1. 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]



2. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Cellular and Molecular Life Sciences (CMLS), 79(565):1-20, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = cmls2022]



3. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Streak-Detection in Dermoscopic Color Images using Localized Radial Flux of Principal Intensity Curvature (Chapter 7). Dermoscopy Image Analysis, pp 211-229, 2015. ISBN: 9781482253269. Keyword(s): Color/Multichannel/Vector-valued, Processing, Segmentation, Anatomical Trees and Tubular Structures, Dermatology. [bibtex-key = crc2015a]



4. 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]



5. Ghassan Hamarneh, Chris McIntosh, Tim McInerney, and Demetri Terzopoulos. Deformable Organisms: An Artificial Life Framework for Automated Medical Image Analysis (Chapter 15). Computational Intelligence In Medical Imaging: Techniques and Applications, pp 433-474, 2009. ISBN: 978-1420060591. Keyword(s): Processing, Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Bifurcation/Junction. [bibtex-key = crc2009]



6. Manku Rana, Ghassan Hamarneh, and James Wakeling. Automated tracking of muscle fascicle orientation in B-mode ultrasound images. Journal of Biomechanics, 42(13):2068-2073, 2009. Keyword(s): Spatio-Temporal, Processing, Segmentation, Tracking. [bibtex-key = jbm2009]



7. Ghassan Hamarneh and Judith Hradsky. Bilateral Filtering of Diffusion Tensor Magnetic Resonance Images. IEEE Transactions on Image Processing (IEEE TIP), 16(10):2463-2475, 2007. Keyword(s): Processing, Diffusion MRI/Tensor-valued. [bibtex-key = tip2007]



8. Vincent Chu and Ghassan Hamarneh. MATITK: Extending MATLAB with ITK. Insight Journal, Aug-Dec:1-8, 2005. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = ij2005]

1. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = ascb2022c]



2. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Goa, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS. In UBC SBME 2022, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = sbme2022]



3. Ben Cardoen and Ghassan Hamarneh. Learning to look beyond what we can see: Leveraging statistical learning to improve scientific discovery from fluorescence microscopy. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Processing, Belief Theory. [bibtex-key = bmiai2021a]



4. 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]



5. 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]



6. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. A computer vision tracking system for pigmented skin lesions. In World Congress of Dermatology (WCD), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Optimization, Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = wcd2015b]



7. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Detecting Streaks from Dermoscopic Images of Pigmented Skin Lesions. In The International Society for Biophysics and Imaging of the Skin (ISBS), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Dermatology. [bibtex-key = isbs2015]



8. Krishna Nand, Ghassan Hamarneh, and Rafeef Abugharbieh. Diffusion Tensor Image Processing using Biquaternions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 538-541, 2012. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = isbi2012b]



9. Krishna Nand, Rafeef Abugharbieh, Brian G. Booth, and Ghassan Hamarneh. Detecting Structure in Diffusion Tensor MR Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6892, pages 90-97, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Processing, Anatomical Trees and Tubular Structures. [bibtex-key = miccai2011c]



10. Peyman Rahmati, Ghassan Hamarneh, Doron Nussbaum, and Andy Adler. A New Preprocessing Filter for Digital Mammograms. In International Conference on Image and Signal Processing (ICISP), pages 585-592, 2010. Keyword(s): Processing. [bibtex-key = icisp2010]



11. Lilong Shi, Brian Funt, and Ghassan Hamarneh. Quaternion Color Curvature. In Color Imaging (IS&T/SID CI), pages 338-341, 2008. Keyword(s): Processing, Color/Multichannel/Vector-valued, Anatomical Trees and Tubular Structures. [bibtex-key = ci2008]



12. Vincent Chu and Ghassan Hamarneh. MATLAB-ITK interface for medical image filtering, segmentation, and registration. In SPIE Medical Imaging, volume 61443T, pages 1-8, 2006. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = spiemi2006a]



13. Ghassan Hamarneh and Judith Hradsky. Bilateral Filtering of Diffusion Tensor MR Images. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 508-512, 2006. Keyword(s): Processing, Diffusion MRI/Tensor-valued. [bibtex-key = isspit2006a]



14. Vincent Chu and Ghassan Hamarneh. MATITK: MATLAB-ITK Interface for Medical Image Processing. In 1st Annual Medical Technology Research Showcase, Vancouver, BC, 2005. Keyword(s): Processing, Segmentation, Registration and Matching, Software and Tools. [bibtex-key = medical_showcase2005a]



15. Josette Chen, Lee Adamson, Leila Baghdadi, Jonathan Bishop, Nick Bock, John Cargill, Lori Davidson, Jun Dazai, Stuart Foster, Ghassan Hamarneh, Natasha Kovacevic, Nir Lifshitz, Brian Nieman, Janet Rossant, John Sled, Yuqing Zhou, and Mark Henkelman. Current Progress of Imaging Screens at the Mouse Imaging Centre. In Integrated Functional Genomics of the Mouse (IFGM), 10 2003. Keyword(s): Imaging, Processing, Segmentation, Registration and Matching. [bibtex-key = ifgm2003]



16. Ghassan Hamarneh, Josette Chen, Brian Nieman, Jeff Henderson, and Mark Henkelman. Processing, Segmentation, Registration, and Deformation Analysis of 3D MR Images of Mice.. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 2879, pages 878-885, 2003. Keyword(s): Processing, Segmentation, Registration and Matching, Deformable Models. [bibtex-key = miccai2003a]



17. Mark Henkelman, Josette Chen, John Cargill, Nick Bock, Brian Nieman, Nir Lifshitz, Stuart Foster, Allison Duckett, John Sled, Jun Dazai, Natasha Kovacevic, Ghassan Hamarneh, Colin McKerlie, Janet Rossant, and Johnathon Walls. An Imaging Centre for Mouse Phenotyping. In 16th International Mouse Genome Conference (IMGC), 2002. Keyword(s): Imaging, Processing, Segmentation, Registration and Matching. [bibtex-key = imgc2002]

1. 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]



2. 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]



3. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Vandevoorde, Joshi, and Cardoen: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report Research Square (Preprint) 1559637, 4 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Image Processing, Belief Theory. [bibtex-key = research_square2022_1559637]



4. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Gp78-mediated basal mitophagy promotes mitochondrial health and limits mitochondrial ROS production (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2021.09.17.460825, 9 2021. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory. [bibtex-key = biorxiv_2021_09_17_460825]



5. 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]

This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All person copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.

This document was translated from BibT_EX by bibtex2html