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Publications about 'Segmentation'
Thesis
  1. Zahra Mirikharaji. Deep Learning for Skin Lesion Segmentation. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2022. [bibtex-key = phd2022mirikharaji]


  2. Kumar Abhishek. Input Space Augmentation For Skin Lesion Segmentation In Dermoscopic Images. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2020. [bibtex-key = msc2020abhishek]


  3. Saeid Asgari Taghanaki. Improved Deep Semantic Medical Image Segmentation. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, November 2019. [bibtex-key = phd2019taghanaki]


  4. Payam Ahmadvand. Machine Learning Driven Active Surfaces for 3D Segmentation of Tumour Lesions in PET Images. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, May 2017. [bibtex-key = msc2017ahmadvand]


  5. Masoud Nosrati. Prior Knowledge for Targeted Object Segmentation in Medical Images. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, March 2015. [bibtex-key = phd2015nosrati]


  6. Andrew Top. Automated Confidence-Based User Guidance for Increasing Efficiency in Interactive 3D Image Segmentation. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, January 2012. [bibtex-key = msc2012top]


  7. Chris McIntosh. Energy Functionals for Medical Image Segmentation: Choices and Consequences. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, November 2011. [bibtex-key = phd2011mcintosh]


  8. Azadeh Yazdan. An Active Contour Approach for Segmentation of Intra-Retinal Layers in Optical Coherence Tomography Images. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, December 2010. [bibtex-key = msc2010yazdan]


  9. 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]


  10. 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]


  11. 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]


Articles in journal, book chapters
  1. 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]


  2. 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]


  3. 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]


  4. 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]


  5. 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]


  6. 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]


  7. 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]


  8. 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]


  9. 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]


  10. 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):99, 2020. Keyword(s): Segmentation, Software and Tools, Multiple Sclerosis, MRI. [bibtex-key = msj2020]


  11. 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]


  12. 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]


  13. 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]


  14. 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]


  15. 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]


  16. 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]


  17. 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]


  18. 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]


  19. 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]


  20. 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]


  21. 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]


  22. 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]


  23. 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]


  24. 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]


  25. 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]


  26. 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]


  27. 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]


  28. 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]


  29. 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]


  30. 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]


  31. 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]


  32. 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]


  33. 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]


  34. 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]


  35. 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]


  36. 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]


  37. 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]


  38. 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]


  39. 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]


  40. 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]


  41. 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]


  42. 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]


  43. 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]


  44. 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]


  45. 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]


  46. 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]


  47. 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]


  48. 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]


  49. 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]


  50. 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]


  51. 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]


  52. 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]


  53. 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]


Conference articles
  1. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Segmentation Style Discovery: Application to Skin Lesion Images. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = miccai_isic2024a]


  2. 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]


  3. 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]


  4. 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]


  5. 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]


  6. 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]


  7. 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]


  8. 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]


  9. 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]


  10. 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]


  11. 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]


  12. 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]


  13. 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]


  14. 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]


  15. 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]


  16. 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]


  17. 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]


  18. 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]


  19. 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]


  20. 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]


  21. 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]


  22. 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]


  23. 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]


  24. 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]


  25. 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]


  26. 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]


  27. 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]


  28. 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]


  29. 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]


  30. 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]


  31. 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]


  32. 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]


  33. 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]


  34. 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]


  35. 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]


  36. 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]


  37. 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]


  38. 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]


  39. 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]


  40. 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]


  41. 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]


  42. 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]


  43. 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]


  44. 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]


  45. 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]


  46. 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]


  47. 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]


  48. 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]


  49. 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]


  50. 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]


  51. 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]


  52. 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]


  53. 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]


  54. 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]


  55. 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]


  56. 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]


  57. 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]


  58. 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]


  59. 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]


  60. 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]


  61. 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]


  62. 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]


  63. 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]


  64. 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]


  65. 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]


  66. 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]


  67. 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]


  68. 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]


  69. 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]


  70. 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]


  71. 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]


  72. 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]


  73. 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]


  74. 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]


  75. 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]


  76. 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]


  77. 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]


  78. 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]


  79. 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]


  80. 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]


  81. 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]


  82. 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]


  83. 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]


  84. 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]


  85. 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]


  86. 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]


  87. 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]


  88. 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]


  89. 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]


  90. 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]


  91. 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]


  92. 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]


  93. 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]


  94. 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]


  95. 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]


  96. 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]


  97. 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]


  98. 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]


  99. 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]


  100. 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]


  101. 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]


  102. 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]


  103. 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]


  104. 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]


  105. 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]


  106. 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]


  107. 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]


  108. 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]


  109. 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]


  110. 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]


  111. 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]


  112. 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]


  113. 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]


  114. 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]


  115. 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]


  116. 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]


  117. 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]


  118. 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]


  119. 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]


Internal reports
  1. 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]


  2. 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]


  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). Technical report arxiv.2305.12621, 5 2023. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = arxiv:2305.12621]


  4. 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]


  5. 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]


  6. 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]


  7. 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]


  8. 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]


  9. 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]


  10. 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]


  11. 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]


  12. 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]


  13. 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]


  14. 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]


  15. 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]


  16. 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]


  17. 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]


  18. 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]


  19. 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]


  20. 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]


  21. 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]


  22. 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]


  23. 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]


  24. 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]


  25. 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]


  26. 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]


  27. 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]


  28. 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]


  29. 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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