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. Ben Cardoen, Hanene Ben Yedder, Ivan Robert Nabi, and Ghassan Hamarneh. Closing the multichannel gap through computational reconstruction of interaction in superresolution microscopy. Cell Patterns, 000(000):000-000, 2025. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures, Survey/Review. [bibtex-key = cellpatterns2025]



2. 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]



3. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. BioInformatics Advances, 3(1-5):000-000, 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility. [bibtex-key = bioinfadv2023]



4. 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]



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. 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]



6. Ben Cardoen, Hanene Ben Yedder, Anmol Sharma, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE Transactions on Medical Imaging (IEEE TMI), 39(6):1942-1956, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = tmi2020]

1. Tanya Gatsak, Kumar Abhishek, Hanene Ben Yedder, Saeid Asgari Taghanaki, and Ghassan Hamarneh. Disentangled PET Lesion Segmentation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), 2025. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = isbi2025]



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. 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]



4. 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. Ben Cardoen, Hanene Ben Yedder, Ivan Robert Nabi, and Ghassan Hamarneh. A review of computational reconstruction of interaction in superresolution microscopy: from colocalization to closing the multichannel gap. Technical report zenodo.14009143, 10 2024. Keyword(s): Survey/Review, Network Modelling and Analysis, Super Resolution Microscopy, Singe Molecule Microscopy, Machine Learning. [bibtex-key = zenodo.14009143]



2. Tanya Gatsak, Kumar Abhishek, Hanene Ben Yedder, Saeid Asgari Taghanaki, and Ghassan Hamarneh. Disentangled PET Lesion Segmentation. Technical report arxiv.2411.01758, 10 2024. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging, Segmentation. [bibtex-key = arxiv:2411.01758]



3. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. Technical report techrxiv:22060118, 2 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility. [bibtex-key = techrxiv_22060118]



4. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. Log-Paradox: Necessary and sufficient conditions for confounding statistically significant pattern reversal under the log-transform. Technical report arxiv.2302.04780, 000 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Statistics, Geometric mean, Log-transform. [bibtex-key = arxiv:2302.04780]



5. 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]



6. 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]



7. 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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