@article{Bezek_analytical_23,
  author = {Can Deniz Bezek and Orcun Goksel},
  title = {Analytical Estimation of Beamforming Speed-of-Sound Using Transmission Geometry},
  journal = {Ultrasonics},
  year = {2023},
  volume = {10},
  number = {860725},
  url = {https://arxiv.org/abs/2211.11553},
  doi = {10.1016/j.ultras.2023.107069}
}

@article{Chintada_spectral_22,
  author = {Bhaskara Rao Chintada and Richard Rau and Orcun Goksel},
  title = {Spectral Ultrasound Imaging of Speed-of-Sound and Attenuation Using an Acoustic Mirror},
  journal = {Frontiers in Physics},
  year = {2022},
  volume = {10},
  number = {860725},
  url = {https://arxiv.org/abs/2201.01435},
  doi = {10.3389/fphy.2022.860725}
}

@article{Gomariz_probabilistic_22,
  author = {Alvaro Gomariz and Tiziano Portenier and C\'esar Nombela-Arrieta and Orcun Goksel},
  title = {Probabilistic Spatial Analysis in Quantitative Microscopy with Uncertainty-Aware Cell Detection using Deep Bayesian Regression},
  journal = {Science Advances},
  year = {2022},
  volume = {8},
  number = {5},
  pages = {eabi8295},
  url = {https://arxiv.org/abs/2102.11865},
  doi = {10.1126/sciadv.abi8295}
}

@article{Pean_computational_22,
  author = {Fabien P\'ean and Philippe Favre and Orcun Goksel},
  title = {Computational Analysis of Subscapularis Tears and Pectoralis Major Transfers on Muscular Activity},
  journal = {Clinical Biomechanics},
  year = {2022},
  volume = {92},
  number = {105541},
  url = {https://arxiv.org/abs/2012.14340},
  doi = {10.1016/j.clinbiomech.2021.105541}
}

@article{Chintada_nonlinear_22,
  author = {Bhaskara R. Chintada and Richard Rau and Orcun Goksel},
  title = {Nonlinear Characterization of Tissue Viscoelasticity with Acoustoelastic Attenuation of Shear-Waves},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2022},
  volume = {69},
  number = {1},
  pages = {38-53},
  url = {https://arxiv.org/abs/2002.12908},
  doi = {10.1109/TUFFC.2021.3105339}
}

@article{Pati_hierarchical_22,
  author = {Pushpak Pati and Guillaume Jaume and Antonio Foncubierta and Florinda Feroce and Anna Maria Anniciello and Giosu\`e Scognamiglio and Nadia Brancati and Maryse Fiche and Estelle Dubruc and Daniel Riccio and Maurizio Di Bonito and Giuseppe De Pietro and Gerardo Botti and Jean-Philippe Thiran and Maria Frucci and Orcun Goksel and Maria Gabrani},
  title = {Hierarchical Graph Representations in Digital Pathology},
  journal = {Medical Image Analysis},
  year = {2022},
  volume = {75},
  number = {102264},
  url = {https://arxiv.org/abs/2102.11057},
  doi = {10.1016/j.media.2021.102264}
}

@article{Chintada_phase-aberration_21,
  author = {Bhaskara Rao Chintada and Richard Rau and Orcun Goksel},
  title = {Phase-Aberration Correction in Shear-wave Elastography Imaging Using Local Speed-of-Sound Adaptive Beamforming},
  journal = {Frontiers in Physics: Medical Physics and Imaging},
  year = {2021},
  volume = {9},
  number = {690385},
  url = {https://arxiv.org/abs/2107.02734},
  doi = {10.3389/fphy.2021.690385}
}

@article{Gomariz_modality_21,
  author = {Alvaro Gomariz and Tiziano Portenier and Patrick M. Helbling and Stephan Isringhausen and Ute Suessbier and C\'esar Nombela-Arrieta and Orcun Goksel},
  title = {Modality Attention and Sampling Enables Deep Learning with Heterogeneous Marker Combinations in Fluorescence Microscopy},
  journal = {Nature Machine Intelligence},
  year = {2021},
  volume = {3},
  number = {9},
  pages = {799-811},
  url = {https://arxiv.org/abs/2008.12380},
  doi = {10.1038/s42256-021-00379-y}
}

@article{Pean_influence_21,
  author = {Fabien P\'ean and Philippe Favre and Orcun Goksel},
  title = {Influence of Rotator Cuff Integrity on Loading and Kinematics Before and After Reverse Shoulder Arthroplasty},
  journal = {Journal of Biomechanics},
  year = {2021},
  volume = {129},
  number = {110778},
  url = {https://arxiv.org/abs/2012.09763},
  doi = {10.1016/j.jbiomech.2021.110778}
}

@article{Robin_hemodynamic_21,
  author = {Justine Robin and Richard Rau and Berkan Lafci and Aileen Schroeter and Michael Reiss and Xos\'e-Lu\'is De\'an-Ben and Orcun Goksel and Daniel Razansky},
  title = {Hemodynamic response to sensory stimulation in mice: Comparison between functional ultrasound and optoacoustic imaging},
  journal = {NeuroImage},
  year = {2021},
  volume = {237},
  pages = {118111},
  doi = {10.1016/j.neuroimage.2021.118111}
}

@article{Rau_speed-of-sound_21,
  author = {Richard Rau and Dieter Schweizer and Valery Vishnevskiy and Orcun Goksel},
  title = {Speed-of-Sound Imaging using Diverging Waves},
  journal = {International Journal of Computer Assisted Radiology and Surgery},
  year = {2021},
  volume = {16},
  pages = {1201-11},
  url = {https://arxiv.org/abs/1910.05935},
  doi = {10.1007/s11548-021-02426-w}
}

@article{Zhang_learning_21,
  author = {Lin Zhang and Tiziano Portenier and Orcun Goksel},
  title = {Learning Ultrasound Rendering from Cross-Sectional Model Slices for Simulated Training},
  journal = {International Journal of Computer Assisted Radiology and Surgery},
  year = {2021},
  volume = {16},
  pages = {721-730},
  url = {https://arxiv.org/abs/2101.08339},
  doi = {10.1007/s11548-021-02349-6}
}

@article{Ruby_quantification_21,
  author = {Lisa Ruby and Sergio J Sanabria and Katharina Martini and Thomas Frauenfelder and Gerrolt Nico Jukema and Orcun Goksel and Marga B Rominger},
  title = {Quantification of immobilization-induced changes in human calf muscle using speed-of-sound ultrasound: An observational pilot study},
  journal = {Medicine},
  year = {2021},
  volume = {100},
  number = {11},
  doi = {10.1097/MD.0000000000023576}
}

@article{Ozdemir_active_21,
  author = {Firat Ozdemir and Zixuan Peng and Philipp Fuernstahl and Christine Tanner and Orcun Goksel},
  title = {Active Learning for Segmentation Based on Bayesian Sample Queries},
  journal = {Knowledge-Based Systems},
  year = {2021},
  volume = {214},
  number = {106531},
  pages = {1-9},
  url = {https://arxiv.org/abs/1912.10493},
  doi = {10.1016/j.knosys.2020.106531}
}

@article{Rau_frequency-dependent_21,
  author = {Richard Rau and Ozan Unal and Dieter Schweizer and Valery Vishnevskiy and Orcun Goksel},
  title = {Frequency-Dependent Attenuation Reconstruction with an Acoustic Reflector},
  journal = {Medical Image Analysis},
  year = {2021},
  volume = {67},
  number = {101875},
  pages = {1-9},
  url = {https://arxiv.org/abs/2003.05658},
  doi = {10.1016/j.media.2020.101875}
}

@article{Pati_reducing_21,
  author = {Pushpak Pati and Antonio Foncubierta-Rodr\'{i}guez and Orcun Goksel and Maria Gabrani},
  title = {Reducing Annotation Effort in Digital Pathology: A Co-Representation Learning Framework for Classification Tasks},
  journal = {Medical Image Analysis},
  year = {2021},
  volume = {67},
  number = {101859},
  pages = {1-17},
  doi = {10.1016/j.media.2020.101859}
}

@article{Zhang_deepN_20,
  author = {Lin Zhang and Valery Vishnevskiy and Orcun Goksel},
  title = {Deep Network for Scatterer Distribution Estimation for Ultrasound Image Simulation},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2020},
  volume = {67},
  number = {12},
  pages = {2553-2564},
  url = {https://arxiv.org/abs/2006.10166},
  doi = {10.1109/TUFFC.2020.3018424}
}

@article{Bernhardt_training_20,
  author = {Melanie Bernhardt and Valery Vishnevskiy and Richard Rau and Orcun Goksel},
  title = {Training Variational Networks with Multi-Domain Simulations: Speed-of-Sound Image Reconstruction},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2020},
  volume = {67},
  number = {12},
  pages = {2584-2594},
  url = {https://arxiv.org/abs/2006.14395},
  doi = {10.1109/TUFFC.2020.3010186}
}

@article{Pean_surface-based_20,
  author = {Fabien P\'ean and Orcun Goksel},
  title = {Surface-based modeling of muscles: Functional simulation of the shoulder},
  journal = {Medical Engineering and Physics},
  year = {2020},
  volume = {82},
  pages = {1-12},
  doi = {10.1016/j.medengphy.2020.04.010}
}

@article{Kling_optical_20,
  author = {Sabine Kling and Hossein Khodadadi and Orcun Goksel},
  title = {Optical coherence elastography based corneal strain imaging during low-amplitude intraocular pressure modulation},
  journal = {Frontiers in Bioengineering and Biotechnology: Biomechanics},
  year = {2020},
  doi = {10.3389/fbioe.2019.00453}
}

@article{Otesteanu_spectral_19,
  author = {Corin F Otesteanu and Bhaskara R Chintada and Marga B Rominger and Sergio J Sanabria and Orcun Goksel},
  title = {Spectral Quantification of Nonlinear Elasticity using Acoustoelasticity and Shear-Wave Dispersion},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2019},
  volume = {66},
  number = {12},
  pages = {1845-1855},
  url = {https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/362253/Otesteanu_spectral_19pre.pdf},
  doi = {10.1109/TUFFC.2019.2933952}
}

@article{Starkov_ultrasound_19d,
  author = {Rastislav Starkov and Lin Zhang and Michael Bajka and Christine Tanner and Orcun Goksel},
  title = {Ultrasound Simulation with Deformable and Patient-Specific Scatterer Maps},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2019},
  volume = {14},
  number = {9},
  pages = {1589-1599},
  doi = {10.1007/s11548-019-02054-5}
}

@article{Ozdemir_extending_19,
  author = {Firat Ozdemir and Orcun Goksel},
  title = {Extending pretrained segmentation networks with additional anatomical structures},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2019},
  volume = {14},
  number = {7},
  pages = {1187-1195},
  url = {https://arxiv.org/abs/1811.04634},
  doi = {10.1007/s11548-019-01984-4}
}

@article{Ruby_breast_19,
  author = {Lisa Ruby and Sergio J. Sanabria and Katharina Martini and Konstantin J. Dedes and Denise Vorburger and Ece Oezkan and Thomas Frauenfelder and Orcun Goksel and Marga B. Rominger},
  title = {Breast Cancer Assessment With Pulse-Echo Speed of Sound Ultrasound From Intrinsic Tissue Reflections: Proof-of-Concept},
  journal = {Investigative Radiology},
  year = {2019},
  volume = {54},
  number = {7},
  pages = {419-427},
  url = {https://www.zora.uzh.ch/id/eprint/170532/1/document.pdf},
  doi = {10.1097/RLI.0000000000000553}
}

@article{Sanabria_speed-of-sound_19,
  author = {Sergio J Sanabria and Marga B Rominger and Orcun Goksel},
  title = {Speed-of-Sound Imaging Based on Reflector Delineation},
  journal = {IEEE Trans Biomedical Engineering},
  year = {2019},
  volume = {66},
  number = {7},
  pages = {1949-1962},
  url = {https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/310433/SoSwithreflector.pdf},
  doi = {10.1109/TBME.2018.2881302}
}

@article{Gong_weighted_19,
  author = {Yuanhao Gong and Orcun Goksel},
  title = {Weighted Mean Curvature},
  journal = {Signal Processing},
  year = {2019},
  volume = {164},
  pages = {329-339},
  url = {https://arxiv.org/abs/1903.07189},
  doi = {10.1016/j.sigpro.2019.06.020}
}

@article{Hess_in-vivo_19,
  author = {Max Hess and Alvaro Gomariz and Orcun Goksel and Collin Ewald},
  title = {In-vivo quantitative image analysis of age-related morphological changes of C. elegans neurons reveals a correlation between neurite bending and novel neurite outgrowths},
  journal = {eNeuro},
  year = {2019},
  volume = {6},
  number = {4},
  doi = {10.1523/ENEURO.0014-19.2019}
}

@article{Ruby_breast-density_19,
  author = {Lisa Ruby and Sergio J Sanabria and Anika S Obrist and Katharina Martini and Serafino Forte and Orcun Goksel and Thomas Frauenfelder and Rahel A Kubik-Huch and Marga B Rominger},
  title = {Breast Density Assessment in Young Women with Handheld Ultrasound Based on Speed of Sound: Influence of the Menstrual Cycle},
  journal = {Medicine},
  year = {2019},
  volume = {98},
  number = {25},
  pages = {e16123},
  doi = {10.1097/MD.0000000000016123}
}

@article{Starkov_ultrasound_19,
  author = {Rastislav Starkov and Christine Tanner and Michael Bajka and Orcun Goksel},
  title = {Ultrasound Simulation with Animated Anatomical Models and On-the-Fly Fusion with Real Images via Path Tracing},
  journal = {Computers & Graphics},
  year = {2019},
  volume = {82},
  pages = {44-52},
  url = {https://www.research-collection.ethz.ch/bitstream/handle/20.500.11850/345177/StarkovR_ComputGraph2019_UltrasoundAnimated.pdf},
  doi = {10.1016/j.cag.2019.05.005}
}

@article{Pean_comprehensive_19,
  author = {Fabien Pean and Christine Tanner and Christian Gerber and Philipp Fuernstahl and Orcun Goksel},
  title = {A comprehensive and volumetric musculoskeletal model for the dynamic simulation of the shoulder function},
  journal = {Computer Methods in Biomechanics and Biomedical Engineering (CMBBE)},
  year = {2019},
  volume = {22},
  number = {7},
  pages = {740-751},
  doi = {10.1080/10255842.2019.1588963}
}

@article{Arar_high_19,
  author = {Nuri Murat Arar and Pushpak Pati and Aditya Kashyap and Anna Fomitcheva Khartchenko and Orcun Goksel and Govind V. Kaigala and Maria Gabrani},
  title = {High-Quality Immunohistochemical Stains through Computational Assay Parameter Optimization},
  journal = {IEEE Trans Biomedical Engineering},
  year = {2019},
  volume = {66},
  number = {10},
  pages = {2952-63},
  doi = {10.1109/TBME.2019.2899156}
}

@article{Mahrenke_comprehensive_19,
  author = {Torben Marhenke and Sergio J. Sanabria and Bhaskara Rao Chintada and Roman Furrer and J{\"u}rg Neuenschwander and Orcun Goksel},
  title = {Fast Spatial Characterization of Acoustic Fields Generated by Medical Array Transducers Based on Single-Plane Hydrophone Measurements},
  journal = {Sensors},
  year = {2019},
  volume = {19},
  number = {4},
  pages = {863},
  doi = {10.3390/s19040863}
}

@article{Ehrbar_elpha_19,
  author = {Stefanie Ehrbar and Alexander J\"ohl and Michael K\"uhni and Mirko Meboldt and Ece Ozkan Elsen and Christine Tanner and Orcun Goksel and Stephan Kl\"ock and Jan Unkelbach and Matthias Guckenberger and Stephanie Tanadini-Lang},
  title = {ELPHA: Dynamically deformable liver phantom for real-time motion-adaptive radiotherapy treatments},
  journal = {Medical Physics},
  year = {2019},
  volume = {46},
  number = {2},
  pages = {839-850},
  doi = {10.1002/mp.13359}
}

@article{Sanabria_speed_19,
  author = {Sergio J Sanabria and Katharina Martini and Gregor Freyst\"{a}tter and Lisa Ruby and Orcun Goksel and Thomas Frauenfelder and Marga B Rominger},
  title = {Speed of sound ultrasound: a pilot study on a novel technique to identify sarcopenia in seniors},
  journal = {European Radiology},
  year = {2019},
  volume = {29},
  number = {1},
  pages = {3-12},
  doi = {10.1007/s00330-018-5742-2}
}

@article{Otesteanu_robust_18,
  author = {Corin F Otesteanu and Sergio J Sanabria and Orcun Goksel},
  title = {Robust Reconstruction of Elasticity Using Ultrasound Imaging and Multi-frequency Excitations},
  journal = {IEEE Trans Medical Imaging},
  year = {2018},
  volume = {37},
  number = {11},
  pages = {2502-2513},
  doi = {10.1109/TMI.2018.2837390}
}

@article{Sanabria_spatial_18,
  author = {Sergio J Sanabria and Ece Ozkan and Marga B Rominger and Orcun Goksel},
  title = {Spatial Domain Reconstruction for Imaging Speed-of-Sound with Pulse-Echo Ultrasound: Simulation and In-Vivo Study},
  journal = {Physics in Medicine and Biology},
  year = {2018},
  volume = {63},
  pages = {215015},
  doi = {10.1088/1361-6560/aae2fb}
}

@article{DeLuca_evaluation_18,
  author = {Valeria De Luca and Jyotirmoy Banerjee and Andre Hallack and Satoshi Kondo and Maxim Makhinya and Daniel Nouri and Lucas Royer and Amalia Cifor and Guillaume Dardenne and Orcun Goksel and Mark J. Gooding and Camiel Klink and Alexandre Krupa and Anthony Le Bras and Maud Marchal and Adriaan Moelker and Wiro J. Niessen and Bartlomiej W. Papiez and Alex Rothberg and Julia A. Schnabel and Theo van Walsum and Erwin Vast and Emma Harris and Muyinatu A. Lediju Bell and Christine Tanner},
  title = {Evaluation of 2D and 3D ultrasound tracking algorithms and impact on ultrasound-guided liver radiotherapy margins},
  journal = {Medical Physics},
  year = {2018},
  volume = {45},
  number = {11},
  pages = {4986-5003},
  doi = {10.1002/mp.13152}
}

@article{Sanabria_breast-density_18,
  author = {Sergio J Sanabria and Orcun Goksel and Katharina Martini and Serafino Forte and Thomas Frauenfelder and Rahel A Kubik-Huch and Marga B Rominger},
  title = {Breast-Density Assessment with Handheld Ultrasound: A Novel Biomarker to Assess Breast Cancer Risk and to Tailor Screening?},
  journal = {European Radiology},
  year = {2018},
  volume = {28},
  number = {8},
  pages = {3165-3175},
  doi = {10.1007/s00330-017-5287-9}
}

@article{Samei_real-time_18,
  author = {Golnoosh Samei and Orcun Goksel and Julio Lobo and Omid Mohareri and Peter Black and Robert Rohling and Septimiu Salcudean},
  title = {Real-time FEM-based Registration of 3D to 2.5D Transrectal Ultrasound Images},
  journal = {IEEE Trans Medical Imaging},
  year = {2018},
  volume = {37},
  number = {8},
  pages = {1877-86},
  doi = {10.1109/TMI.2018.2810778}
}

@article{Gomariz_quantitative_18,
  author = {Alvaro Gomariz and Stephan Isringhausen and Patrick Helbling and Ute Suessbier and Anton Becker and Andreas Boss and Takashi Nagasawa and Gr\'egory Paul and Orcun Goksel and G\'abor Sz\'ekely and Szymon Stoma and Simon F. N\/orrelykke and Markus G. Manz and C\'esar Nombela-Arrieta},
  title = {Quantitative spatial analysis of hematopoiesis-regulating stromal cells in the bone marrow microenvironment by multiscale 3D microscopy},
  journal = {Nature Communications},
  year = {2018},
  volume = {9},
  number = {2532},
  doi = {10.1038/s41467-018-04770-z}
}

@article{Otesteanu_fem_18,
  author = {Corin F Otesteanu and Valeriy Vishnevskiy and Orcun Goksel},
  title = {FEM Based Elasticity Reconstruction Using Ultrasound For Imaging Tissue Ablation},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2018},
  volume = {13},
  number = {6},
  pages = {885-894},
  doi = {10.1007/s11548-018-1714-x}
}

@article{Ciganovic_registration_18,
  author = {Matija Ciganovic and Firat Ozdemir and Fabien Pean and Philipp Fuernstahl and Christine Tanner and Orcun Goksel},
  title = {Registration of 3D Freehand Ultrasound to a Bone Model for Orthopaedic Procedures of the Forearm},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2018},
  volume = {13},
  number = {6},
  pages = {827-836},
  doi = {10.1007/s11548-018-1756-0}
}

@article{Mattausch_image-based_18,
  author = {Oliver Mattausch and Orcun Goksel},
  title = {Image-based Reconstruction of Tissue Scatterers using Beam Steering for Ultrasound Simulation},
  journal = {IEEE Trans Medical Imaging},
  year = {2018},
  volume = {37},
  number = {3},
  pages = {767-780},
  doi = {10.1109/TMI.2017.2770118}
}

@article{Ozkan_inverse_18,
  author = {Ece Ozkan and Valeriy Vishnevsky and Orcun Goksel},
  title = {Inverse Problem of Ultrasound Beamforming with Sparsity Constraints and Regularization},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2018},
  volume = {65},
  number = {3},
  pages = {356-365},
  doi = {10.1109/TUFFC.2017.2757880}
}

@article{Mattausch_realistic_18,
  author = {Oliver Mattausch and Maxim Makhinya and Orcun Goksel},
  title = {Realistic Ultrasound Simulation of Complex Surface Models Using Interactive Monte-Carlo Path Tracing},
  journal = {Computer Graphics Forum},
  year = {2018},
  volume = {37},
  number = {1},
  pages = {202-213},
  doi = {10.1111/cgf.13260}
}

@article{Ozkan_compliance_18,
  author = {Ece Ozkan and Orcun Goksel},
  title = {Compliance Boundary Conditions for Patient-Specific Deformation Simulation Using the Finite Element Method},
  journal = {Biomedical Physics & Engineering Express},
  year = {2018},
  volume = {4},
  number = {2},
  pages = {025003},
  doi = {10.1088/2057-1976/aa918d}
}

@article{Lundin_automatic_17,
  author = {Elin L. Lundin and Martin Stauber and Panagiota Papageorgiou and Martin Ehrbar and Chafik Ghayord and Franz E. Weber and Christine Tanner and Orcun Goksel},
  title = {Automatic Registration of 2D Histological Sections to 3D microCT Volumes: Trabecular Bone},
  journal = {Bone},
  year = {2017},
  volume = {105},
  pages = {173-183},
  doi = {10.1016/j.bone.2017.08.021}
}

@article{Tanner_consistent_17,
  author = {Christine Tanner and Barbara Flach and C\'{e}line Eggenberger and Oliver Mattausch and Michael Bajka and Orcun Goksel},
  title = {Consistent Reconstruction of 4D Fetal Heart Ultrasound Images to Cope with Fetal Motion},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2017},
  volume = {12},
  number = {8},
  pages = {1307-17},
  doi = {10.1007/s11548-017-1624-3}
}

@article{Ozdemir_interactive_17,
  author = {Firat Ozdemir and Neerav Karani and Philipp Fuernstahl and Orcun Goksel},
  title = {Interactive Segmentation in MRI for Orthopedic Surgery Planning: Bone Tissue},
  journal = {Int J Comp. Assisted Radiol. Surgery},
  year = {2017},
  volume = {12},
  number = {6},
  pages = {1031-9},
  doi = {10.1007/s11548-017-1570-0}
}

@article{Ozkan_robust_17,
  author = {Ece Ozkan and Christine Tanner and Matej Kastelic and Oliver Mattausch and Maxim Makhinya and Orcun Goksel},
  title = {Robust Motion Tracking in Liver from 2D Ultrasound Images Using Supporters},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2017},
  volume = {12},
  number = {6},
  pages = {941-950},
  doi = {10.1007/s11548-017-1559-8}
}

@article{Vishnevskiy_isotropic_17,
  author = {Valeriy Vishnevskiy and Tobias Gass and Gabor Szekely and Christine Tanner and Orcun Goksel},
  title = {Isotropic Total Variation Regularization of Displacements in Parametric Image Registration},
  journal = {IEEE Trans Medical Imaging},
  year = {2017},
  volume = {36},
  number = {2},
  pages = {385-395},
  doi = {10.1109/tmi.2016.2610583}
}

@article{Knopf_required_16,
  author = {Antje-Christin Knopf and Kristin St\"utzer and Christian Richter and Antoni Rucinsk and Joakim da Silva and Justin Phillips and Martijn Engelsman and Shinichi Shimizu and Rene Werner and Annika Jakobi and Orcun Goksel and Ye Zhang and Tuathan Oshea and Martin Fast and Rosalind Perrin and Christoph Bert and EriK Korevaar and Jamie McClelland},
  title = {Required transition from research to clinical application: report on the 4D treatment planning workshops 2014 and 2015},
  journal = {Physica Medica: European J Medical Physics},
  year = {2016},
  volume = {32},
  number = {7},
  pages = {874-82},
  doi = {10.1016/j.ejmp.2016.05.064}
}

@article{Jimenez_cloud-based_16,
  author = {Oscar Alfonso {Jim\'enez-del-Toro} and Henning M\"uller and Markus Krenn and Katharina Gruenberg and Abdel Aziz Taha and Marianne Winterstein and Ivan Eggel and Antonio Foncubierta-Rodr\'iguez and Orcun Goksel and Andr\'as Jakab and Georgios Kontokotsios and Georg Langs and Bjoern Menze and Tom\`as Salas Fernandez and Roger Schaer and Anna Walley and Marc-Andr/e Weber and Yashin Dicente Cid and Tobias Gass and Mattias Heinrich and Fucang Jia and Fredrik Kahl and Razmig Kechichian and Dominic Mai and Assaf B. Spanier and Graham Vincent and Chunliang Wang and Daniel Wyeth and Allan Hanbury},
  title = {Cloud-based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms:  VISCERAL Anatomy Benchmarks},
  journal = {IEEE Trans Medical Imaging},
  year = {2016},
  volume = {35},
  number = {11},
  pages = {2459-75},
  doi = {10.1109/tmi.2016.2578680}
}

@article{Vlachopoulos_computer_16,
  author = {Lazaros Vlachopoulos and Celestine D\"unner and Tobias Gass and Matthias Graf and Orcun Goksel and Christian Gerber and G\'abor Sz\'ekely and Philipp F\"urnstahl},
  title = {Computer algorithms for three-dimensional measurement of humeral anatomy: analysis of 140 paired humeri},
  journal = {J Shoulder and Elbow Surgery},
  year = {2016},
  volume = {25},
  number = {2},
  pages = {e38-e48},
  doi = {10.1016/j.jse.2015.07.027}
}

@article{Crimi_automatic_16,
  author = {Alessandro Crimi and Maxim Makhinya and Ulrich Baumann and Christoph Thalhammer and Gabor Szekely and Orcun Goksel},
  title = {Automatic Measurement of Venous Pressure Using B-Mode Ultrasound},
  journal = {IEEE Trans Biomedical Engineering},
  year = {2016},
  volume = {63},
  number = {2},
  pages = {288-299},
  doi = {10.1109/TBME.2015.2455953}
}

@article{Khallaghi_biomechanically_15,
  author = {Siavash Khallaghi and C. Antonio S\'{a}nchez and Joy Sun and Farhad Imani and Amir Khojaste Galesh Khale and Orcun Goksel and Abtin Rasoulian and Cesare Romagnoli and Hamidreza Abdi and Silvia Chang and Parvin Mousavi and Aaron Fenster and Aaron Ward and Sidney Fels and Purang Abolmaesumi},
  title = {Biomechanically Constrained Surface Registration: Application to MR-TRUS Fusion for Prostate Interventions},
  journal = {IEEE Trans Med Imag},
  year = {2015},
  volume = {34},
  number = {11},
  pages = {2404-14},
  doi = {10.1109/TMI.2015.2440253}
}

@article{Gass_consistency-based_15,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Consistency-Based Rectification of Non-Rigid Registrations},
  journal = {SPIE J Medical Imaging},
  year = {2015},
  volume = {2},
  number = {1},
  pages = {014005},
  doi = {10.1117/1.JMI.2.1.014005}
}

@article{Baki_thermal_15,
  author = {Peter Baki and Sergio J Sanabria and Gabor Kosa and Gabor Szekely and Orcun Goksel},
  title = {Thermal Expansion Imaging for Monitoring Lesion Depth using M-Mode Ultrasound during Cardiac RF Ablation: In-vitro Study},
  journal = {Int J Computer Assisted Radiology and Surgery},
  year = {2015},
  volume = {10},
  number = {6},
  pages = {681-693},
  doi = {10.1007/s11548-015-1203-4}
}

@article{Gass_simultaneous_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Simultaneous Segmentation and Multi-Resolution Nonrigid Atlas Registration},
  journal = {IEEE Trans Image Processing},
  year = {2014},
  volume = {23},
  number = {7},
  pages = {2931-43},
  doi = {10.1109/TIP.2014.2322447}
}

@article{Goksel_prostate_13,
  author = {Orcun Goksel and Kirill Sapchuk and William James Morris and Septimiu E. Salcudean},
  title = {Prostate Brachytherapy Training with Simulated Ultrasound and Fluoroscopy Images},
  journal = {IEEE Trans Biomedical Engineering},
  year = {2013},
  volume = {60},
  number = {4},
  pages = {1002-12},
  doi = {10.1109/TBME.2012.2222642}
}

@article{Goksel_mesh_13,
  author = {Orcun Goksel and Hani Eskandari and Septimiu E. Salcudean},
  title = {Mesh Adaptation for Improving Elasticity Reconstruction using the FEM Inverse Problem},
  journal = {IEEE Trans Medical Imaging},
  year = {2013},
  volume = {32},
  number = {2},
  pages = {408-418},
  doi = {10.1109/TMI.2012.2228664}
}

@article{Luethi_statismo_12,
  author = {Marcel L\"uthi and Remi Blanc and Thomas Albrecht and Tobias Gass and Orcun Goksel and Philippe B\"uchler and Michael Kistler and Habib Bousleiman and Mauricio Reyes and Philippe Cattin and Thomas Vetter},
  title = {Statismo - A framework for PCA based statistical models},
  journal = {Insight Journal},
  year = {2012},
  url = {http://hdl.handle.net/10380/3371}
}

@article{Eskandari_dilatation_12,
  author = {Hani Eskandari and Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {Dilatation parameterization for two dimensional modeling of nearly incompressible isotropic materials},
  journal = {Physics in Medicine and Biology},
  year = {2012},
  volume = {57},
  number = {12},
  pages = {4055-73},
  doi = {10.1088/0031-9155/57/12/4055}
}

@article{Abeysekera_analysis_12,
  author = {Jeffrey M. Abeysekera and Reza Zahiri-Azar and Orcun Goksel and Robert Rohling and Septimiu E. Salcudean},
  title = {Analysis of 2-D Motion Tracking in Ultrasound with Dual Transducers},
  journal = {Ultrasonics},
  year = {2012},
  volume = {52},
  number = {1},
  pages = {156-168},
  doi = {10.1016/j.ultras.2011.07.011}
}

@article{Azar_comparison_11,
  author = {Reza Zahiri Azar and Orcun Goksel and Septimiu E. Salcudean},
  title = {Comparison Between 2-D Cross Correlation With 2-D Sub-Sampling and 2-D Tracking Using Beam Steering},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2011},
  volume = {58},
  number = {8},
  pages = {1534-7},
  doi = {10.1109/TUFFC.2011.1978}
}

@article{Eskandari_bandpass_11,
  author = {Hani Eskandari and Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {Bandpass Sampling of High Frequency Tissue Motion},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2011},
  volume = {58},
  number = {7},
  pages = {1332-43},
  doi = {10.1109/TUFFC.2011.1953}
}

@article{Goksel_haptic_11,
  author = {Orcun Goksel and Kirill Sapchuk and Septimiu E. Salcudean},
  title = {Haptic Simulator for Prostate Brachytherapy with Simulated Needle and Probe Interaction},
  journal = {IEEE Trans Haptics},
  year = {2011},
  volume = {4},
  number = {3},
  pages = {188-198},
  doi = {10.1109/TOH.2011.34}
}

@article{Goksel_image-based_11,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {Image-Based Variational Meshing},
  journal = {IEEE Trans Medical Imaging},
  year = {2011},
  volume = {30},
  number = {1},
  pages = {11-21},
  doi = {10.1109/TMI.2010.2055884}
}

@article{Zahiri-Azar_sub-sample_10,
  author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
  title = {Sub-sample Displacement Estimation from Digitized Ultrasound RF Signals Using Multi-Dimensional Polynomial Fitting of the Cross-correlation Function},
  journal = {IEEE Trans Ultrasonics, Ferroelectrics, and Frequency Control},
  year = {2010},
  volume = {57},
  number = {11},
  pages = {2403-20},
  doi = {10.1109/TUFFC.2010.1708}
}

@article{Goksel_b-mode_09,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {B-Mode Ultrasound Image Simulation in Deformable 3-D Medium},
  journal = {IEEE Trans Medical Imaging},
  year = {2009},
  volume = {28},
  number = {11},
  pages = {1657-69},
  doi = {10.1109/TMI.2009.2016561}
}

@article{Goksel_modeling_09,
  author = {Orcun Goksel and Ehsan Dehghan and Septimiu E. Salcudean},
  title = {Modeling and Simulation of Flexible Needles},
  journal = {Medical Engineering and Physics},
  year = {2009},
  volume = {31},
  number = {9},
  pages = {1069-78},
  doi = {10.1016/j.medengphy.2009.07.007}
}

@article{Goksel_3d_06,
  author = {Orcun Goksel and Septimiu E. Salcudean and Simon P. DiMaio},
  title = {3D Simulation of Needle-Tissue Interaction with Application to Prostate Brachytherapy},
  journal = {Computer Aided Surgery},
  year = {2006},
  volume = {11},
  number = {6},
  pages = {279-288},
  doi = {10.3109/10929080601089997}
}

@article{French_computing_05,
  author = {Danny G. French and James Morris and Mira Keyes and Orcun Goksel and Septimiu E. Salcudean},
  title = {Computing Intraoperative Dosimetry for Prostate Brachytherapy Using TRUS and Fluoroscopy},
  journal = {Academic Radiology},
  year = {2005},
  volume = {12},
  number = {10},
  pages = {1262-72},
  doi = {10.1016/j.acra.2005.05.026}
}

@incollection{Pati_graph_22,
  author = {Pushpak Pati and Guillaume Jaume and Antonio Foncubierta-Rodriguez and Florinda Feroce and Giosue Scognamiglio and Anna Maria Anniciello and Nadia Brancati and Maria Frucci and Daniel Riccio and Jean-Philippe Thiran and Orcun Goksel and Maria Gabrani},
  title = {Graph Representation Learning and Explainability in Breast Cancer Pathology: Bridging the Gap between AI and Pathology Practice},
  booktitle = {Artificial Intelligence Applications In Human Pathology},
  publisher = {World Scientific Publishing Europe},
  year = {2022},
  pages = {243-285},
  doi = {10.1142/9781800611399_0010}
}

@incollection{Goksel_visceral_17,
  author = {Goksel, Orcun and Foncubierta-Rodr{\'\i}guez, Antonio},
  title = {VISCERAL Anatomy Benchmarks for Organ Segmentation and Landmark Localization: Tasks and Results},
  booktitle = {Cloud-Based Benchmarking of Medical Image Analysis},
  publisher = {Springer},
  year = {2017},
  pages = {107--125},
  doi = {10.1007/978-3-319-49644-3_7}
}

@incollection{Fuernstahl_surgical_16,
  author = {Philipp F\"urnstahl and Andreas Schweizer and Matthias Graf and Lazaros Vlachopoulos and Sandro Fucentese and Stephan Wirth and Ladislav Nagy and Gabor Szekely and Orcun Goksel},
  title = {Surgical Treatment of Long-bone Deformities: 3D Preoperative Planning and Patient-specific Instrumentation},
  booktitle = {Computational Radiology for Orthopaedic Interventions},
  editor = {Guoyan Zheng and Shuo Li},
  publisher = {Springer},
  year = {2016},
  pages = {123-149},
  url = {http://www.springer.com/us/book/9783319234816},
  doi = {10.1007/978-3-319-23482-3_7}
}

@incollection{Goksel_computational_14,
  author = {Or\c{c}un G\"oksel and Gabor Sz\'ekely},
  title = {Computational Support for Intraoperative Imaging and IGT},
  booktitle = {Intraoperative Imaging and Image-Guided Therapy},
  editor = {Ferenc A. Jolesz},
  publisher = {Springer},
  year = {2014},
  pages = {63-77},
  doi = {10.1007/978-1-4614-7657-3_4}
}

@incollection{Salcudean_biomechanical_12,
  author = {Septimiu E. Salcudean and Ramin S. Sahebjavaher and Orcun Goksel and Ali Baghani and Sara S. Mahdavi and Guy Nir and Ralph Sinkus and Mehdi Moradi},
  title = {Biomechanical Modeling of the Prostate for Procedure Guidance and Simulation},
  booktitle = {Soft Tissue Biomechanical Modeling for Computer Assisted Surgery},
  editor = {Yohan Payan},
  publisher = {Springer},
  year = {2012},
  volume = {11},
  pages = {169-198},
  doi = {10.1007/978-3-642-29014-5}
}

@incollection{Goksel_overview_15,
  author = {Orcun Goksel and Antonio Foncubierta--Rodr\'iguez and Oscar Alfonso Jim\'enez del Toro and Henning M\"uller and Georg Langs and Marc-Andr\'e Weber and Bjoern Menze and Ivan Eggel and Katharina Gruenberg and Marianne Winterstein and Markus Holzer and Markus Krenn and Georgios Kontokotsios and Sokratis Metallidis and Roger Schaer and Abdel Aziz Taha and Andr\'as Jakab and Tom\`as Salas Fernandez and Allan Hanbury},
  title = {Overview of the VISCERAL Challenge at ISBI 2015},
  booktitle = {Proceedings of VISCERAL Challenge at ISBI},
  editor = {Orcun Goksel et al.},
  publisher = {CEUR-WS},
  year = {2015},
  number = {1390},
  pages = {6-11},
  url = {http://ceur-ws.org/Vol-1390/visceralISBI15-0.pdf}
}

@incollection{Jimenez_visceral_14,
  author = {Jim\'enez del Toro, Oscar Alfonso and Orcun Goksel and Bjoern Menze and Henning M\"uller and Georg Langs and Marc-Andr\'e Weber and Ivan Eggel and Katharina Gruenberg and Markus Holzer and Andr\'as Jakab and Georgios Kotsios-Kontokotsios and Markus Krenn and Tom\`as Salas Fernandez and Roger Schaer and Abdel Aziz Taha and Marianne Winterstein and Allan Hanbury},
  title = {VISCERAL - VISual Concept Extraction challenge in RAdioLogy : ISBI 2014 Challenge Organization},
  booktitle = {VISCERAL Challenge at ISBI},
  editor = {Orcun Goksel},
  publisher = {CEUR-WS},
  year = {2014},
  number = {1194},
  pages = {6-15},
  url = {http://ceur-ws.org/Vol-1194/visceralISBI14-0.pdf}
}

@inproceedings{Bezek_global_22,
  author = {Can Deniz Bezek and Mert Bilgin and Lin Zhang and Orcun Goksel},
  title = {Global Speed-of-Sound Prediction Using Transmission Geometry},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2022},
  number = {arxiv:2208.08377},
  url = {https://arxiv.org/abs/2208.08377}
}

@inproceedings{Thandiackal_differentiable_22,
  author = {Kevin Thandiackal and Boqi Chen and Pushpak Pati and Guillaume Jaume and Drew FK Williamson and Maria Gabrani and Orcun Goksel},
  title = {Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images},
  booktitle = {European Conference on Computer Vision (ECCV)},
  year = {2022},
  url = {https://arxiv.org/abs/2204.12454},
  doi = {10.1007/978-3-031-19803-8_41}
}

@inproceedings{Gomariz_unsupervised_22,
  author = {Alvaro Gomariz and Huanxiang Lu and Yun Yvonna Li and Thomas Albrecht and Andreas Maunz and Fethallah Benmansour and Alessandra M Valcarcel and Jennifer Luu and Daniela Ferrara and Orcun Goksel},
  title = {Unsupervised Domain Adaptation with Contrastive Learning for OCT Segmentation},
  booktitle = {MICCAI},
  year = {2022},
  url = {https://arxiv.org/abs/2203.03664},
  doi = {10.1007/978-3-031-16452-1_34}
}

@inproceedings{Gomariz_unified_22,
  author = {Alvaro Gomariz and Huanxiang Lu and Yun Li and Thomas Albrecht and Andreas Maunz and Fethallah Benmansour and Jennifer Luu and Orcun Goksel and Daniela Ferrara},
  title = {A unified deep learning approach for OCT segmentation from different devices and retinal diseases},
  booktitle = {ARVO Annual Meeting Procs in Investigative Ophthalmology and Visual Science},
  year = {2022},
  volume = {63},
  number = {7},
  pages = {2053-F0042},
  url = {https://iovs.arvojournals.org/article.aspx?articleid=2782139}
}

@inproceedings{Tomar_content-preserving_21,
  author = {Devavrat Tomar and Lin Zhang and Tiziano Portenier and Orcun Goksel},
  title = {Content-Preserving Unpaired Translation from Simulated to Realistic Ultrasound Images},
  booktitle = {MICCAI},
  year = {2021},
  url = {https://arxiv.org/abs/2103.05745},
  doi = {10.1007/978-3-030-87237-3_63}
}

@inproceedings{Anklin_learning_21,
  author = {Valentin Anklin and Pushpak Pati and Guillaume Jaume and Behzad Bozorgtabar and Antonio Foncubierta-Rodriguez and Jean-Philippe Thiran and Mathilde Sibony and Maria Gabrani and Orcun Goksel},
  title = {Learning Whole-Slide Segmentation from Inexact and Incomplete Labels using Tissue Graphs},
  booktitle = {MICCAI},
  year = {2021},
  pages = {636-646},
  url = {https://arxiv.org/abs/2103.03129},
  doi = {10.1007/978-3-030-87196-3_59}
}

@inproceedings{Augustin_estimating_21,
  author = {Xenia Augustin and Lin Zhang and Orcun Goksel},
  title = {Estimating Mean Speed-of-Sound from Sequence-Dependent Geometric Disparities},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2021},
  pages = {1-4},
  url = {https://arxiv.org/abs/2109.11819},
  doi = {10.1109/IUS52206.2021.9593742}
}

@inproceedings{Jaume_quantifying_21,
  author = {Guillaume Jaume and Pushpak Pati and Behzad Bozorgtabar and Antonio Foncubierta-Rodr\'iguez and Florinda Feroce and Anna Maria Anniciello and Tilman Rau and Jean-Philippe Thiran and Maria Gabrani and Orcun Goksel},
  title = {Quantifying Explainers of Graph Neural Networks in Computational Pathology},
  booktitle = {Computer Vision and Pattern Recognition (CVPR)},
  year = {2021},
  pages = {8102-12},
  url = {https://arxiv.org/abs/2011.12646},
  doi = {10.1109/CVPR46437.2021.00801}
}

@inproceedings{Gomariz_utilizing_21,
  author = {Alvaro Gomariz and Raphael Egli and Tiziano Portenier and C\'esar Nombela-Arrieta and Orcun Goksel},
  title = {Utilizing Uncertainty Estimation in Deep Learning Segmentation of Fluorescence Microscopy Images with Missing Markers},
  booktitle = {IEEE Int Symposium on Biomedical Imaging (ISBI)},
  year = {2021},
  pages = {371-4},
  url = {https://arxiv.org/abs/2101.11476},
  doi = {10.1109/ISBI48211.2021.9434158}
}

@inproceedings{Chintada_time_21,
  author = {Bhaskara Rao Chintada and Richard Rau and Orcun Goksel},
  title = {Time of Arrival Delineation In Echo Traces For Reflection Ultrasound Tomography},
  booktitle = {IEEE Int Symposium on Biomedical Imaging (ISBI)},
  year = {2021},
  pages = {1342-5},
  url = {pub/Chintada_time_21pre.pdf},
  doi = {10.1109/ISBI48211.2021.9433846}
}

@inproceedings{Portenier_gramgan_20,
  author = {Tiziano Portenier and Siavash Bigdeli and Orcun Goksel},
  title = {GramGAN: Deep 3D Texture Synthesis From 2D Exemplars},
  booktitle = {Neural Information Processing Systems (NeurIPS)},
  year = {2020},
  pages = {1-11},
  url = {https://arxiv.org/abs/2006.16112}
}

@inproceedings{Pati_hact-net_20,
  author = {Pushpak Pati and Guillaume Jaume and Lauren Alisha Fernandes and Antonio Foncubierta-Rodriguez and Florinda Feroce and Anna Maria Anniciello and Giosue Scognamiglio and Nadia Brancati and Daniel Riccio and Maurizio Di Bonito and Giuseppe De Pietro and Gerardo Botti and Orcun Goksel and Jean-Philippe Thiran and Maria Frucci and Maria Gabrani},
  title = {HACT-Net: A Hierarchical Cell-to-Tissue Graph Neural Network for Histopathological Image Classification},
  booktitle = {MICCAI Workshop on Graphs in Biomedical Image Analysis (GRAIL)},
  year = {2020},
  pages = {208-219},
  url = {https://arxiv.org/abs/2007.00584},
  doi = {10.1007/978-3-030-60365-6_20}
}

@inproceedings{Joos_recurrent_20,
  author = {Emanuel Joos and Fabien P\'ean and Orcun Goksel},
  title = {Reinforcement Learning of Musculoskeletal Control from Functional Simulations},
  booktitle = {MICCAI},
  year = {2020},
  pages = {135-145},
  url = {https://arxiv.org/abs/2007.06669},
  doi = {10.1007/978-3-030-59716-0_14}
}

@inproceedings{Zhang_deepI_20,
  author = {Lin Zhang and Tiziano Portenier and Christoph Paulus and Orcun Goksel},
  title = {Deep Image Translation for Enhancing Simulated Ultrasound Images},
  booktitle = {MICCAI Workshop on Advances in Simplifying Medical Ultrasound},
  year = {2020},
  pages = {85-94},
  url = {https://arxiv.org/abs/2006.10850},
  doi = {10.1007/978-3-030-60334-2_9}
}

@inproceedings{Rau_displacement_20,
  author = {Richard Rau and Ece Ozkan and Batu M. Ozturkler and Leila Gastli and Orcun Goksel},
  title = {Displacement Estimation Methods for Speed-of-Sound Imaging in Pulse-Echo},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2020},
  pages = {2007-2010},
  doi = {10.1109/IUS46767.2020.9251781}
}

@inproceedings{Rau_functional_20,
  author = {Richard Rau and Justine Robin and Berkan Lafci and Aileen Schroeter and Michael Reiss and X Luis Dean Ben and Orcun Goksel and Daniel Razansky},
  title = {Functional Neuroimaging of Mice Using Ultrasound and Optoacoustics},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2020}
}

@inproceedings{Chintada_model-independent_20,
  author = {Bhaskara Rao Chintada and Richard Rau and Orcun Goksel},
  title = {Model-Independent Quantification of Complex Shear Modulus via Speed and Attenuation of Surface Waves},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2020},
  pages = {1269-1272},
  url = {pub/Chintada_model-independent_20.pdf},
  doi = {10.1109/IUS46767.2020.9251721}
}

@inproceedings{Jaume_towards_20,
  author = {Guillaume Jaume and Pushpak Pati and Antonio Foncubierta-Rodriguez and Florinda Feroce and Giosue Scognamiglio and Anna Maria Anniciello and Jean-Philippe Thiran and Orcun Goksel and Maria Gabrani},
  title = {Towards Explainable Graph Representations in Digital Pathology},
  booktitle = {ICML Workshop on Computational Biology},
  year = {2020},
  pages = {1-5},
  url = {https://arxiv.org/abs/2007.00311}
}

@inproceedings{Pati_mitosis_20,
  author = {Pushpak Pati and Antonio Foncubierta-Rodr\'{i}guez and Orcun Goksel and Maria Gabrani},
  title = {Mitosis Detection under Limited Annotation: A Joint Learning Approach},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2020},
  pages = {486-489},
  url = {https://arxiv.org/abs/2006.09772},
  doi = {10.1109/ISBI45749.2020.9098431}
}

@inproceedings{Rau_attenuation_19,
  author = {Rau, Richard and Ozan Unal and Dieter Schweizer and Valery Vishnevskiy and Orcun Goksel},
  title = {Attenuation Imaging with Pulse-Echo Ultrasound based on an Acoustic Reflector},
  booktitle = {MICCAI},
  year = {2019},
  pages = {601-609},
  url = {https://arxiv.org/abs/1906.11615},
  doi = {10.1007/978-3-030-32254-0_67}
}

@inproceedings{Vishnevskiy_deep_19,
  author = {Valery Vishnevskiy and Richard Rau and Orcun Goksel},
  title = {Deep Variational Networks with Exponential Weighting for Learning Computed Tomography},
  booktitle = {MICCAI},
  year = {2019},
  pages = {310-318},
  url = {https://arxiv.org/abs/1906.05528},
  doi = {10.1007/978-3-030-32226-7_35}
}

@inproceedings{Rau_ultrasound_19,
  author = {Richard Rau and Dieter Schweizer and Valery Vishnevskiy and Orcun Goksel},
  title = {Ultrasound Aberration Correction based on Local Speed-of-Sound Map Estimation},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2019},
  pages = {1-4},
  url = {https://arxiv.org/abs/1909.10254}
}

@inproceedings{Chintada_acousto_19,
  author = {Bhaskara Rao Chintada and Richard Rau and Orcun Goksel},
  title = {Acoustoelasticity analysis of shear waves for nonlinear biomechanical characterization of oil-gelatin phantoms},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2019},
  pages = {423-6},
  url = {https://www.research-collection.ethz.ch/handle/20.500.11850/403888},
  doi = {10.1109/ULTSYM.2019.8925670}
}

@inproceedings{AlBahou_scatgan_19,
  author = {Al Bahou, Andrawes and Christine Tanner and Orcun Goksel},
  title = {ScatGAN for Reconstruction of Ultrasound Scatterers using Generative Adversarial Networks},
  booktitle = {IEEE Int Symposium on Biomedical Imaging (ISBI)},
  year = {2019},
  pages = {1674-7},
  url = {https://arxiv.org/abs/1902.00469},
  doi = {10.1109/ISBI.2019.8759251}
}

@inproceedings{Zhang_implicit_19,
  author = {Lin Zhang and Valery Vishnevsky and Andras Jakab and Orcun Goksel},
  title = {Implicit modeling with uncertainty estimation for intravoxel incoherent motion imaging},
  booktitle = {IEEE Int Symposium on Biomedical Imaging (ISBI)},
  year = {2019},
  pages = {1003-7},
  url = {https://arxiv.org/abs/1810.10358},
  doi = {10.1109/ISBI.2019.8759391}
}

@inproceedings{Gomariz_siamese_19,
  author = {Alvaro Gomariz and Weiye Li and Ece Ozkan and Christine Tanner and Orcun Goksel},
  title = {Siamese Networks with Location Prior for Landmark Tracking in Liver Ultrasound Sequences},
  booktitle = {IEEE Int Symposium on Biomedical Imaging (ISBI)},
  year = {2019},
  pages = {1757-60},
  url = {https://arxiv.org/abs/1901.08109},
  doi = {10.1109/ISBI.2019.8759382}
}

@inproceedings{Ciganovic_deep_19,
  author = {Matija Ciganovic and Firat Ozdemir and Mazda Farshad and Orcun Goksel},
  title = {Deep learning techniques for bone surface delineation in ultrasound},
  booktitle = {SPIE Medical Imaging},
  year = {2019},
  pages = {10955-33},
  url = {https://www.research-collection.ethz.ch/handle/20.500.11850/350278},
  doi = {10.1117/12.2512997}
}

@inproceedings{Pati_deep_19,
  author = {Pushpak Pati and Raul Catena and Orcun Goksel and Maria Gabrani},
  title = {A deep learning framework for context-aware mitotic activity estimation in whole slide images},
  booktitle = {SPIE Medical Imaging},
  year = {2019},
  pages = {10956-09},
  doi = {10.1117/12.2512705}
}

@inproceedings{Vishnevskiy_image_18,
  author = {Valery Vishnevskiy and Sergio J Sanabria and Orcun Goksel},
  title = {Image Reconstruction via Variational Network for Real-Time Hand-Held Sound-Speed Imaging},
  booktitle = {MICCAI Workshop on Machine Learning for Medical Image Reconstruction},
  year = {2018},
  pages = {120-128},
  url = {https://arxiv.org/abs/1807.07416},
  doi = {10.1007/978-3-030-00129-2_14}
}

@inproceedings{Ozdemir_learn_18,
  author = {Firat Ozdemir and Philipp Fuernstahl and Orcun Goksel},
  title = {Learn the New, Keep the Old: Extending Pretrained Models with New Anatomy and Images},
  booktitle = {MICCAI},
  year = {2018},
  pages = {361-369},
  url = {https://arxiv.org/abs/1806.00265},
  doi = {10.1007/978-3-030-00937-3_42}
}

@inproceedings{Tanner_combining_18,
  author = {Christine Tanner and Rastislav Starkov and Michael Bajka and Orcun Goksel},
  title = {Framework for Fusion of Data- and Model-Based Approaches for Ultrasound Simulation},
  booktitle = {MICCAI},
  year = {2018},
  pages = {332-339},
  doi = {10.1007/978-3-030-00937-3_39}
}

@inproceedings{Ozdemir_active_18,
  author = {Firat Ozdemir and Zixuan Peng and Christine Tanner and Philipp Fuernstahl and Orcun Goksel},
  title = {Active Learning for Segmentation by Optimizing Content Information for Maximal Entropy},
  booktitle = {MICCAI Workshop on Deep Learning in Medical Image Analysis},
  year = {2018},
  pages = {183-191},
  url = {https://arxiv.org/abs/1807.07349},
  doi = {10.1007/978-3-030-00889-5_21}
}

@inproceedings{Thandiackal_structure-aware_18,
  author = {Kevin Thandiackal and Orcun Goksel},
  title = {A Structure-aware Convolutional Neural Network for Skin Lesion Classification},
  booktitle = {MICCAI Workshop on ISIC Skin Image Analysis},
  year = {2018},
  pages = {312-319},
  doi = {10.1007/978-3-030-01201-4_34}
}

@inproceedings{Otesteanu_ultrasound_18,
  author = {Corin F. Otesteanu and Valeriy Vishnevskiy and Christian Guenthner and Sebastian Kozerke and Orcun Goksel},
  title = {Ultrasound and Magnetic-Resonance Harmonic Elastography with Hybrid Inverse-Problem Formulation of FEM Viscoelasticity Reconstruction},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2018}
}

@inproceedings{Ruby_menstrual_18,
  author = {Lisa Ruby and Sergio J Sanabria and Anika S Obrist and Katharina Martini and Serafino Forte and Orcun Goksel and Thomas Frauenfelder and Rahel Kubik-Huch and Marga B Rominger},
  title = {Menstrual cycle-related changes in breast density using hand-held Speed-of-Sound Ultrasound},
  booktitle = {Dreiländertreffen Ultraschall},
  journal = {Ultraschall in der Medizin},
  year = {2018},
  volume = {39},
  pages = {S43-4},
  doi = {10.1055/s-0038-1670479}
}

@inproceedings{Jakab_neuroshape_18,
  author = {A. Jakab and Z. Goey and O. Goksel and R. Tuura and R. Bauer and L. Stieglitz and G. Szekely and E. Martin and B. Werner},
  title = {NeuroShape: a novel software implementing state-of-the-art targeting for MRI-guided focused ultrasound neurosurgery},
  booktitle = {Swiss Congress of Radiology},
  year = {2018},
  doi = {10.13140/RG.2.2.16998.73283}
}

@inproceedings{Pean_musculoskeletal_18,
  author = {Fabien P\'{e}an and Philipp F\u{u}rnstahl and Orcun Goksel},
  title = {A musculoskeletal model of the shoulder combining multibody dynamics and FEM using B-Spline elements},
  booktitle = {Int Symp Computer Methods in Biomechanics and Biomedical Engineering (CMBBE)},
  year = {2018},
  url = {http://cmbbe2018.tecnico.ulisboa.pt/pen_cmbbe2018/pdf/WEB_ABSTRACTS/Abstracts_CMBBE2018_149.pdf}
}

@inproceedings{Sanabria_breast_18,
  author = {Sergio Sanabria and Katharina Martini and Marga Rominger and Konstantin Dedes and D. Vorburger and Thomas Frauenfelder and Orcun Goksel},
  title = {Breast cancer assessment with hand-held ultrasound based Speed of Sound: preliminary results},
  booktitle = {European Conference on Radiology (ECR)},
  year = {2018},
  doi = {10.1594/ecr2018/C-1388}
}

@inproceedings{Metzger_sarcopenia_18,
  author = {M-L Metzger and Gregor Freyst\"{a}tter and Katharina Martini and Thomas Frauenfelder and Orcun Goksel and Sergio J Sanabria and Marga B. Rominger},
  title = {Sarcopenia assessment with handheld ultrasound: a novel technique based on speed of sound},
  booktitle = {European Conference on Radiology (ECR)},
  year = {2018},
  doi = {10.1594/ecr2018/C-1211}
}

@inproceedings{Martini_hand-held_18,
  author = {Katharina Martini and Sergio J Sanabria and Serafino Forte and Rahel A Kubik-Huch and Thomas Frauenfelder and Orcun Goksel and Marga B. Rominger},
  title = {Hand-held speed-of-sound ultrasound -- a novel cost-efficient biomarker for breast density assessment},
  booktitle = {European Conference on Radiology (ECR)},
  year = {2018},
  doi = {10.1594/ecr2018/C-0037}
}

@inproceedings{Sanabria_can_17,
  author = {Sergio J Sanabria and Marga B Rominger and Corin F Otesteanu and Farrukh I Sheikh and Volker Klingmueller and Orcun Goksel},
  title = {Can speed of sound be better than conventional elastography for breast characterization?},
  booktitle = {Annual Meeting of Radiological Society of North America (RSNA)},
  year = {2017}
}

@inproceedings{Farrukh_interpreting_17,
  author = {Waleed Farrukh and Antonio Foncubierta-Rodriguez and Anca-Nicoleta Ciubotaru and Guillaume Jaume and Costas Bekas and Orcun Goksel and Maria Gabrani},
  title = {Interpreting data from scanned tables},
  booktitle = {GREC 2017: 12th IAPR International Workshop on Graphics Recognition},
  year = {2017},
  doi = {10.1109/ICDAR.2017.250}
}

@inproceedings{Pati_computational_17,
  author = {Pushpak Pati and Murat Arar and Govind Kaigala and Kashyap Aditya and Orcun Goksel and Maria Gabrani},
  title = {Computational Immunohistochemistry: Recipes for Standardization of Immunostaining},
  booktitle = {MICCAI},
  year = {2017},
  doi = {10.1007/978-3-319-66185-8_6}
}

@inproceedings{Otesteanu_quantification_17,
  author = {Corin F. Otesteanu and Bhaskara R. Chintada and Edoardo Mazza and Sergio J. Sanabria and Orcun Goksel},
  title = {Quantification of nonlinear elastic constants using polynomials in quasi-incompressible soft solids},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2017},
  doi = {10.1109/ULTSYM.2017.8091737}
}

@inproceedings{Chintada_reflector-based_17,
  author = {Bhaskara R. Chintada and Sergio J. Sanabria and Wolfgang Bost and Orcun Goksel},
  title = {Reflector-Based 3D Tomographic Ultrasound Reconstruction: Simulation Study},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2017},
  doi = {10.1109/ULTSYM.2017.8092257}
}

@inproceedings{Pean_physical_17,
  author = {Fabien Pean and Fabio Carrillo and Philipp Fuernstahl and Orcun Goksel},
  title = {Physical Simulation of the Interosseous Ligaments During Forearm Rotation},
  booktitle = {Computer Assisted Orthopaedic Surgery},
  year = {2017},
  url = {https://easychair.org/publications/paper/350665},
  doi = {10.29007/74wg}
}

@inproceedings{Gomariz_multiscale_17,
  author = {Gomariz, A and Helbling, P and Isringhausen, S and Suessbier, U and Becker, A and Boss, A and Nagasawa, T and Paul, G and Goksel, O and Szekely, G and others},
  title = {Multiscale Image-Based Quantitative Analysis of Bone Marrow Stromal Network Topology Reveals Strict Spatial Constraints for Hematopoietic-Stromal Cellular Interactions},
  booktitle = {Haematologica},
  year = {2017},
  volume = {102},
  pages = {78-79}
}

@inproceedings{Mattausch_comparison_17,
  author = {Oliver Mattausch and Elisabeth Ren and Michael Bajka and Kenneth Vanhoey and Orcun Goksel},
  title = {Comparison of Texture Synthesis Methods for Content Generation in Ultrasound Training Simulation},
  booktitle = {SPIE Medical Imaging},
  year = {2017},
  pages = {1-8},
  doi = {10.1117/12.2250604}
}

@inproceedings{Goksel_abdominal_16,
  author = {Orcun Goksel and Valeria DeLuca and Maxim Makhinya and Christine Tanner},
  title = {Abdominal Motion Tracking and Prediction in 2D Ultrasound},
  booktitle = {4D Treatment Planning (4DTP) Workshop},
  year = {2016}
}

@inproceedings{Vishnevskiy_accurate_16,
  author = {Valeriy Vishnevskiy and Christine Tanner and Orcun Goksel},
  title = {Accurate and Fast Deformable Image Registration Allowing For Sliding Interfaces},
  booktitle = {4D Treatment Planning (4DTP) Workshop},
  year = {2016}
}

@inproceedings{Sanabria_hand-held_16,
  author = {Sergio J. Sanabria and Orcun Goksel},
  title = {Hand-held Sound-Speed Mammography Based on Ultrasound Reflector Tracking},
  booktitle = {MICCAI},
  year = {2016},
  pages = {568-576},
  doi = {10.1007/978-3-319-46720-7_66}
}

@inproceedings{Ozdemir_graphical_16,
  author = {Firat Ozdemir and Ece Ozkan and Orcun Goksel},
  title = {Graphical Modeling of Ultrasound Propagation in Tissue for Automatic Bone Segmentation},
  booktitle = {MICCAI},
  year = {2016},
  pages = {256-264},
  doi = {10.1007/978-3-319-46723-8_30}
}

@inproceedings{Tanner_4D_16,
  author = {Christine Tanner and Celine Eggenberger and Barbara Flach and Oliver Mattausch and Michael Bajka and Orcun Goksel},
  title = {4D Reconstruction of Fetal Heart Ultrasound Images in Presence of Fetal Motion},
  booktitle = {MICCAI},
  year = {2016},
  pages = {593-601},
  doi = {10.1007/978-3-319-46720-7_69}
}

@inproceedings{Mattausch_image-based_16,
  author = {Oliver Mattausch and Orcun Goksel},
  title = {Image-based PSF Estimation for Ultrasound Training Simulation},
  booktitle = {MICCAI W Simulation and Synthesis in Medical Imaging (SASHIMI)},
  year = {2016},
  pages = {23-33},
  doi = {10.1007/978-3-319-46630-9_3}
}

@inproceedings{Flach_pure_16,
  author = {Barbara Flach and Maxim Makhinya and Orcun Goksel},
  title = {PURE: Panoramic Ultrasound Reconstruction by Seamless Stitching of Volumes},
  booktitle = {MICCAI W Simulation and Synthesis in Medical Imaging (SASHIMI)},
  year = {2016},
  pages = {75-84},
  doi = {10.1007/978-3-319-46630-9_8}
}

@inproceedings{Thoma_automatic_16,
  author = {Janine Thoma and Firat Ozdemir and Orcun Goksel},
  title = {Automatic Segmentation of Abdominal MRI Using Selective Sampling and Random Walker},
  booktitle = {MICCAI W Medical Computer Vision (MCV)},
  year = {2016},
  pages = {83-93},
  doi = {10.1007/978-3-319-61188-4_8}
}

@inproceedings{Sanabria_non-linear_16,
  author = {Sergio J Sanabria and Marga Rominger and Corin F. Otesteanu and Edoardo Mazza and Orcun Goksel},
  title = {Non-Linear Characterization of the Liver by Combining Shear and Longitudinal Wave Speed With Strain Observations},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2016}
}

@inproceedings{Ozkan_compliance_16,
  author = {Ece Ozkan and Orcun Goksel},
  title = {Compliance Boundary Conditions for Elasticity Reconstruction Using FEM Inverse Problem},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2016}
}

@inproceedings{Otesteanu_low-cost_16,
  author = {Corin F. Otesteanu and Sergio J Sanabria and Orcun Goksel},
  title = {Low Cost Alternative for Ultrasound Harmonic Elastography},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2016}
}

@inproceedings{Kurth_mobile_16,
  author = {Andreas Kurth and Andreas Tretter and Pascal A. Hager and Sergio Sanabria and Orcun Goksel and Lothar Thiele and Luca Benini},
  title = {Mobile Ultrasound Imaging on Heterogeneous Multi-Core Platform},
  booktitle = {ACM/IEEE Symp on Embedded Systems for Real-time Multimedia (ESTIMedia)},
  year = {2016},
  pages = {9-18},
  doi = {10.1145/2993452.2993565}
}

@inproceedings{Ozkan_inverse_16,
  author = {Ece Ozkan and Orcun Goksel},
  title = {Inverse Problem of Ultrasound Beamforming with Sparsity in Time and Frequency Domain},
  booktitle = {IEEE Int Ultrasonics Symp (IUS)},
  year = {2016},
  doi = {10.1109/ULTSYM.2016.7728892}
}

@inproceedings{Mattausch_monte-carlo_16,
  author = {Oliver Mattausch and Orcun Goksel},
  title = {Monte-Carlo Ray-Tracing for Realistic Interactive Ultrasound Simulation},
  booktitle = {Eurographics W Visual Computing for Biology and Medicine (VCBM)},
  year = {2016},
  pages = {1-9},
  doi = {dx.doi.org/10.2312/vcbm.20161285}
}

@inproceedings{Chen_temporal_16,
  author = {Chen, Xiaoran and Tanner, Christine and G\"oksel, Or\ccun and Sz\'ekely, G\'abor and Luca, Valeria},
  title = {Temporal Prediction of Respiratory Motion Using a Trained Ensemble of Forecasting Methods},
  booktitle = {Medical Imaging and Augmented Reality (MIAR)},
  year = {2016},
  pages = {383-391},
  doi = {10.1007/978-3-319-43775-0_35}
}

@inproceedings{Otesteanu_analysis_16,
  author = {Corin Felix Otesteanu and Sergio J Sanabria and Orcun Goksel},
  title = {Analysis of Excitation Frequency in Elasticity Reconstruction Using the FEM Inverse-Problem},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2016},
  pages = {485-8},
  doi = {10.1109/ISBI.2016.7493313}
}

@inproceedings{Goksel_imaging_16,
  author = {Orcun Goksel and Valery Vishnevsky and Alvaro Gomariz Carrillo and Christine Tanner},
  title = {Imaging of Sliding Visceral Interfaces During Breathing},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2016},
  pages = {298-301},
  doi = {10.1109/ISBI.2016.7493268}
}

@inproceedings{Flach_model-based_16,
  author = {Barbara Flach and Maxim Makhinya and Orcun Goksel},
  title = {Model-based Compensation of Tissue Deformation During Data Acquisition for Interpolative Ultrasound Simulation},
  booktitle = {IEEE Int Symp Biomed Imaging (ISBI)},
  year = {2016},
  pages = {502-5},
  doi = {10.1109/ISBI.2016.7493317}
}

@inproceedings{Makhinya_real-time_15,
  author = {Maxim Makhinya and Orcun Goksel},
  title = {Real-time Tracking of Liver Landmarks in 2D Ultrasound Sequences},
  booktitle = {4D Treatment Planning (4DTP) Workshop},
  year = {2015}
}

@inproceedings{Makhinya_motion_15,
  author = {Maxim Makhinya and Orcun Goksel},
  title = {Motion Tracking in 2D Ultrasound Using Vessel Models and Robust Optic-Flow},
  booktitle = {MICCAI Challenge on Liver Motion Tracking (CLUST)},
  year = {2015},
  url = {http://clust.ethz.ch/opendownload/CLUST2015/makhinya_clust15.pdf}
}

@inproceedings{Sanabria_hand-held_15,
  author = {Sergio J. Sanabria and Corin F. Otesteanu and Orcun Goksel},
  title = {Hand-held Sound-speed Imaging for the Reconstruction of Bulk Modulus and Poisson Ratio in a Commercial Tissue-Mimicking Phantom},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2015}
}

@inproceedings{Sanabria_total-variation_15,
  author = {Sergio J. Sanabria and Orcun Goksel},
  title = {Total-Variation Regularization of Hand-held Limited-Angle Sound-Speed Tomography Based on Coherent Reflector for Breast Cancer Detection},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2015}
}

@inproceedings{Ozkan_compliance_15,
  author = {Ece Ozkan and Orcun Goksel},
  title = {Compliance Boundary Conditions for Simulating Deformations in a Limited Region of Interest},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2015},
  pages = {929-32},
  doi = {10.1109/EMBC.2015.7318515}
}

@inproceedings{Mattausch_scatterer_15,
  author = {Oliver Mattausch and Orcun Goksel},
  title = {Scatterer Reconstruction and Parametrization of Homogeneous Tissue for Ultrasound Image Simulation},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2015},
  pages = {6350-3},
  doi = {10.1109/EMBC.2015.7319845}
}

@inproceedings{Baki_thermal_15t,
  author = {Peter Baki and Sergio J. Sanabria and Gabor Kosa and Gabor Szekely and Orcun Goksel},
  title = {Thermal Expansion Imaging for Monitoring Lesion Depth using M-Mode Ultrasound during Cardiac RF Ablation: In-vitro Study},
  booktitle = {Information Processing in Computer-Assisted Interventions (IPCAI)},
  year = {2015}
}

@inproceedings{Vishnevsky_unsupervised_15,
  author = {Valery Vishnevsky and Tobias Gass and Gabor Szekely and Christine Tanner and Orcun Goksel},
  title = {Unsupervised Detection of Local Errors in Image Registration},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2015},
  pages = {841-4},
  doi = {10.1109/ISBI.2015.7164002}
}

@inproceedings{Gass_multi-atlas_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Multi-Atlas Segmentation and Landmark Localization in Images with Large Fields of View},
  booktitle = {MICCAI W Medical Computer Vision (MCV): Algorithms for Big Data},
  year = {2014},
  pages = {171-80},
  doi = {10.1007/978-3-319-13972-2_16}
}

@inproceedings{Vishnevskiy_total_14,
  author = {Valeriy Vishnevskiy and Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Total Variation Regularization of Displacements in Parametric Image Registration},
  booktitle = {MICCAI W Abdominal Imaging: Computational and Clinical Apps},
  year = {2014},
  pages = {211-220},
  doi = {10.1007/978-3-319-13692-9_20}
}

@inproceedings{Gass_registration_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Registration Fusion using Markov Random Fields},
  booktitle = {Workshop on Biomedical Image Registration (WBIR)},
  year = {2014},
  pages = {213-222},
  doi = {10.1007/978-3-319-08554-8_22}
}

@inproceedings{Gass_consistent_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Consistent Dense Correspondences from Pairwise Registrations},
  booktitle = {SHAPE Symp on Statistical Shape Models and Applications},
  year = {2014},
  pages = {10}
}

@inproceedings{Goksel_segmentation_14,
  author = {Orcun Goksel and Tobias Gass and Gabor Szekely},
  title = {Segmentation and Landmark Localization Based on Multiple Atlases},
  booktitle = {IEEE ISBI VISCERAL Challenge},
  year = {2014},
  number = {1194},
  pages = {37-43},
  url = {http://ceur-ws.org/Vol-1194/visceralISBI14-5.pdf}
}

@inproceedings{Crimi_vessel_14,
  author = {Alessandro Crimi and Maxim Makhinya and Ulrich Baumann and Gabor Szekely and Orcun Goksel},
  title = {Vessel tracking for Ultrasound-based venous pressure measurement},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2014},
  pages = {306-9},
  doi = {10.1109/ISBI.2014.6867870}
}

@inproceedings{Gass_detection_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Detection and correction of inconsistency-based errors in non-rigid registration},
  booktitle = {SPIE Medical Imaging},
  year = {2014},
  pages = {90341B},
  doi = {10.1117/12.2042757}
}

@inproceedings{Gass_auxiliary_14,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Auxiliary anatomical labels for joint segmentation and atlas registration},
  booktitle = {SPIE Medical Imaging},
  year = {2014},
  pages = {90343T},
  doi = {10.1117/12.2042876}
}

@inproceedings{Goksel_improving_13,
  author = {Or\c{c}un G\"oksel and Gabor Sz\'ekely},
  title = {Improving FEM Inverse Problem Reconstructions By Incorporating All Displacement Observations Using Element Shape Function Interpolations},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2013},
  pages = {78},
  url = {http://www.elasticityconference.org/PDF/2013/2013ITECProceedings.pdf}
}

@inproceedings{Baki_thermal_13,
  author = {P\'eter Baki and Gabor Sz\'ekely and Or\c{c}un G\"oksel},
  title = {Thermal Expansion Imaging For Real-time Lesion Depth Assessment During RF Catheter Ablation},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2013},
  pages = {70},
  url = {http://www.elasticityconference.org/PDF/2013/2013ITECProceedings.pdf}
}

@inproceedings{Shahim_accuracy_13,
  author = {Kamal Shahim and Orcun Goksel and Philipp J\"urgens and Mauricio Reyes},
  title = {Accuracy Improvement In Cranio-Maxillofacial Soft Tissue Simulation Using A Muscle Embedded Meshing Approach},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2013},
  pages = {7156-9},
  doi = {10.1109/EMBC.2013.6611208}
}

@inproceedings{Ma_supervised_13,
  author = {Hua Ma and Thomas Coradi and Gabor Szekely and Benjamin Haas and Orcun Goksel},
  title = {Supervised Learning with Global Features for Image Retrieval in Atlas-Based Segmentation of Thoracic CT},
  booktitle = {Int Congress on Computer Assisted Radiology and Surgery (CARS)},
  year = {2013},
  pages = {S302}
}

@inproceedings{Goksel_estimation_13,
  author = {Orcun Goksel and Tobias Gass and Valery Vishnevsky and Gabor Szekely},
  title = {Estimation of Atlas-Based Segmentation Outcome: Leveraging Information From Unsegmented Images},
  booktitle = {IEEE Int Symp Biomedical Imaging (ISBI)},
  year = {2013},
  pages = {1203-6},
  doi = {10.1109/ISBI.2013.6556699}
}

@inproceedings{Goksel_deformable_13,
  author = {Orcun Goksel and Seokhee Jeon and Matthias Harders and Gabor Szekely},
  title = {Deformable Haptic Model Generation Through Manual Exploration},
  booktitle = {IEEE World Haptics Conference},
  year = {2013},
  pages = {543-8},
  doi = {10.1109/WHC.2013.6548466}
}

@inproceedings{Bolis_exploiting_12a,
  author = {Dimitris Bolis and Andras Jakab and Orcun Goksel and Gabor Szekely},
  title = {On exploiting the connectomics for thalamic nuclei localization: application of pattern recognition techniques},
  booktitle = {European Society for Magnetic Resonance in Medicine and Biology (ESMRMB)},
  year = {2012}
}

@inproceedings{Gass_semi-supervised_12,
  author = {Tobias Gass and Gabor Szekely and Orcun Goksel},
  title = {Semi-supervised Segmentation Using Multiple Segmentation Hypotheses from a Single Atlas},
  booktitle = {MICCAI W Medical Computer Vision (MCV)},
  year = {2012},
  pages = {29-37},
  doi = {10.1007/978-3-642-36620-8_4}
}

@inproceedings{Bolis_exploiting_12,
  author = {Dimitris Bolis and Andr\'as Jakab and Or\ccun G\"oksel and G\'abor Sz\'ekely},
  title = {On Exploiting Connectomics for Thalamic Nuclei Localization: A Supervised Learning Approach},
  booktitle = {Int Conf on Machine Learning (ICML) Workshop on Statistics, Machine Learning and Neuroscience},
  year = {2012},
  url = {https://sites.google.com/site/stamlins/proceedings}
}

@inproceedings{Bolis_application_12,
  author = {Dimitris Bolis and Andras Jakab and Orcun Goksel and Gabor Szekely},
  title = {Application of pattern recognition techniques to locate the Vim thalamic nucleus based on thalamocortical tractography},
  booktitle = {European Congress on Radiology (ECR)},
  year = {2012},
  pages = {C-1991}
}

@inproceedings{Taquee_deformable_12,
  author = {Farheen Taquee and Orcun Goksel and S. Sara Mahdavi and Mira Keyes and W. James Morris and Ingrid Spadinger and Septimiu Salcudean},
  title = {Deformable Prostate Registration from MR and TRUS Images Using Surface Error Driven FEM models},
  booktitle = {SPIE Medical Imaging},
  year = {2012},
  doi = {10.1117/12.911688}
}

@inproceedings{Goksel_haptic_11n,
  author = {Orcun Goksel and Kirill Sapchuk and Septimiu E. Salcudean},
  title = {Haptic simulation of needle and probe interaction with tissue for prostate brachytherapy training},
  booktitle = {IEEE World Haptics Conference (WHC)},
  year = {2011},
  pages = {7-12},
  doi = {10.1109/WHC.2011.5945453}
}

@inproceedings{Goksel_fem_10,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {FEM Simulation of Harmonic Tissue Excitation for Prostate Elastography},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2010},
  pages = {93}
}

@inproceedings{Eskandari_bandpass_10,
  author = {Hani Eskandari and Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {Bandpass Sampling of High Frequency Tissue Motion},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2010},
  pages = {71}
}

@inproceedings{Goksel_mesh_10,
  author = {Orcun Goksel and Hani Eskandari and Septimiu E. Salcudean},
  title = {Mesh Adaptation for Improving Inverse-Problem Reconstruction},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2010},
  pages = {96}
}

@inproceedings{Haddadi_controllability_10,
  author = {Amir Haddadi and Orcun Goksel and Septimiu E. Salcudean and Keyvan Hashtrudi-Zaad},
  title = {On the Controllability of Dynamic Model-Based Needle Insertion in Soft Tissue},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2010},
  pages = {2287-2291},
  doi = {10.1109/IEMBS.2010.5627676}
}

@inproceedings{Goksel_haptic_10,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {Haptic Simulator for Prostate Brachytherapy with Simulated Ultrasound},
  booktitle = {Int Symp Biomedical Simulation (ISBMS)},
  year = {2010},
  pages = {150-9},
  doi = {10.1007/978-3-642-11615-5_16}
}

@inproceedings{Zahiri-Azar_multi-dimensional_09,
  author = {Reza Zahiri-Azar and Orcun Goksel and T.S. Yao and Ehsan Dehghan and Joseph Yan and Septimiu E. Salcudean},
  title = {Multi-Dimensional Sub-Sample Motion Estimation: Initial Results},
  booktitle = {IEEE Int Ultrasonics Symposium (IUS)},
  year = {2009},
  doi = {10.1109/ULTSYM.2009.0595}
}

@inproceedings{Goksel_automatic_09,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {Automatic Prostate Segmentation from Transrectal Ultrasound Elastography Images Using Geometric Active Contours},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2009},
  pages = {34}
}

@inproceedings{Zahiri-Azar_application_09,
  author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
  title = {Application of 2D Polynomial Fitting to Beam Steering for Motion Estimation with Sub-Sample Accuracy},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2009},
  pages = {124}
}

@inproceedings{Zahiri-Azar_methods_09,
  author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
  title = {Methods for the Estimation of the Sub-Sample Motion Using Digitized Ultrasound Echo Signals in Three Dimensions},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2009},
  pages = {88}
}

@inproceedings{Goksel_high-quality_09,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {High-Quality Model Generation for Finite Element Simulation of Tissue Deformation},
  booktitle = {MICCAI},
  year = {2009},
  pages = {248-256},
  doi = {10.1007/978-3-642-04271-3_31}
}

@inproceedings{Mahdavi_3d_09,
  author = {Sara Mahdavi and Orcun Goksel and Septimiu E. Salcudean},
  title = {3D Prostate Segmentation in Ultrasound Images Based on Tapered and Deformed Ellipsoids},
  booktitle = {MICCAI},
  year = {2009},
  pages = {960-7},
  doi = {10.1007/978-3-642-04271-3_116}
}

@inproceedings{Zahiri-Azar_methods_08,
  author = {Reza Zahiri-Azar and Orcun Goksel and T.S. Yao and Ehsan Dehghan and Joseph Yan and Septimiu E. Salcudean},
  title = {Methods for the Estimation of Sub-sample Motion of Digitized Ultrasound Echo Signals in 2D},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2008},
  pages = {5581-4},
  doi = {10.1109/IEMBS.2008.4650479}
}

@inproceedings{Zahiri-Azar_real-time_07,
  author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
  title = {Real-Time Tissue Deformation Visualization},
  booktitle = {Int Tissue Elasticity Conf (ITEC)},
  year = {2007},
  pages = {117}
}

@inproceedings{Goksel_real-time_07,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {Real-time Synthesis of Image Slices in Deformed Tissue from Nominal Volume Images},
  booktitle = {MICCAI},
  year = {2007},
  pages = {401-8},
  doi = {10.1007/978-3-540-75757-3_49}
}

@inproceedings{Goksel_fast_07,
  author = {Orcun Goksel and Septimiu E. Salcudean},
  title = {Fast B-Mode Ultrasound Image Simulation of Deformed Tissue},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2007},
  pages = {87-90},
  doi = {10.1109/IEMBS.2007.4352229}
}

@inproceedings{Goksel_simulation_07,
  author = {Orcun Goksel and Reza Zahiri-Azar and Septimiu E. Salcudean},
  title = {Simulation of Ultrasound Radio-Frequency Signals in Deformed Tissue for Validation of 2D Motion Estimation with Sub-Sample Accuracy},
  booktitle = {IEEE Eng Medicine and Biology Conf (EMBC)},
  year = {2007},
  pages = {2159-62},
  doi = {10.1109/IEMBS.2007.4352750}
}

@inproceedings{Dehghan_comparison_06,
  author = {Ehsan Dehghan and Orcun Goksel and Septimiu E. Salcudean},
  title = {A Comparison of Needle Bending Models},
  booktitle = {MICCAI},
  year = {2006},
  pages = {305-312},
  doi = {10.1007/11866565_38}
}

@inproceedings{Goksel_image_06,
  author = {Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {Image Synthesis of Deformed Tissue with Application to Ultrasound for Prostate Brachytherapy},
  booktitle = {Canadian Medical and Biological Engineering Conf (CMBEC)},
  year = {2006}
}

@inproceedings{Goksel_3d_05,
  author = {Orcun Goksel and Simon P. DiMaio and Septimiu E. Salcudean and Robert Rohling and James Morris},
  title = {3D Needle-Tissue Interaction Simulation for Prostate Brachytherapy},
  booktitle = {MICCAI},
  year = {2005},
  pages = {827-834},
  doi = {10.1007/11566465_102}
}

@inproceedings{Goksel_3Dis_05,
  author = {Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {3D Needle-Tissue Interaction Simulation for Prostate Brachytherapy},
  booktitle = {Annual Canadian Conference on Intelligent Systems (IS 2005)},
  year = {2005}
}

@inproceedings{Goksel_towards_04,
  author = {Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
  title = {Towards a Prostate Brachytherapy Haptic Simulator},
  booktitle = {BC Advanced Systems Institute (ASI) Exchange},
  year = {2004}
}

@phdthesis{Goksel_meshing_09,
  author = {Orcun Goksel},
  title = {Meshing and Rendering of Patient-Specific Deformation Models With Application to Needle Insertion Simulation},
  school = {University of British Columbia},
  year = {2009},
  url = {http://hdl.handle.net/2429/17418},
  doi = {10.14288/1.0068717}
}

@mastersthesis{Goksel_ultrasound_05,
  author = {Orcun Goksel},
  title = {Ultrasound Image and 3D Finite Element based Tissue Deformation Simulator for Prostate Brachytherapy},
  school = {University of British Columbia},
  year = {2005},
  url = {http://hdl.handle.net/2429/16194},
  doi = {10.14288/1.0065481}
}

@book{Franz_ipcai_21,
  author = {Alfred Franz and Orcun Goksel},
  title = {(eds.) IJCARS-IPCAI 2021 Special Issue: Proceedings of Information Processing for Computer-Assisted Interventions},
  publisher = {Springer},
  year = {2021},
  doi = {10.1007/s11548-021-02401-5}
}

@book{Spiclin_wbir_20,
  author = {Spiclin, Z. and McClelland, J. and Kybic, J. and Goksel, O},
  title = {(eds.) Proceedings of International Workshop on Biomedical Image Registration (WBIR)},
  publisher = {Springer},
  year = {2020},
  doi = {10.1007/978-3-030-50120-4}
}

@book{Gooya_sashimi_18,
  author = {Gooya, A. and Goksel, O. and Oguz, I. and Burgos, N.},
  title = {(eds.) Proceedings of Simulation and Synthesis in Medical Imaging (SASHIMI)},
  publisher = {Springer},
  year = {2018},
  doi = {10.1007/978-3-030-00536-8}
}

@book{Goksel_visceral_15,
  author = {Orcun Goksel and Jim\'enez del Toro, Oscar Alfonso and Antonio Foncubierta and Henning M\"uller},
  title = {(eds.) Proceedings of the VISCERAL Challenge at ISBI},
  publisher = {CEUR-WS.org},
  year = {2015},
  number = {1390},
  url = {http://ceur-ws.org/Vol-1390/}
}

@book{Goksel_visceral_14,
  author = {Orcun Goksel},
  title = {(ed.) Proceedings of the VISCERAL Challenge at ISBI},
  publisher = {CEUR-WS.org},
  year = {2014},
  number = {1194},
  url = {http://ceur-ws.org/Vol-1194}
}

@unpublished{Zhang_unpaired_23,
  author = {Lin Zhang and Tiziano Portenier and Orcun Goksel},
  title = {Unpaired Translation from Semantic Label Maps to Images by Leveraging Domain-Specific Simulations},
  year = {2023},
  number = {arxiv:2302.10698},
  doi = {10.48550/ARXIV.2302.10698}
}

@unpublished{Schweizer_robust_23,
  author = {Dieter Schweizer and Richard Rau and Can Deniz Bezek and Rahel A. Kubik-Huch and Orcun Goksel},
  title = {Robust Imaging of Speed-of-Sound Using Virtual Source Transmission},
  year = {2023},
  number = {arxiv:2303.11262},
  doi = {10.48550/arXiv.2303.11262}
}

@unpublished{Thandiackal_multi-scale_23,
  author = {Kevin Thandiackal and Luigi Piccinelli and Pushpak Pati and Orcun Goksel},
  title = {Multi-scale Feature Alignment for Continual Learning of Unlabeled Domains},
  year = {2023},
  number = {arxiv:2302.01287},
  doi = {10.48550/ARXIV.2302.01287}
}

@unpublished{Pati_weakly_23,
  author = {Pushpak Pati and Guillame Jaume and Z Ayadi and K Thandiackal and B Bozorgtabar and M Gabrani and Orcun Goksel},
  title = {Weakly Supervised Joint Whole-Slide Segmentation and Classification in Prostate Cancer},
  year = {2023},
  number = {arxiv:2301.02933},
  doi = {10.48550/ARXIV.2301.02933}
}

@unpublished{Chen_generative_23,
  author = {Boqi Chen and Kevin Thandiackal and Pushpak Pati and Orcun Goksel},
  title = {Generative appearance replay for continual unsupervised domain adaptation},
  year = {2023},
  number = {arxiv:2301.01211},
  doi = {10.48550/ARXIV.2301.01211}
}

@unpublished{Thandiackal_match_21,
  author = {Kevin Thandiackal and Tiziano Portenier and Andrea Giovannini and Maria Gabrani and Orcun Goksel},
  title = {Generative Feature-driven Image Replay for Continual Learning},
  year = {2022},
  number = {arxiv:2106.05350},
  url = {https://arxiv.org/abs/2106.05350},
  doi = {10.48550/arxiv.2106.05350}
}

@unpublished{Zhu_hdrfeat_22,
  author = {Zhu, Lingkai and Zhou, Fei and Liu, Bozhi and Göksel, Orcun},
  title = {HDRfeat: A Feature-Rich Network for High Dynamic Range Image Reconstruction},
  year = {2022},
  number = {arxiv:2211.04238},
  doi = {10.48550/arxiv.2211.04238}
}

@unpublished{Teuscher_mechanotransduction_22,
  author = {Alina C Teuscher and Cyril Statzer and Anita Goyala and Seraina A Domenig and Ingmar Schoen and Max Hess and Alexander M. Hofer and Andrea Fossati and Viola Vogel and Orcun Goksel and Ruedi Aebersold and Collin Y. Ewald},
  title = {Mechanotransduction Coordinates Extracellular Matrix Protein Homeostasis Promoting Longevity in C. Elegans},
  year = {2022},
  doi = {10.1101/2022.08.30.505802}
}

@unpublished{Khodadadi_motion_21,
  author = {Hossein Khodadadi and Orcun Goksel and Sabine Kling},
  title = {Motion Estimation for Optical Coherence Elastography Using Signal Phase and Intensity},
  year = {2021},
  number = {arxiv:2103.10784},
  url = {https://arxiv.org/abs/2103.10784}
}

@unpublished{Ozdemir_delineating_20,
  author = {Firat Ozdemir and Christine Tanner and Orcun Goksel},
  title = {Delineating Bone Surfaces in B-Mode Images Constrained by Physics of Ultrasound Propagation},
  year = {2020},
  number = {arxiv:2001.02001},
  pages = {1-11},
  url = {https://arxiv.org/abs/2001.02001}
}

@unpublished{Tanner_generative_18,
  author = {Christine Tanner and Firat Ozdemir and Romy Profanter and Valeriy Vishnevsky and Ender Konukoglu and Orcun Goksel},
  title = {Generative Adversarial Networks for MR-CT Deformable Image Registration},
  year = {2018},
  number = {arXiv:1807.07349},
  pages = {1-11},
  url = {https://arxiv.org/abs/1807.07349}
}

@unpublished{Ozkan_herding_17,
  author = {Ece Ozkan and Gemma Roig and Orcun Goksel and Xavier Boix},
  title = {Herding Generalizes Diverse M-Best Solutions},
  year = {2016},
  number = {arXiv:1611.04353},
  pages = {1-8},
  url = {https://arxiv.org/abs/1611.04353}
}

@unpublished{Azar_strain_11,
  author = {Reza Zahiri Azar and Orcun Goksel and Ehsan Dehghan and Septimiu E Salcudean},
  title = {Strain Tensor Visualization Using Glyph Objects: Application to Elastography},
  year = {2011},
  pages = {1-4},
  doi = {10.13140/RG.2.2.31558.37446}
}