1. Hanene Ben Yedder. Deep Learning Methods for Reconstruction and Analysis of Diffuse Optical Tomography Images of Breast Cancer Lesions. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, September 2023. [bibtex-key = phd2023benyedder]

1. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Deep Orthogonal Multi-Wavelength Fusion for Tomogram-Free Diagnosis in Diffuse Optical Imaging. Computers in Biology and Medicine (CIBM), 000:000, 2024. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = cibm2024]



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



3. 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]



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

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



2. 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, Diffuse Optical Tomography. [bibtex-key = miccai2019c]



3. 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]



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



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



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



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



8. 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]

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, Diffuse Optical Tomography. [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, Diffuse Optical Tomography. [bibtex-key = techrxiv_13150805]

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