1. Ali Majd, Mohammed AlJasser, Hengameh Mirzaalian, Jerry Shapiro, Ghassan Hamarneh, Harvey Lui, Leopoldo Duailibe Nogueira Santos, Thomas Chu, and Tim K. Lee. A novel automated approach to rapid and precise in vivo measurement of hair morphometrics using a smartphone. Skin Research and Technology (SRT), 27:1128–1134, 2021. Keyword(s): Anatomical Trees and Tubular Structures, Dermatology, Color/Multichannel/Vector-valued, Software and Tools. [bibtex-key = srt2021]



2. Alborz Amir-Khalili, Ghassan Hamarneh, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, and Rafeef Abugharbieh. Automatic Segmentation of Occluded Vasculature via Pulsatile Motion Analysis in Endoscopic Robot-Assisted Partial Nephrectomy Video. Medical Image Analysis (MedIA) (Special Issue: Invited best papers of the 2014 Conference on Medical Image Computing and Computer Assisted Intervention), 25(1):103-110, 2015. Keyword(s): Spatio-Temporal, Segmentation, Image-Guided Surgery, Anatomical Trees and Tubular Structures. [bibtex-key = media2015b]



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. Preet Jassi and Ghassan Hamarneh. VascuSynth: Vascular Tree Synthesis Software. Insight Journal, January-June:1-12, 2011. Keyword(s): Segmentation, Validation, Shape Modelling and Analysis, Software and Tools, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = ij2011]



6. Ghassan Hamarneh and Preet Jassi. VascuSynth: Simulating Vascular Trees for Generating Volumetric Image data with Ground Truth Segmentation and Tree Analysis. Computerized Medical Imaging and Graphics (CMIG), 34(8):605-616, 2010. Keyword(s): Segmentation, Validation, Shape Modelling and Analysis, Software and Tools, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = cmig2010]

1. Mengliu Zhao and Ghassan Hamarneh. Retinal Image Classification via Vasculature-guided Sequential Attention. In International Conference on Computer Vision workshop on Visual Recognition for Medical Images (ICCV VRMI), pages 381-387, 2019. Keyword(s): Anatomical Trees and Tubular Structures, Classification, Shape Modelling and Analysis, Machine Learning, Deep Learning. [bibtex-key = iccv_vrmi2019a]



2. Mengliu Zhao and Ghassan Hamarneh. Tree-LSTM: Using LSTM to Encode Memory in Anatomical Tree Prediction from 3D Images. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 637-645, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = miccai_mlmi2019a]



3. Mengliu Zhao and Ghassan Hamarneh. TreeNet: Multi-Loss Deep Learning Network to Predict Branch Direction for Extracting 3D Anatomical Trees. In Medical Image Computing and Computer-Assisted Intervention Workshop on Deep Learning in Medical Image Analysis (MICCAI DLMIA), volume 11045, pages 47-55, 2018. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Machine Learning, Deep Learning, Bifurcation/Junction. [bibtex-key = miccai_dlmia2018]



4. Mian Huang and Ghassan Hamarneh. SwifTree: Interactive Extraction of 3D Trees Supporting Gaming and Crowdsourcing. In Medical Image Computing and Computer-Assisted Intervention Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis (MICCAI LABELS), volume 10552, pages 116-125, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Gaming, Crowdsourcing. [bibtex-key = miccai_labels2017b]



5. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction. [bibtex-key = healthtech2017e]



6. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths (Mirikharaji and Zhao: Joint first authors). In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10434, pages 242-250, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction. [bibtex-key = miccai2017a]



7. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Localization in 3D Images via Evolutionary Geometric Deformable Templates. In Canadian Conference on Computer and Robot Vision (CRV), pages 124-130, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Deformable Models, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = crv2017a]



8. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Leveraging Tree Statistics for Extracting Anatomical Trees from 3D Medical Images. In Canadian Conference on Computer and Robot Vision (CRV), pages 131-138, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = crv2017b]



9. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Tree Structure Analysis in 3D Medical Images. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = healthtech2017f]



10. Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Vessel Segmentation from Pulsatile Radial Motion. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9351, pages 403-410, 2015. Keyword(s): Anatomical Trees and Tubular Structures, Tracking. [bibtex-key = miccai2015d]



11. Ali Majd, Mohammed AlJasser, Hengameh Mirzaalian, Jerry Shapiro, Ghassan Hamarneh, and Tim K. Lee. Automated Counting of Hair Using an iPhone. In World Congress of Dermatology (WCD), 2015. Keyword(s): Anatomical Trees and Tubular Structures, Dermatology, Color/Multichannel/Vector-valued, Software and Tools. [bibtex-key = wcd2015c]



12. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Detection in 3D Vascular Images Using Novel Features and Random Forest. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 421-424, 2014. Keyword(s): Anatomical Trees and Tubular Structures, Machine Learning, Bifurcation/Junction. [bibtex-key = isbi2014a]



13. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Globally Optimal Spinal Cord Segmentation using A Minimal Path in High Dimensions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 836-839, 2013. Keyword(s): Segmentation, Optimization, Anatomical Trees and Tubular Structures, Graph based, Multiple Sclerosis, MRI. [bibtex-key = isbi2013b]



14. Daniel Baboiu and Ghassan Hamarneh. Vascular Bifurcation Detection in Scale-Space. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 41-46, 2012. Keyword(s): Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = mmbia2012b]



15. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Learning Features for Streak Detection in Dermoscopic Color Images using Localized Radial Flux of Principal Intensity Curvature. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 97-101, 2012. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Anatomical Trees and Tubular Structures, Dermatology. [bibtex-key = mmbia2012d]



16. Chris McIntosh, Ghassan Hamarneh, Matt Toom, and Roger Tam. Spinal Cord Segmentation for Volume Estimation in Healthy and Multiple Sclerosis Subjects using Crawlers and Minimal Paths. In IEEE Conference on Healthcare Informatics, Imaging and Systems Biology (IEEE HISB), pages 25-31, 2011. Keyword(s): Artificial Life, Deformable Organisms, Segmentation, Anatomical Trees and Tubular Structures, Multiple Sclerosis, MRI. [bibtex-key = hisb2011b]



17. 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]



18. Hengameh Mirzaalian and Ghassan Hamarneh. Vessel Scale Selection using MRF Optimization. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 3273-3278, 2010. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Graph based. [bibtex-key = cvpr2010a]



19. Ghassan Hamarneh. Airway Segmentation using Crawlers and Optimal Paths. In First International Workshop on Dynamic Modeling of the Oral, Pharyngeal and Laryngeal Complex for Biomedical Applications (OPAL), pages 43, 2009. Keyword(s): Deformable Organisms, Segmentation, Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = opal2009]



20. 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]



21. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-Vessel: Extending Livewire for Simultaneous Extraction of Optimal Medial and Boundary Paths in Vascular Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 444-451, 2007. Keyword(s): Deformable Models, Segmentation, Anatomical Trees and Tubular Structures, Graph based. [bibtex-key = miccai2007a]



22. Chris McIntosh and Ghassan Hamarneh. Spinal Crawlers: Deformable Organisms for Spinal Cord Segmentation and Analysis. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4190, pages 808-815, 2006. Keyword(s): Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Anatomical Trees and Tubular Structures. [bibtex-key = miccai2006]



23. Chris McIntosh and Ghassan Hamarneh. Vessel Crawlers: 3D Physically-based Deformable Organisms for Vasculature Segmentation and Analysis. In IEEE Conference on Computer Vision and Pattern Recognition (IEEE CVPR), pages 1084-1091, 2006. Keyword(s): Segmentation, Deformable Models, Deformable Organisms, Artificial Life, Anatomical Trees and Tubular Structures, Bifurcation/Junction. [bibtex-key = cvpr2006]

1. Ashwin Samudre, Guang Gao, Ben Cardoen, Ivan Robert Nabi, and Ghassan Hamarneh. nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors). Technical report biorxiv:2024.02.20.581259, 2 2024. Keyword(s): Super Resolution Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning, Deep Learning, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = biorxiv_2024_02_20_581259]



2. Ashish Sinha and Ghassan Hamarneh. Representing Anatomical Trees by Denoising Diffusion of Implicit Neural Fields. Technical report arxiv.2403.08974, 3 2024. Keyword(s): Deep Learning, Diffusion Models, Anatomical Trees and Tubular Structures. [bibtex-key = arxiv:2403.08974]



3. Ryan Dickie, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-vessel: Interactive vascular image segmentation with simultaneous extraction of optimal medial and boundary paths. Technical report TR 2009-23, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 11 2009. Keyword(s): Segmentation, Anatomical Trees and Tubular Structures, Color/Multichannel/Vector-valued, Optimization, Software and Tools, User Interaction, Medial-based Shape Representation, Graph based, Bifurcation/Junction. [bibtex-key = sfu_cs2009_23]

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