swedish Symposium on Image Analysis (SSIA), pages 129-132, 1998. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = ssab1998b]



315. Ghassan Hamarneh, Rafeef Abugharbieh, and Tomas Gustavsson. Review - Active Shape Models - Part I: Modeling Shape and Gray Level Variation. In Swedish Symposium on Image Analysis (SSIA), pages 125-128, 1998. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = ssab1998a]



316. Tomas Gustavsson, Rafeef Abugharbieh, Ghassan Hamarneh, and Quan Liang. Implementation and Comparison of Four Different Boundary Detection Algorithms for Quantitative Ultrasonic Measurements of the Human Carotid Artery. In IEEE Computers in Cardiology (IEEE CinC), volume 24, pages 69-72, 1997. Keyword(s): Segmentation. [bibtex-key = cinc1997]

1. Kumar Abhishek, Aditi Jain, and Ghassan Hamarneh. Investigating the Quality of DermaMNIST and Fitzpatrick17k Dermatological Image Datasets. Technical report arXiv:2401.14497, 1 2024. Keyword(s): Dermatology, Machine Learning, Deep Learning, Software and Tools, Datasets. [bibtex-key = arxiv:2401.14497]



2. Y. Lydia Li, Ismail M. Khater, Christian Hallgrimson, Timothy H. Wong, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution single molecule network analysis (SuperResNET) detects changes to clathrin structure by small molecule inhibitors (Wong and Khater: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2024.03.07.583946, 3 2024. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction. [bibtex-key = biorxiv_2024_03_07_583946]



3. Y. Lydia Li, Ismail M. Khater, Christian Hallgrimson, Timothy H. Wong, Ghassan Hamarneh, and Ivan Robert Nabi. SuperResNET single molecule localization microscopy model-free network analysis of Nup96 achieves molecular resolution (Li and Khater: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2024.03.12.584716, 3 2024. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction. [bibtex-key = biorxiv_2024_03_12_584716]



4. Ashwin Samudre, Guang Gao, Ben Cardoen, Ivan Robert Nabi, and Ghassan Hamarneh. nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors). Technical report biorxiv:2024.02.20.581259, 2 2024. Keyword(s): Super Resolution Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning, Deep Learning, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = biorxiv_2024_02_20_581259]



5. Ashish Sinha and Ghassan Hamarneh. Representing Anatomical Trees by Denoising Diffusion of Implicit Neural Fields. Technical report arxiv.2403.08974, 3 2024. Keyword(s): Deep Learning, Diffusion Models, Anatomical Trees and Tubular Structures. [bibtex-key = arxiv:2403.08974]



6. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. Technical report techrxiv:22060118, 2 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility. [bibtex-key = techrxiv_22060118]



7. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. Log-Paradox: Necessary and sufficient conditions for confounding statistically significant pattern reversal under the log-transform. Technical report arxiv.2302.04780, 000 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Statistics, Geometric mean, Log-transform. [bibtex-key = arxiv:2302.04780]



8. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. Counting Objects in Images using Deep Learning: Methods and Current Challenges. Technical report Research Square (Preprint) 2986682, 6 2023. Keyword(s): Deep Learning, Counting, Survey/Review, Dermatology. [bibtex-key = research_square2023_2986682]



9. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. SYRAC: Synthesize, Rank, and Count. Technical report arxiv.2310.01662, 10 2023. Keyword(s): Deep Learning, Counting, Ranking. [bibtex-key = arxiv:2310.01662]



10. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. MDViT: Multi-domain Vision Transformer for Small Medical Image Segmentation Datasets Segmentation. Technical report arxiv.2307.02100, 7 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Transformers, Classification. [bibtex-key = arxiv:2307.02100]



11. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, and Ghassan Hamarneh. Invisible Users: Uncovering End-Users' Requirements for Explainable AI via Explanation Forms and Goals. Technical report arxiv.2302.06609, 2 2023. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal, Software and Tools. [bibtex-key = arxiv:2302.06609]



12. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. The XAI Alignment Problem: Rethinking How Should We Evaluate Human-Centered AI Explainability Techniques. Technical report arxiv.2303.17707, 4 2023. Keyword(s): Explainable AI (XAI). [bibtex-key = arxiv:2303.17707]



13. Aliasghar Khani, Saeid Asgari Taghanaki, Aditya Sanghi, Ali Mahdavi-Amiri, and Ghassan Hamarneh. SLiMe: Segment Like Me. Technical report arxiv.2309.03179, 9 2023. Keyword(s): Deep Learning, Segmentation. [bibtex-key = arxiv:2309.03179]



14. Ivan Robert Nabi, Ben Cardoen, Ismail M. Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. Technical report arxiv.2305.17193, 5 2023. Keyword(s): Machine Learning, Deep Learning, Weak Supervision, Super Resolution Microscopy, Validation. [bibtex-key = arxiv:2305.17193]



15. Ashish Sinha, Jeremy Kawahara, Arezou Pakzad, Kumar Abhishek, Matthieu Ruthven, Enjie Ghorbel, Anis Kacem, Djamila Aouada, and Ghassan Hamarneh. DermSynth3D: Synthesis of in-the-wild Annotated Dermatology Images (Sinha, Kawahara, Pakzad: Joint first authors). Technical report arxiv.2305.12621, 5 2023. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = arxiv:2305.12621]



16. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample \(\zeta\)-mixup: Richer, More Realistic Synthetic Samples from a \(p\)-Series Interpolant. Technical report arXiv:2204.03323, 4 2022. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = arxiv:2204.03323]



17. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Vandevoorde, Joshi, and Cardoen: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report Research Square (Preprint) 1559637, 4 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Image Processing, Belief Theory. [bibtex-key = research_square2022_1559637]



18. Ben Cardoen, Guang Gao, Kurt Vandevoorde, Parsa Alan, William Liu, Ghassan Hamarneh, and Ivan Robert Nabi. Automatic sub-precision membrane contact site detection identifies convoluted tubular riboMERCs (Cardoen, Gao, Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2022.06.23.497346, 6 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction. [bibtex-key = biorxiv_2022_06_23_497346]



19. Siyi Du, Ben Her, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. FairDisCo: Fairer AI in Dermatology via Disentanglement Contrastive Learning. Technical report arXiv:2208.10013, 8 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = arxiv:2208.10013]



20. Saurabh Garg, Haoyao Ruan, Ghassan Hamarneh, Dawn M. Behne, Allard Jongman, Joan Sereno, and Yue Wang. Mouth2audio: Intelligible Audio Synthesis from Videos with Distinctive Vowel Articulation. Technical report SSRN Electronic Journal 4146179, 6 2022. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal, Deep Learning. [bibtex-key = ssrn2022_4146179]



21. Saeed Izadi, Isaac Shiri, Carlos Uribe, Parham Geramifar, Habib Zaidi, Arman Rahmim, and Ghassan Hamarneh. Enhanced Direct Joint Attenuation and Scatter Correction of Whole-Body PET Images via Context-Aware Deep Networks. Technical report medRxiv 2022.05.26.22275662, May 2022. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = medrxiv2022_20220526]



22. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Denoising in the Deep Learning Era. Technical report Research Square (Preprint) 1806416, 6 2022. Keyword(s): Deep Learning, Enhancement/Restoration/Denoising, Survey/Review. [bibtex-key = research_square2022_1806416]



23. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, and Ghassan Hamarneh. EUCA: the End-User-Centered Explainable AI Framework. Technical report arXiv:2102.02437, 2 2022. Keyword(s): Explainable AI (XAI). [bibtex-key = arxiv:2102.02437]



24. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, Xiaoxiao Li, and Ghassan Hamarneh. Transcending XAI Algorithm Boundaries through End-User-Inspired Design. Technical report arXiv:2208.08739, 8 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal. [bibtex-key = arxiv:2208.08739]



25. Weina Jin, Mostafa Fatehi, Ru Guo, and Ghassan Hamarneh. Evaluating the Clinical Utility of Artificial Intelligence Assistance and its Explanation on Glioma Grading Task. Technical report medRxiv 2022.12.07.22282726, December 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal. [bibtex-key = medrxiv2022_22282726]



26. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Guidelines and evaluation for clinical explainable AI on medical image analysis. Technical report arXiv:2202.10553, 2 2022. Keyword(s): Deep Learning, Explainable AI (XAI). [bibtex-key = arxiv:2202.10553]



27. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. Evaluating Explainable AI on a Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?. Technical report arXiv:2203.06487, 3 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal. [bibtex-key = arxiv:2203.06487]



28. Mayur Mallya and Ghassan Hamarneh. Deep Multimodal Guidance for Medical Image Classification. Technical report arXiv:2203.05683, 3 2022. Keyword(s): Dermatology, Deep Learning, MRI, Microscopy, Multimodal. [bibtex-key = arxiv:2203.05683]



29. Zahra Mirikharaji, Kumar Abhishek, Alceu Bissoto, Catarina Barata, Sandra Avila, Eduardo Valle, M. Emre Celebi, and Ghassan Hamarneh. A Survey on Deep Learning for Skin Lesion Segmentation (Mirikharaji and Abhishek: Joint first authors; Celebi and Hamarneh: Joint senior authors). Technical report arXiv:2206.00356, 6 2022. Keyword(s): Machine Learning, Deep Learning, Segmentation, Survey/Review, Dermatology. [bibtex-key = arxiv:2206.00356]



30. Arezou Pakzad, Kumar Abhishek, and Ghassan Hamarneh. CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. Technical report arXiv:2208.13528, 8 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = arxiv:2208.13528]



31. Darren Sutton, Zamir K. Punja, and Ghassan Hamarneh. Characterization of Trichome Phenotypes to Assess Maturation and Flower Development in Cannabis sativa L. (Cannabis) by Automatic Trichome Gland Analysis. Technical report SSRN Electronic Journal 4141209, 6 2022. Keyword(s): Agritech, Precision Agriculture, Plant Phenotyping, Trichomes, Medicinal Cannabis. [bibtex-key = ssrn2022_4141209]



32. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Orthogonal Multi-frequency Fusion Based Image Reconstruction and Diagnosis in Diffuse Optical Tomography. Technical report techrxiv:21574533, 11 2022. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = techrxiv_21574533]



33. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Gp78-mediated basal mitophagy promotes mitochondrial health and limits mitochondrial ROS production (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2021.09.17.460825, 9 2021. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = biorxiv_2021_09_17_460825]



34. Mengliu Zhao, Jeremy Kawahara, Sajjad Shamanian, Kumar Abhishek, Priyanka Chandrashekar, and Ghassan Hamarneh. Detection and Longitudinal Tracking of Pigmented Skin Lesions in 3D Total-Body Skin Textured Meshes (Zhao and Kawahara: Joint first authors). Technical report arXiv:2105.00374, 5 2021. Keyword(s): Dermatology, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graph based, Tracking. [bibtex-key = arxiv:2105.00374]



35. Kumar Abhishek and Ghassan Hamarneh. Matthews Correlation Coefficient Loss for Deep Convolutional Networks: Application to Skin Lesion Segmentation. Technical report arXiv:2010.13454, 10 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2010.13454]



36. Kumar Abhishek, Ghassan Hamarneh, and Mark S. Drew. Illumination-based Transformations Improve Skin Lesion Segmentation in Dermoscopic Images. Technical report arxiv:2003.10111, 3 2020. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2003.10111]



37. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Predicting the Clinical Management of Skin Lesions Using Deep Learning. Technical report medRxiv 2020.11.02.20223941, November 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Clinical Management. [bibtex-key = medrxiv2020_20223941]



38. Ben Cardoen and Ghassan Hamarneh. Introduction to Causality. Technical report SFU-Summit-20939, 12 2020. Keyword(s): Machine Learning, Deep Learning, Causality. [bibtex-key = sfu_summit_cardoen_2021a]



39. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). Technical report techrxiv:12971051, 9 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory, Object Detection, Datasets. [bibtex-key = techrxiv_12971051]



40. Saeed Izadi and Ghassan Hamarneh. Patch-based Non-Local Bayesian Networks for Blind Confocal Microscopy Denoising. Technical report arxiv:2003.11177, 3 2020. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = arxiv:2003.11177]



41. Ivan Klyuzhin, Yixi Xu, Anthony Ortiz, Juan Lavista Ferres, Ghassan Hamarneh, and Arman Rahmim. Testing the Ability of Convolutional Neural Networks to Learn Radiomic Features. Technical report medrxiv:20198077, September 2020. Keyword(s): Deep Learning, Machine Learning, Radiomics, Functional/Molecular/Dynamic Imaging. [bibtex-key = medrxiv2020_20198077]



42. Rory Long, Kathleen Moriarty, Ben Cardoen, Guang Gao, A. Wayne Vogl, François Jean, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum (Long and Moriarty: Joint first authors; Hamarneh and Nabi: Joint senior authors. Technical report biorxiv:091611, 5 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning. [bibtex-key = biorxiv_2020_091611]



43. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations - Application to Skin Lesion Segmentation. Technical report arXiv:2012.07206, 12 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2012.07206]



44. Hanene Ben Yedder, Ben Cardoen, and Ghassan Hamarneh. Deep Learning for Biomedical Image Reconstruction: A Survey. Technical report arxiv:2002.12351, 2 2020. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = arxiv:2002.12351]



45. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography. Technical report techrxiv:13150805, 10 2020. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = techrxiv_13150805]



46. Kumar Abhishek and Ghassan Hamarneh. Mask2Lesion: Mask-Constrained Adversarial Skin Lesion Image Synthesis. Technical report arxiv:1906.05845, 6 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1906.05845]



47. Shahab Aslani, Vittorio Murino, Michael Dayan, Roger Tam, Diego Sona, and Ghassan Hamarneh. Scanner Invariant Multiple Sclerosis Lesion Segmentation from MRI. Technical report arxiv:1910.10035, 10 2019. Keyword(s): Segmentation, Machine Learning, Deep Learning, Multiple Sclerosis, MRI. [bibtex-key = arxiv:1910.10035]



48. Aicha BenTaieb and Ghassan Hamarneh. Deep Learning Models for Digital Pathology. Technical report arxiv:1910.12329, 10 2019. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Generative Adversarial Network, Survey/Review. [bibtex-key = arxiv:1910.12329]



49. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy. Technical report arxiv:1906.07802, 6 2019. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = arxiv:1906.07802]



50. Weina Jin, Mostafa Fatehi, Kumar Abhishek, Mayur Mallya, Brian Toyota, and Ghassan Hamarneh. Artificial Intelligence in Glioma Imaging: Challenges and Advances. Technical report arxiv:1911.12886, 11 2019. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning. [bibtex-key = arxiv:1911.12886]



51. Jeremy Kawahara and Ghassan Hamarneh. Visual Diagnosis of Dermatological Disorders: Human and Machine Performance. Technical report arxiv:1906.01256, 6 2019. Keyword(s): Survey/Review, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Dermatology, Classification. [bibtex-key = arxiv:1906.01256]



52. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. Technical report biorxiv:495382, 1 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Network Modelling and Analysis, Machine Learning. [bibtex-key = biorxiv_2019_526327]



53. Zahra Mirikharaji, Yiqi Yan, and Ghassan Hamarneh. Learning to Segment Skin Lesions from Noisy Annotations. Technical report arxiv:1906.03815, 6 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1906.03815]



54. Anmol Sharma and Ghassan Hamarneh. Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network. Technical report arxiv:1904.12200, 4 2019. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning, Generative Adversarial Network, Multimodal. [bibtex-key = arxiv:1904.12200]



55. Saeid Asgari Taghanaki, Kumar Abhishek, Joseph Paul Cohen, Julien Cohen-Adad, and Ghassan Hamarneh. Deep Semantic Segmentation of Natural and Medical Images: A Review. Technical report arxiv:1910.07655, 10 2019. Keyword(s): Survey/Review, Segmentation, Machine Learning, Deep Learning. [bibtex-key = arxiv:1910.07655]



56. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Improved Inference via Deep Input Transfer. Technical report arxiv:1904.02307, 4 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1904.02307]



57. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Signed Input Regularization. Technical report arxiv:1911.07086, 12 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1911.07086]



58. Saeid Asgari Taghanaki, Mohammad Havaei, Tess Berthier, Francis Dutil, Lisa Di Jorio, Ghassan Hamarneh, and Yoshua Bengio. InfoMask: Masked Variational Latent Representation to Localize Chest Disease. Technical report arxiv:1903.11741, 3 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1903.11741]



59. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows that polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Technical report biorxiv:495382, 12 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = biorxiv_2018_495382]



60. Saeid Asgari Taghanaki, Aicha BenTaieb, Anmol Sharma, S. Kevin Zhou, Yefeng Zheng, Bogdan Georgescu, Puneet Sharma, Sasa Grbic, Zhoubing Xu, Dorin Comaniciu, and Ghassan Hamarneh. Select, Attend, and Transfer: Light, Learnable Skip Connections. Technical report arxiv:1703.04559, 4 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1804.05181]



61. Saeid Asgari Taghanaki, Yefeng Zheng, S. Kevin Zhou, Bogdan Georgescu, Puneet Sharma, Daguang Xu, Dorin Comaniciu, and Ghassan Hamarneh. Combo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation. Technical report arxiv:1703.04559, 5 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1805.02798]



62. Jeremy Kawahara and Ghassan Hamarneh. Fully Convolutional Networks to Detect Clinical Dermoscopic Features. Technical report arxiv:1703.04559, 3 2017. Keyword(s): Machine Learning, Deep Learning, Dermatology, Challenge. [bibtex-key = arxiv:1703.04559]



63. 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. [bibtex-key = arxiv:1607.04174]



64. 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. [bibtex-key = arxiv:1611.08699]



65. 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. [bibtex-key = arxiv:1607.01092]



66. 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. [bibtex-key = arxiv:1509.07244]



67. Shawn Andrews, Chris McIntosh, and Ghassan Hamarneh. Convex Multi-Region Probabilistic Segmentation with Shape Prior in the Isometric Logratio Transformation Space. Technical report TR 2011-03, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, July 2011. Keyword(s): Optimization, Segmentation, Uncertainty. [bibtex-key = sfu_cs2011_03]



68. Ghassan Hamarneh. The Optimizability-Fidelty Trade-Off in Image Analysis. Technical report SFU-Summit-10897, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 9 2011. Keyword(s): Optimization, Segmentation, Registration and Matching. [bibtex-key = scia2011_g4a2011]



69. Shawn Andrews, Ghassan Hamarneh, and Ahmed Saad. Fast Random Walker with Priors using Precomputation for Interactive Medical Image Segmentation. Technical report TR 2010-07, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 6 2010. Keyword(s): Segmentation, Graph based, Fast MIA. [bibtex-key = sfu_cs2010_07]



70. Neda Changizi and Ghassan Hamarneh. Probabilistic Multi-Shape Representation using an Isometric Log-Ratio Mapping. Technical report TR 2010-05, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 4 2010. Keyword(s): Shape Modelling and Analysis, Uncertainty. [bibtex-key = sfu_cs2010_05]



71. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Spatial Normalization of Human Back Images for Dermatological Studies. Technical report TR 2010-01, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 2010. Keyword(s): Registration and Matching, Dermatology. [bibtex-key = sfu_cs2010_01]



72. Josna Rao, Rafeef Abugharbieh, and Ghassan Hamarneh. Adaptive Regularization for Image Segmentation Using Local Image Curvature Cues. Technical report TR 2010-08, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 6 2010. Keyword(s): Segmentation, Graph based. [bibtex-key = sfu_cs2010_08]



73. Ryan Dickie, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-vessel: Interactive vascular image segmentation with simultaneous extraction of optimal medial and boundary paths. Technical report TR 2009-23, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 11 2009. Keyword(s): Segmentation, Anatomical Trees and Tubular Structures, Color/Multichannel/Vector-valued, Optimization, Software and Tools, User Interaction, Medial-based Shape Representation, Graph based, Bifurcation/Junction. [bibtex-key = sfu_cs2009_23]



74. Ghassan Hamarneh. Multi-Label MRF Optimization via Least Squares s-t Cuts. Technical report TR 2009-08, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 4 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = sfu_cs2009_08]



75. Ghassan Hamarneh. Multi-Label MRF Optimization via Least Squares s-t Cuts. Technical report arxiv:0907.0204, 7 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = arxiv:0907.0204]



76. Ghassan Hamarneh and Neda Changizi. Barycentric Label Space. Technical report TR 2009-13, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 4 2009. Keyword(s): Shape Modelling and Analysis, Uncertainty. [bibtex-key = sfu_cs2009_13]



77. Ghassan Hamarneh, Chris McIntosh, and Mark S. Drew. Perception-based Visualization of High-Dimensional Medical Images Using Distance Preserving Dimensionality Reduction. Technical report TR 2009-22, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 11 2009. Keyword(s): Color/Multichannel/Vector-valued, Visualization, Diffusion MRI/Tensor-valued, Functional/Molecular/Dynamic Imaging. [bibtex-key = sfu_cs2009_22]



78. Chris McIntosh and Ghassan Hamarneh. Optimal Weights in Convex Functionals: Taking the Guesswork Out of Segmentation. Technical report TR 2009-14, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 6 2009. Keyword(s): Optimization, Segmentation. [bibtex-key = sfu_cs2009_14]



79. Josna Rao, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Spatially-Adaptive Balancing of Energy Terms for Image Segmentation. Technical report arxiv:0906.4131, 6 2009. Keyword(s): Segmentation, Graph based. [bibtex-key = arxiv:0906.4131]



80. Josna Rao, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Spatially-Adaptive Balancing of Energy Terms for Image Segmentation. Technical report TR 2009-10, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 4 2009. Keyword(s): Optimization, Segmentation. [bibtex-key = sfu_cs2009_10]



81. Aaron Ward and Ghassan Hamarneh. GMAT: The Groupwise Medial Axis Transform for Fuzzy Skeletonization and Intelligent Pruning. Technical report TR 2008-07, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 3 2008. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation. [bibtex-key = sfu_cs2008_07]



82. Ghassan Hamarneh and Tim McInerney. Physics-Based Shape Deformations for Medical Image Analysis. Technical report CSRG-436, Department of Computer Science, University of Toronto, Toronto, ON, Canada, 2001. Keyword(s): Shape Modelling and Analysis, Medial-based Shape Representation, Deformable Models. [bibtex-key = csrg2001_436]



83. Ghassan Hamarneh, Tim McInerney, and Demetri Terzopoulos. Intelligent Deformable Organisms: An ALife Approach to Medical Image Analysis. Technical report CSRG-432, Department of Computer Science, University of Toronto, Toronto, ON, Canada, 2001. Keyword(s): Segmentation, Deformable Organisms, Artificial Life. [bibtex-key = csrg2001_432]



84. Ghassan Hamarneh. Digital Image Analysis of Fundus Photographs on the WWW. Technical report R002/1999 (S2-IAG-99-1), Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, Goteborg, Sweden, 2 1999. Keyword(s): Software and Tools. [bibtex-key = s2iag1999_1]



85. Ghassan Hamarneh. Active Shape Models, Modeling Shape Variations and Gray Level Information and an Application to Image Search and Classification. Technical report R005/1998 (S2-IAG-98-1), Department of Signals and Systems, School of Electrical and Computer Engineering, Chalmers University of Technology, Goteborg, Sweden, 9 1998. Keyword(s): Segmentation, Shape Modelling and Analysis, Deformable Models. [bibtex-key = s2iag1998_1]

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