1. Ben Cardoen, Hanene Ben Yedder, Ivan Robert Nabi, and Ghassan Hamarneh. Closing the multichannel gap through computational reconstruction of interaction in superresolution microscopy. Cell Patterns, 6(5):101181, 2025. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graphs/Networks, Biomarkers/Biosignatures, Survey/Review, Point Cloud. [bibtex-key = cellpatterns2025]



2. Ashwin Samudre, Guang Gao, Ben Cardoen, Ivan Robert Nabi, and Ghassan Hamarneh. nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors). Communications Biology, 000(000):000-000, 2025. Keyword(s): Super Resolution Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning, Deep Learning, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation, Graphs/Networks. [bibtex-key = nature_commbio2025]



3. 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. The Journal Of Cell Biology (JCB), 223(8):e202311073, 8 2024. Keyword(s): Super Resolution Microscopy, Deep Learning, Machine Learning, Weak Supervision, Survey/Review, Point Cloud, Graphs/Networks. [bibtex-key = jcb2024]



4. 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/Skin, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graphs/Networks, Tracking, Datasets. [bibtex-key = media2022]



5. 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). Scientific Reports, 11(7810):1-14, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Graphs/Networks, Point Cloud. [bibtex-key = nature_sr2021]



6. 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, Graphs/Networks, Point Cloud, Biomarkers/Biosignatures, Survey/Review. [bibtex-key = cellpatterns2020]



7. 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, Graphs/Networks, Point Cloud, Biomarkers/Biosignatures. [bibtex-key = plosone2019]



8. 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. Scientific reports, 9(9888):1-10, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphs/Networks, Point Cloud. [bibtex-key = nature_sr2019]



9. 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, Graphs/Networks, Point Cloud, Biomarkers/Biosignatures. [bibtex-key = bioinformatics2019]



10. 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. Scientific reports, 8(9009):1-15, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphs/Networks, Point Cloud. [bibtex-key = nature_sr2018]



11. 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, Graphs/Networks, Dermatology/Skin, Machine Learning. [bibtex-key = media2015]



12. 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, Graphs/Networks, Optimization, Machine Learning, Registration and Matching. [bibtex-key = tmi2015b]



13. 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, Graphs/Networks, Dermatology/Skin. [bibtex-key = jbhi2013]



14. 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, Graphs/Networks. [bibtex-key = tmi2012b]



15. 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, Graphs/Networks. [bibtex-key = mia2012b]



16. 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, Graphs/Networks. [bibtex-key = cmig2008]

1. 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, Graphs/Networks, Point Cloud. [bibtex-key = smlms2022]



2. 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, Graphs/Networks, Point Cloud. [bibtex-key = ascb2022b]



3. 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, Graphs/Networks, Point Cloud. [bibtex-key = smlms2021]



4. 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, Graphs/Networks, Point Cloud. [bibtex-key = tricluster2020b]



5. 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, Graphs/Networks, Point Cloud. [bibtex-key = smlms2020]



6. 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, Graphs/Networks, Point Cloud. [bibtex-key = embo2019a]



7. 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, Graphs/Networks, Point Cloud. [bibtex-key = embo2019b]



8. 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, Graphs/Networks, Point Cloud. [bibtex-key = embo2019c]



9. 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, Graphs/Networks, Graphs/Networks, Point Cloud. [bibtex-key = ascb2018b]



10. 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, Graphs/Networks, Biomarkers/Biosignatures, Graphs/Networks, Point Cloud. [bibtex-key = ascb2018a]



11. 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, Graphs/Networks, Biomarkers/Biosignatures, Graphs/Networks, Point Cloud. [bibtex-key = bme2018]



12. 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/Skin, Color/Multichannel/Vector-valued, Deep Learning, Graphs/Networks. [bibtex-key = miccai_grail2017]



13. 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, Graphs/Networks, Point Cloud. [bibtex-key = ascb2017]



14. 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, Graphs/Networks, Point Cloud. [bibtex-key = gordon2017a]



15. 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, Graphs/Networks, Point Cloud. [bibtex-key = siam2017a]



16. 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, Graphs/Networks, Point Cloud. [bibtex-key = healthtech2017d]



17. 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, Graphs/Networks, Point Cloud. [bibtex-key = frontiers_biophysics2017]



18. 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, Graphs/Networks, Point Cloud. [bibtex-key = ascb2016]



19. 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, Graphs/Networks, Point Cloud. [bibtex-key = superres2016]



20. 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, Graphs/Networks, Point Cloud. [bibtex-key = ascblsi2016]



21. 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, Graphs/Networks, Point Cloud. [bibtex-key = cinc2016]



22. 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, Graphs/Networks, Point Cloud. [bibtex-key = nanolytica2015]



23. 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, Graphs/Networks, Point Cloud. [bibtex-key = asci2015]



24. 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, Graphs/Networks, Point Cloud. [bibtex-key = ccma2015]



25. 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, Graphs/Networks, Dermatology/Skin. [bibtex-key = wcd2015b]



26. 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, Graphs/Networks, Multiple Sclerosis, MRI. [bibtex-key = isbi2013b]



27. 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, Graphs/Networks. [bibtex-key = can-acn2012]



28. 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, Graphs/Networks. [bibtex-key = isbi2011]



29. 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, Graphs/Networks. [bibtex-key = miccai2010b]



30. 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, Graphs/Networks. [bibtex-key = cvpr2010a]



31. 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, Graphs/Networks. [bibtex-key = cvpr2010b]



32. 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, Graphs/Networks. [bibtex-key = miccai2010d]



33. 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, Graphs/Networks. [bibtex-key = eccv2010]



34. 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, Graphs/Networks. [bibtex-key = mmbia2010]



35. 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, Graphs/Networks. [bibtex-key = isvc2009a]



36. 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, Graphs/Networks, Dermatology/Skin. [bibtex-key = cvpr2009]



37. 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, Graphs/Networks, Dermatology/Skin. [bibtex-key = skin2009]



38. 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, Graphs/Networks. [bibtex-key = miccai_fmri2009]



39. 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, Graphs/Networks. [bibtex-key = spiemi2009]



40. 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, Graphs/Networks. [bibtex-key = miccai2008a]



41. 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, Graphs/Networks. [bibtex-key = miccai2007a]



42. 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, Graphs/Networks. [bibtex-key = spiemi2007a]



43. 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, Graphs/Networks. [bibtex-key = miccai2007b]



44. 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, Graphs/Networks. [bibtex-key = spiemi2007b]



45. 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, Graphs/Networks. [bibtex-key = isspit2006b]



46. 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): Dermatology/Skin, Segmentation, Deformable Models, Color/Multichannel/Vector-valued, Graphs/Networks. [bibtex-key = spiemi2005d]

1. 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, Simon Fraser Universiry, 3 2024. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction, Graphs/Networks, Point Cloud. [bibtex-key = biorxiv_2024_03_12_584716]



2. 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, Simon Fraser Universiry, 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, Graphs/Networks. [bibtex-key = biorxiv_2024_02_20_581259]



3. Timothy H. Wong, Ismail M. Khater, Christian Hallgrimson, Y. Lydia Li, 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, Simon Fraser University, 3 2024. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Graphs/Networks, Point Cloud. [bibtex-key = biorxiv_2024_03_07_583946]



4. 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, Simon Fraser Universiry, 5 2023. Keyword(s): Machine Learning, Deep Learning, Weak Supervision, Super Resolution Microscopy, Validation, Graphs/Networks, Point Cloud. [bibtex-key = arxiv:2305.17193]



5. 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, Simon Fraser Universiry, 5 2021. Keyword(s): Dermatology/Skin, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graphs/Networks, Tracking. [bibtex-key = arxiv:2105.00374]



6. 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, Simon Fraser University, 1 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Network Modelling and Analysis, Machine Learning, Graphs/Networks, Point Cloud. [bibtex-key = biorxiv_2019_526327]



7. 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, Simon Fraser University, 12 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphs/Networks, Point Cloud. [bibtex-key = biorxiv_2018_495382]



8. Shawn Andrews and Ghassan Hamarneh. Multi-Region Probabilistic Dice Similarity Coefficient using the Aitchison Distance and Bipartite Graph Matching. Technical report arxiv:1509.07244, Simon Fraser University, 9 2015. Keyword(s): Segmentation, Validation, Graphs/Networks, Registration and Matching. [bibtex-key = arxiv:1509.07244]



9. 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, Graphs/Networks, Fast MIA. [bibtex-key = sfu_cs2010_07]



10. 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, Graphs/Networks. [bibtex-key = sfu_cs2010_08]



11. 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, Graphs/Networks, Bifurcation/Junction. [bibtex-key = sfu_cs2009_23]



12. Ghassan Hamarneh. Multi-Label MRF Optimization via Least Squares s-t Cuts. Technical report arxiv:0907.0204, Simon Fraser University, 7 2009. Keyword(s): Optimization, Segmentation, Graphs/Networks. [bibtex-key = arxiv:0907.0204]



13. 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, Graphs/Networks. [bibtex-key = sfu_cs2009_08]



14. Josna Rao, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Spatially-Adaptive Balancing of Energy Terms for Image Segmentation. Technical report arxiv:0906.4131, Simon Fraser University, 6 2009. Keyword(s): Segmentation, Graphs/Networks. [bibtex-key = arxiv:0906.4131]

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