1. Ivan Robert Nabi, Ben Cardoen, Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. The Journal Of Cell Biology (JCB), 000(jcb.000):000-000, 000 2024. Keyword(s): Super Resolution Microscopy, Deep Learning, Machine Learning, Weak Supervision, Survey/Review. [bibtex-key = jcb2024]



2. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). PLOS ONE, 17(12):e0276726, 2022. Keyword(s): Super Resolution Microscopy, Machine Learning, Classification, Belief Theory, Biomarkers/Biosignatures, Generalizability. [bibtex-key = plosone2022]



3. Timothy H. Wong, Ismail M. Khater, Bharat Joshi, Mona Shahsavari, Ghassan Hamarneh, and Ivan Robert Nabi. Single molecule network analysis identifies structural changes to caveolae and scaffolds due to mutation of the caveolin-1 scaffolding domain (Wong and Khater: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific Reports, 11(7810):1-14, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = nature_sr2021]



4. Ismail M. Khater, Fanrui Meng, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Nature - Scientific reports, 8(9009):1-15, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2018]

1. Ismail M. Khater, Timothy H. Wong, Christian Hallgrimson, Satish Moparthi, Stéphane Vassilopoulos, Ghassan Hamarneh, and Ivan Robert Nabi. Molecular architecture of clathrin plaques and pits defined by super-resolution network analysis (SuperResNET) (Khater and Wong: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2022b]



2. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Self-tuning Weakly Supervised Object Detection (SPECHT) of Sub-Diffraction Limited Caveolae and Scaffold and Amyloid-Beta Deposits. In American Society of Cell Biology -- Cell Bio 2021, 2021. Keyword(s): Object Detection, Super Resolution Microscopy, Belief Theory, Datasets. [bibtex-key = cellbio2021]



3. Ben Cardoen, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables detection of Caveolae in superresolution microscopy.. In Microscopy Societies Symposium - Advanced Imaging and Analysis at Nanoscale, November 2021. Keyword(s): Object Detection, Super Resolution Microscopy, Belief Theory. [bibtex-key = jsm2021]



4. Ismail M. Khater, Timothy H. Wong, Stéphane Vassilopoulos, Ivan Robert Nabi, and Ghassan Hamarneh. SuperResNET: a GUI software package for single molecule localization microscopy cluster analysis (Nabi and Hamarneh: Joint senior authors). In Single Molecule Localization Microscopy Symposium - Current Trends, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2021]



5. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Automatic identification of protein complexes in multi-scale microscopy with applications tometastasis and Alzheimer disease. In The 2nd Annual Tri-Cluster Research Day, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = tricluster2020b]



6. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables identification of protein complexes in multi-scale microscopy with applications to metastasis and Alzheimer disease. In Centre for Artificial Intelligence Decision-making and Action (CAIDA), BC's AI Showcase, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = caida2020b]



7. Timothy H. Wong, Mona Shahsavari, Ismail M. Khater, Bharat Joshi, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy Identification of Focal Adhesion-Associated Caveolin-1 Domains (Wong and Shahsavari: Joint first authors). In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis. [bibtex-key = embo2019c]

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. Ivan Robert Nabi, Ben Cardoen, Ismail M. Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. Technical report arxiv.2305.17193, 5 2023. Keyword(s): Machine Learning, Deep Learning, Weak Supervision, Super Resolution Microscopy, Validation. [bibtex-key = arxiv:2305.17193]



4. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). Technical report techrxiv:12971051, 9 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory, Object Detection, Datasets. [bibtex-key = techrxiv_12971051]

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