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



2. 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]

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



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

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



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



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



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



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



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

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