1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample $\zeta$-mixup: Richer, More Realistic Synthetic Samples from a $p$-Series Interpolant. Journal of Big Data, 11(43):1-41, 3 2024. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation, Classification, Dermatology. [bibtex-key = jbd2024]



2. 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]



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



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



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



6. Brian G. Booth, Steven Miller, Colin J. Brown, Kenneth Poskitt, Vann Chau, Ruth Grunau, Anne Synnes, and Ghassan Hamarneh. STEAM - Statistical Template Estimation for Abnormality Mapping: a Personalized DTI Analysis Technique with Applications to the Screening of Preterm Infants. NeuroImage, 125:705-723, 2015. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Datasets, Synthesis/Simulation/Augmentation. [bibtex-key = neuroimage2015]



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



8. 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]



9. 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]

1. Ashish Sinha and Ghassan Hamarneh. TrIND: Representing Anatomical Trees by Denoising Diffusion of Implicit Neural Fields. In , volume 000, pages 000-000, 2024. Keyword(s): Deep Learning, Diffusion Models, Anatomical Trees and Tubular Structures, Neural Fields, Synthesis/Simulation/Augmentation. [bibtex-key = miccai2024b]



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



3. 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]



4. Colin J. Brown, Steven Miller, Brian G. Booth, Ken Poskitt, Vann Chau, Anne Synnes, Jill Zwicker, Ruth Grunau, and Ghassan Hamarneh. Prediction of Motor Function in Very Preterm Infants using Connectome Features and Local Synthetic Instances. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 69-76, 2015. Keyword(s): Neurodevelopment, Machine Learning, Synthesis/Simulation/Augmentation. [bibtex-key = miccai2015a]



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



6. 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]

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



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



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



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

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