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ORCIDJohn A. Onofrey
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2020 – today
- 2025
[j12]Siyuan Dong, Zhuotong Cai
, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Yaqing Huang, Qinghao Liang, Chenyu You, Chathura Kumaragamage, Robert K. Fulbright, Amit Mahajan, Amin Karbasi, John A. Onofrey, Robin A. de Graaf, James S. Duncan:
A Flow-based Truncated Denoising Diffusion Model for super-resolution Magnetic Resonance Spectroscopic Imaging. Medical Image Anal. 99: 103358 (2025)- 2024
- [j11]Tal Ze'evi, Michael S. Leapman, Preston C. Sprenkle, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey:
Reliable Prostate Cancer Risk Mapping From MRI Using Targeted and Systematic Core Needle Biopsy Histopathology. IEEE Trans. Biomed. Eng. 71(3): 1084-1091 (2024) - [j10]Daniel H. Pak, Minliang Liu, Theodore Kim, Liang Liang, Andrés Caballero, John A. Onofrey, Shawn S. Ahn, Yilin Xu, Raymond McKay, Wei Sun, Rudolph L. Gleason, James S. Duncan:
Patient-Specific Heart Geometry Modeling for Solid Biomechanics Using Deep Learning. IEEE Trans. Medical Imaging 43(1): 203-215 (2024) - [c27]Zhuotong Cai, Jingmin Xin, Siyuan Dong, John A. Onofrey, Nanning Zheng, James S. Duncan:
Symmetric Consistency with Cross-Domain Mixup for Cross-Modality Cardiac Segmentation. ICASSP 2024: 1536-1540 - [c26]Tal Ze'evi, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey:
Monte-Carlo Frequency Dropout for Predictive Uncertainty Estimation in Deep Learning. ISBI 2024: 1-5 - [i8]Yuexi Du, John A. Onofrey, Nicha C. Dvornek:
Multi-View and Multi-Scale Alignment for Contrastive Language-Image Pre-training in Mammography. CoRR abs/2409.18119 (2024) - [i7]Siyuan Dong, Zhuotong Cai, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Yaqing Huang, Qinghao Liang, Chenyu You, Chathura Kumaragamage, Robert K. Fulbright, Amit Mahajan, Amin Karbasi, John A. Onofrey, Robin A. de Graaf, James S. Duncan:
A Flow-based Truncated Denoising Diffusion Model for Super-resolution Magnetic Resonance Spectroscopic Imaging. CoRR abs/2410.19288 (2024) - [i6]Tal Zeevi, Ravid Shwartz-Ziv, Yann LeCun, Lawrence H. Staib, John A. Onofrey:
Rate-In: Information-Driven Adaptive Dropout Rates for Improved Inference-Time Uncertainty Estimation. CoRR abs/2412.07169 (2024) - 2023
- [j9]Shawn S. Ahn, Kevinminh Ta, Stephanie Thorn, John A. Onofrey, Inga H. Melvinsdottir, Supum Lee, Jonathan Langdon, Albert J. Sinusas, James S. Duncan:
Co-attention spatial transformer network for unsupervised motion tracking and cardiac strain analysis in 3D echocardiography. Medical Image Anal. 84: 102711 (2023) - [j8]Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, James S. Duncan, Edward J. Miller, Albert J. Sinusas, John A. Onofrey, Chi Liu:
DuSFE: Dual-Channel Squeeze-Fusion-Excitation co-attention for cross-modality registration of cardiac SPECT and CT. Medical Image Anal. 88: 102840 (2023) - [c25]Zhuotong Cai, Jingmin Xin, Siyuan Dong, Chenyu You, Peiwen Shi, Tianyi Zeng, Jiazhen Zhang, John A. Onofrey, Nanning Zheng, James S. Duncan:
Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation. BIBM 2023: 819-824 - [c24]Eléonore V. Lieffrig, Tianyi Zeng, Jiazhen Zhang, Kathryn Fontaine, Xi Fang, Enette Mae Revilla, Yihuan Lu, John A. Onofrey:
Multi-Task Deep Learning and Uncertainty Estimation for Pet Head Motion Correction. ISBI 2023: 1-5 - [c23]Jiayang Zhong, Lawrence H. Staib, Rajesh Venkataraman, John A. Onofrey:
Integrating Prostate Specific Antigen Density Biomarker Into Deep Learning Prostate MRI Lesion Segmentation Models. ISBI 2023: 1-5 - [c22]Zhuotong Cai, Tianyi Zeng, Eléonore V. Lieffrig, Jiazhen Zhang, Fuyao Chen, Takuya Toyonaga, Chenyu You, Jingmin Xin, Nanning Zheng, Yihuan Lu, James S. Duncan, John A. Onofrey:
Cross-Attention for Improved Motion Correction in Brain PET. MLCN@MICCAI 2023: 34-45 - [c21]Tianyi Zeng, Jiazhen Zhang, Eléonore V. Lieffrig, Zhuotong Cai, Fuyao Chen, Chenyu You, Mika Naganawa, Yihuan Lu, John A. Onofrey:
Fast Reconstruction for Deep Learning PET Head Motion Correction. MICCAI (10) 2023: 710-719 - 2022
- [j7]Enette Mae Revilla, Jean-Dominique Gallezot, Mika Naganawa, Takuya Toyonaga, Kathryn Fontaine, Tim Mulnix, John A. Onofrey, Richard E. Carson, Yihuan Lu:
Adaptive data-driven motion detection and optimized correction for brain PET. NeuroImage 252: 119031 (2022) - [j6]Chen Sun, Enette Mae Revilla, Jiazhen Zhang, Kathryn Fontaine, Takuya Toyonaga, Jean-Dominique Gallezot, Tim Mulnix, John A. Onofrey, Richard E. Carson, Yihuan Lu:
An objective evaluation method for head motion estimation in PET - Motion corrected centroid-of-distribution. NeuroImage 264: 119678 (2022) - [c20]Siyuan Dong, Gilbert Hangel, Eric Z. Chen, Shanhui Sun, Wolfgang Bogner, Georg Widhalm, Chenyu You, John A. Onofrey, Robin A. de Graaf, James S. Duncan:
Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging. DGM4MICCAI@MICCAI 2022: 3-13 - [c19]Chenyu You, Jinlin Xiang, Kun Su, Xiaoran Zhang, Siyuan Dong, John A. Onofrey, Lawrence H. Staib, James S. Duncan:
Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. DeCaF/FAIR@MICCAI 2022: 3-16 - [c18]Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, Albert J. Sinusas, John A. Onofrey, Chi Liu:
Dual-Branch Squeeze-Fusion-Excitation Module for Cross-Modality Registration of Cardiac SPECT and CT. MICCAI (6) 2022: 46-55 - [c17]Tianyi Zeng, Jiazhen Zhang, Enette Mae Revilla, Eléonore V. Lieffrig, Xi Fang, Yihuan Lu, John A. Onofrey:
Supervised Deep Learning for Head Motion Correction in PET. MICCAI (4) 2022: 194-203 - [c16]Siyuan Dong, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Karl Rössler, Siegfried Trattnig, Chenyu You, Robin A. de Graaf, John A. Onofrey, James S. Duncan:
Multi-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. MICCAI (6) 2022: 410-420 - [c15]Jiazhen Zhang, Rajesh Venkataraman, Lawrence H. Staib, John A. Onofrey:
Atlas-Based Semantic Segmentation of Prostate Zones. MICCAI (5) 2022: 570-579 - [i5]Chenyu You, Jinlin Xiang, Kun Su, Xiaoran Zhang, Siyuan Dong, John A. Onofrey, Lawrence H. Staib, James S. Duncan:
Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation. CoRR abs/2206.01369 (2022) - [i4]Xiongchao Chen, Bo Zhou, Huidong Xie, Xueqi Guo, Jiazhen Zhang, Albert J. Sinusas, John A. Onofrey, Chi Liu:
Dual-Branch Squeeze-Fusion-Excitation Module for Cross-Modality Registration of Cardiac SPECT and CT. CoRR abs/2206.05278 (2022) - [i3]Siyuan Dong, Gilbert Hangel, Wolfgang Bogner, Georg Widhalm, Karl Rössler, Siegfried Trattnig, Chenyu You, Robin A. de Graaf, John A. Onofrey, James S. Duncan:
Multi-scale Super-resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness. CoRR abs/2206.08984 (2022) - [i2]Siyuan Dong, Gilbert Hangel, Eric Z. Chen, Shanhui Sun, Wolfgang Bogner, Georg Widhalm, Chenyu You, John A. Onofrey, Robin A. de Graaf, James S. Duncan:
Flow-based Visual Quality Enhancer for Super-resolution Magnetic Resonance Spectroscopic Imaging. CoRR abs/2207.10181 (2022) - 2021
- [c14]Daniel H. Pak, Minliang Liu, Shawn S. Ahn, Andrés Caballero, John A. Onofrey, Liang Liang, Wei Sun, James S. Duncan:
Weakly Supervised Deep Learning for Aortic Valve Finite Element Mesh Generation from 3D CT Images. IPMI 2021: 637-648 - [c13]Ricardo A. Gonzales, Jérôme Lamy, Felicia Seemann, Einar Heiberg, John A. Onofrey, Dana C. Peters:
TVnet: Automated Time-Resolved Tracking of the Tricuspid Valve Plane in MRI Long-Axis Cine Images with a Dual-Stage Deep Learning Pipeline. MICCAI (6) 2021: 567-576
2010 – 2019
- 2019
- [j5]Praneeth Sadda, Metehan Imamoglu, Michael Dombrowski, Xenophon Papademetris, Mert Ozan Bahtiyar, John A. Onofrey:
Deep-learned placental vessel segmentation for intraoperative video enhancement in fetoscopic surgery. Int. J. Comput. Assist. Radiol. Surg. 14(2): 227-235 (2019) - [j4]John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris:
Segmenting the Brain Surface From CT Images With Artifacts Using Locally Oriented Appearance and Dictionary Learning. IEEE Trans. Medical Imaging 38(2): 596-607 (2019) - [c12]John A. Onofrey, Dana I. Casetti-Dinescu, Andreas D. Lauritzen, Saradwata Sarkar, Rajesh Venkataraman, Richard E. Fan, Geoffrey A. Sonn, Preston C. Sprenkle, Lawrence H. Staib, Xenophon Papademetris:
Generalizable Multi-Site Training and Testing Of Deep Neural Networks Using Image Normalization. ISBI 2019: 348-351 - [c11]Luyao Shi, John A. Onofrey, Enette Mae Revilla, Takuya Toyonaga, David Menard, Joseph Ankrah, Richard E. Carson, Chi Liu, Yihuan Lu:
A Novel Loss Function Incorporating Imaging Acquisition Physics for PET Attenuation Map Generation Using Deep Learning. MICCAI (4) 2019: 723-731 - [i1]Luyao Shi, John A. Onofrey, Enette Mae Revilla, Takuya Toyonaga, David Menard, Joseph Ankrah, Richard E. Carson, Chi Liu, Yihuan Lu:
A Novel Loss Function Incorporating Imaging Acquisition Physics for PET Attenuation Map Generation using Deep Learning. CoRR abs/1909.01394 (2019) - 2018
- [j3]Chung Chan, John A. Onofrey, Yiqiang Jian, Mary Germino, Xenophon Papademetris, Richard E. Carson, Chi Liu:
Non-Rigid Event-by-Event Continuous Respiratory Motion Compensated List-Mode Reconstruction for PET. IEEE Trans. Medical Imaging 37(2): 504-515 (2018) - [c10]Dustin Scheinost, John A. Onofrey, Soo Hyun Kwon, Sarah N. Cross, Gordon Sze, Laura R. Ment, Xenophon Papademetris:
A fetal fMRI specific motion correction algorithm using 2nd order edge features. ISBI 2018: 1288-1292 - [c9]Praneeth Sadda, John A. Onofrey, Xenophon Papademetris:
Deep Learning Retinal Vessel Segmentation from a Single Annotated Example: An Application of Cyclic Generative Adversarial Neural Networks. CVII-STENT/LABELS@MICCAI 2018: 82-91 - [c8]Praneeth Sadda, John A. Onofrey, Mert Ozan Bahtiyar, Xenophon Papademetris:
Better Feature Matching for Placental Panorama Construction. DATRA/PIPPI@MICCAI 2018: 128-137 - 2017
- [j2]John A. Onofrey, Lawrence H. Staib, Saradwata Sarkar, Rajesh Venkataraman, Cayce B. Nawaf, Preston C. Sprenkle, Xenophon Papademetris:
Learning Non-rigid Deformations for Robust, Constrained Point-based Registration in Image-Guided MR-TRUS Prostate Intervention. Medical Image Anal. 39: 29-43 (2017) - 2016
- [c7]John A. Onofrey, Ilkay Öksüz, Saradwata Sarkar, Rajesh Venkataraman, Lawrence H. Staib, Xenophon Papademetris:
MRI-TRUS Image Synthesis with Application to Image-Guided Prostate Intervention. SASHIMI@MICCAI 2016: 157-166 - 2015
- [j1]John A. Onofrey, Xenophon Papademetris, Lawrence H. Staib:
Low-Dimensional Non-Rigid Image Registration Using Statistical Deformation Models From Semi-Supervised Training Data. IEEE Trans. Medical Imaging 34(7): 1522-1532 (2015) - [c6]Shaogang Ren, Shuai Huang, John A. Onofrey, Xenios Papademetris, Xiaoning Qian:
A Scalable Algorithm for Structured Kernel Feature Selection. AISTATS 2015 - [c5]John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris:
Segmenting the Brain Surface from CT Images with Artifacts Using Dictionary Learning for Non-rigid MR-CT Registration. IPMI 2015: 662-674 - [c4]John A. Onofrey, Lawrence H. Staib, Saradwata Sarkar, Rajesh Venkataraman, Xenophon Papademetris:
Learning nonrigid deformations for constrained point-based registration for image-guided MR-TRUS prostate intervention. ISBI 2015: 1592-1595 - 2013
- [c3]John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris:
Fast nonrigid image registration using statistical deformation models learned from richly-annotated data. ISBI 2013: 580-583 - [c2]John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris:
Semi-supervised Learning of Nonrigid Deformations for Image Registration. MCV 2013: 13-23 - [c1]John A. Onofrey, Lawrence H. Staib, Xenophon Papademetris:
Learning Nonrigid Deformations for Constrained Multi-modal Image Registration. MICCAI (3) 2013: 171-178
Coauthor Index
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