publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

Journal Articles

2025

  1. An Evaluation of Image-Based and Statistical Techniques for Harmonizing Brain Volume Measurements
    Yuan-Chiao Lu, Lianrui Zuo, Yi-Yu Chou, Blake E Dewey, Samuel Remedios, Russell T Shinohara, Sonya U Steele, Govind Nair, Daniel S Reich, Jerry L Prince, and others
    Imaging Neuroscience, 2025
  2. The relationship of white matter tract orientation to vascular geometry in the human brain
    Kurt G Schilling, Allen Newton, Chantal MW Tax, Maxime Chamberland, Samuel W Remedios, Yurui Gao, Muwei Li, Catie Chang, Francois Rheault, Farshid Sepherband, and others
    Scientific Reports, 2025
  3. Super-Resolution in Clinically Available Spinal Cord MRIs Enables Automated Atrophy Analysis
    Blake E Dewey, Samuel W Remedios, Muraleetharan Sanjayan, Nicole Bou Rjeily, Alexandra Zambriczki Lee, Chelsea Wyche, Safiya Duncan, Jerry L Prince, Peter A Calabresi, Kathryn C Fitzgerald, and others
    American Journal of Neuroradiology, 2025
  4. Influence of early through late fusion on pancreas segmentation from imperfectly registered multimodal magnetic resonance imaging
    Lucas W Remedios, Han Liu, Samuel W Remedios, Lianrui Zuo, Adam M Saunders, Shunxing Bao, Yuankai Huo, Alvin C Powers, John Virostko, and Bennett A Landman
    Journal of Medical Imaging, 2025

2024

  1. Data-driven nucleus subclassification on colon hematoxylin and eosin using style-transferred digital pathology
    Lucas W Remedios, Shunxing Bao, Samuel W Remedios, Ho Hin Lee, Leon Y Cai, Thomas Li, Ruining Deng, Nancy R Newlin, Adam M Saunders, Can Cui, and others
    Journal of Medical Imaging, 2024
  2. Super-resolution multi-contrast unbiased eye atlases with deep probabilistic refinement
    Ho Hin Lee, Adam M Saunders, Michael E Kim, Samuel W Remedios, Lucas W Remedios, Yucheng Tang, Qi Yang, Xin Yu, Shunxing Bao, Chloe Cho, and others
    Journal of Medical Imaging, 2024

2023

  1. No ultrasounds detected from fungi when dehydrated
    Neil Phillips, Samuel W. Remedios, Anna Nikolaidou, Zlatko Baracskai, and Andrew Adamatzky
    Ultrasonics, 2023
  2. HACA3: A unified approach for multi-site MR image harmonization
    Lianrui Zuo, Yihao Liu, Yuan Xue, Blake E. Dewey, Samuel W. Remedios, Savannah P. Hays, Murat Bilgel, Ellen M. Mowry, Scott D. Newsome, Peter A. Calabresi, Susan M. Resnick, Jerry L. Prince, and Aaron Carass
    Computerized Medical Imaging and Graphics, 2023
  3. ESPRESO: An algorithm to estimate the slice profile of a single magnetic resonance image
    Shuo Han, Samuel W Remedios, Michael Schär, Aaron Carass, and Jerry L Prince
    Magnetic Resonance Imaging, 2023
  4. Enlarged perivascular space burden associations with arterial stiffness and cognition
    Corey W Bown, Omair A Khan, Dandan Liu, Samuel W Remedios, Kimberly R Pechman, James G Terry, Sangeeta Nair, L Taylor Davis, Bennett A Landman, Katherine A Gifford, and others
    Neurobiology of Aging, 2023

2022

  1. Automated classification of resting-state fMRI ICA components using a deep Siamese Network
    Yiyu Chou, Catie Chang, Samuel W Remedios, John A Butman, Leighton Chan, and Dzung L Pham
    Frontiers in neuroscience, 2022

2021

  1. Comparison of convolutional neural networks for detecting large vessel occlusion on computed tomography angiography
    Lucas W. Remedios, Sneha Lingam, Samuel W. Remedios, Riqiang Gao, Stephen W. Clark, Larry T. Davis, and Bennett A. Landman
    Medical Physics, 2021

2020

  1. Generalizing deep whole-brain segmentation for post-contrast MRI with transfer learning
    Camilo Bermudez, Samuel W. Remedios, Karthik Ramadass, Maureen McHugo, Stephan Heckers, Yuankai Huo, and Bennett A. Landman
    Journal of Medical Imaging, 2020
  2. Brain connections derived from diffusion MRI tractography can be highly anatomically accurate—if we know where white matter pathways start, where they end, and where they do not go
    Kurt G Schilling, Laurent Petit, Francois Rheault, Samuel Remedios, Carlo Pierpaoli, Adam W Anderson, Bennett A Landman, and Maxime Descoteaux
    Brain Structure and Function, 2020

2019

  1. Distributed deep learning across multisite datasets for generalized CT hemorrhage segmentation
    Samuel W. Remedios, Snehashis Roy, Camilo Bermudez, Mayur B. Patel, John A. Butman, Bennett A. Landman, and Dzung L. Pham
    Medical Physics, 2019

  1. ECLARE: Efficient Cross-Planar Learning for Anisotropic Resolution Enhancement
    Samuel W Remedios, Shuwen Wei, Shuo Han, Jinwei Zhang, Aaron Carass, Kurt G Schilling, Dzung L Pham, Jerry L Prince, and Blake E Dewey
    2019
    In review at the Journal of Medical Imaging.
  2. Diffusion-Driven Generation of Minimally Preprocessed Brain MRI
    Samuel W Remedios, Aaron Carass, Jerry L Prince, and Blake E Dewey
    2019
    In revision for submission to Nature Scientific Reports.
  3. Background Removal in Whole Head MRI with Foundation Models
    2019
    In preparation for submission to the Journal of Medical Imaging.

Theses

2025

  1. Through-plane super-resolution of anisotropic multi-slice magnetic resonance images
    Samuel W. Remedios
    Oct 2025

Authored Books

2027

  1. Super-resolution in Magnetic Resonance Imaging: A Tutorial
    Samuel W. Remedios, Aaron Carass, Jerry L. Prince, and Blake E. Dewey
    2027
    Under contract.

Book Chapters

2022

  1. Medical image super-resolution with deep networks
    Can Zhao, Samuel W. Remedios, Shuo Han, Bowen Li, and Jerry L. Prince
    In Biomedical Image Synthesis and Simulation, Jan 2022

Accepted Conference Submissions

2025

  1. Optical Coherence Tomography Harmonization with Anatomy-Guided Latent Metric Schrödinger Bridges
    Shuwen Wei, Samuel W. Remedios, Blake E. Dewey, Zhangxing Bian, Shimeng Wang, Junyu Chen, Bruno Michel Jedynak, saidha, Peter A. Calabresi, Aaron Carass, and Jerry L Prince
    In The Thirty-ninth Annual Conference on Neural Information Processing Systems, 2025
  2. Exploring the Feasibility of Zero-Shot Super-Resolution in Preclinical Imaging
    Omar A. M. Gharib, Samuel W. Remedios, Blake E. Dewey, Jerry L. Prince, and Aaron Carass
    In Medical Image Computing and Computer Assisted Intervention – MICCAI 2025, 2025
  3. Unsupervised OCT Image Interpolation Using Deformable Registration and generative models
    Shuwen Wei, Samuel W. Remedios, Zhangxing Bian, Shimeng Wang, Junyu Chen, Yihao Liu, Bruno Jedynak, Tin Y. A. Liu, Shiv Saidha, Peter A. Calabresi, Jerry L. Prince, and Aaron Carass
    In Medical Image Computing and Computer Assisted Intervention – MICCAI 2025, 2025
  4. Segmenting Thalamic Nuclei: T1 Maps Provide a Reliable and Efficient Solution
    Anqi Feng, Zhangxing Bian, Samuel W Remedios, Savannah P Hays, Blake E Dewey, Jiachen Zhuo, Dan Benjamini, and Jerry L Prince
    In Proceedings of the iMIMIC Workshop at MICCAI 2025, Sep 2025
  5. Cycle-Consistent Zero-Shot Through-Plane Super-Resolution for Anisotropic Head MRI
    Samuel W Remedios, Shuwen Wei, Aaron Carass, Blake E Dewey, and Jerry L Prince
    In International Conference on Information Processing in Medical Imaging, Sep 2025
  6. Brightness-Invariant Tracking Estimation in Tagged MRI
    Zhangxing Bian, Shuwen Wei, Xiao Liang, Yuan-Chiao Lu, Samuel W Remedios, Fangxu Xing, Jonghye Woo, Dzung L Pham, Aaron Carass, Philip V Bayly, and others
    In International Conference on Information Processing in Medical Imaging, Sep 2025
  7. Measuring Impact of Super-Resolution on Spinal Cord MRI Scans: Lesion Detection Sensitivity, Variability, and Clinical Impact
    Greyson A Wintergerst, Samuel W Remedios, Allen T Newton, Seth A Smith, Bennett A Landman, and Kurt G Schilling
    In 2025 IEEE 22nd International Symposium on Biomedical Imaging (ISBI), Sep 2025
  8. Unique MS lesion identification from MRI
    Carlos A Rivas, Jinwei Zhang, Shuwen Wei, Samuel W Remedios, Aaron Carass, and Jerry L Prince
    In Medical Imaging 2025: Image Processing, Sep 2025
  9. Bi-directional MS lesion filling and synthesis using denoising diffusion implicit model-based lesion repainting
    Jinwei Zhang, Lianrui Zuo, Yihao Liu, Samuel Remedios, Bennett A Landman, Jerry L Prince, and Aaron Carass
    In Medical Imaging 2025: Image Processing, Sep 2025
  10. An Unsupervised Approach for Artifact Severity Scoring in Multi-Contrast MR Images
    Savannah Hays, Lianrui Zuo, Blake E Dewey, Samuel Remedios, Jinwei Zhang, Ellen M Mowry, Scott D Newsome, Aaron Carass, and Jerry L Prince
    In Medical Imaging with Deep Learning, Sep 2025

2024

  1. TS-SR3: Time-Strided Denoising Diffusion Probabilistic Model for MR Super-Resolution
    Zejun Wu, Samuel W Remedios, Blake E Dewey, Aaron Carass, and Jerry L Prince
    In International Workshop on Machine Learning in Medical Imaging, Sep 2024
  2. Beyond MR Image Harmonization: Resolution Matters Too
    Savannah P Hays, Samuel W Remedios, Lianrui Zuo, Ellen M Mowry, Scott D Newsome, Peter A Calabresi, Aaron Carass, Blake E Dewey, and Jerry L Prince
    In International Workshop on Simulation and Synthesis in Medical Imaging, Sep 2024
  3. Towards an accurate and generalizable multiple sclerosis lesion segmentation model using self-ensembled lesion fusion
    Jinwei Zhang, Lianrui Zuo, Blake E Dewey, Samuel W Remedios, Dzung L Pham, Aaron Carass, and Jerry L Prince
    In 2024 IEEE International Symposium on Biomedical Imaging (ISBI), Sep 2024
  4. Parameter Maps Synthesis From Magnetic Resonance Images Used in a Clinical Study of People With Multiple Sclerosis.
    Savannah P Hays, Lianrui Zuo, Blake E Dewey, Samuel W Remedios, Sandra D Cassard, Ann Fishman, Jiachen Zhuo, Aaron Carass, Ellen M Mowry, Scott D Newsome, and others
    In International Journal of MS Care, Sep 2024
  5. Assessing Central Vein Sign Visibility Across Various Anisotropic MRI Resolutions for Multiple Sclerosis Diagnosis.
    Samuel W Remedios, Blake E Dewey, Aaron Carass, Sandra D Cassard, Carolyn Koch, Ann Fishman, Jerry L Prince, Ellen M Mowry, Scott D Newsome, and Peter A Calabresi
    In International Journal of MS Care, Sep 2024
  6. Pushing the limits of zero-shot self-supervised super-resolution of anisotropic MR images
    Samuel W. Remedios, Shuwen Wei, Blake E. Dewey, Aaron Carass, Dzung L. Pham, and Jerry L. Prince
    In Medical Imaging 2024: Image Processing, Sep 2024
  7. Nucleus subtype classification using inter-modality learning
    Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios, Ho Hin Lee, Leon Cai, Thomas Li, Ruining Deng, Can Cui, Jia Li, Qi Liu, Ken S. Lau, Joseph T. Roland, Mary K. Washington, Lori A. Coburn, Keith T. Wilson, Yuankai Huo, and Bennett A. Landman
    In Medical Imaging 2024: Digital and Computational Pathology, Sep 2024
  8. Self-supervised super-resolution of 2-D pre-clinical MRI acquisitions
    Lin Guo, Samuel W. Remedios, Alexandru Korotcov, and Dzung L. Pham
    In Medical Imaging 2024: Clinical and Biomedical Imaging, Sep 2024
  9. Deep learning-based segmentation of hydrocephalus brain ventricle from ultrasound
    Yuli Wang, Yihao Liu, Shuwen Wei, Yuan Xue, Lianrui Zuo, Samuel W. Remedios, Zhangxing Bian, Michael Meggyesy, Jheesoo Ahn, Ryan P. Lee, Mark G. Luciano, Jerry L. Prince, and Aaron Carass
    In Medical Imaging 2024: Image Processing, Sep 2024
  10. AniRes2D: Anisotropic Residual-enhanced Diffusion for 2D MR Super-Resolution
    Zejun Wu, Samuel W. Remedios, Blake E. Dewey, Aaron Carass, and Jerry L. Prince
    In Medical Imaging 2024: Image Processing, Sep 2024
  11. Harmonization-enriched domain adaptation with light fine-tuning for multiple sclerosis lesion segmentation
    Jinwei Zhang, Lianrui Zuo, Blake E. Dewey, Samuel W. Remedios, Savannah P. Hays, Dzung L. Pham, Jerry L. Prince, and Aaron Carass
    In Medical Imaging 2024: Clinical and Biomedical Imaging, Sep 2024

2023

  1. Self-Supervised Super-Resolution for Anisotropic MR Images with and Without Slice Gap
    Samuel W. Remedios, Shuo Han, Lianrui Zuo, Aaron Carass, Dzung L. Pham, Jerry L. Prince, and Blake E. Dewey
    In Simulation and Synthesis in Medical Imaging, Sep 2023
  2. Cautions in Anisotropy: Thick Slices and Slice Gaps in 2D Magnetic Resonance Acquisition Tarnish Volumetrics
    Samuel W. Remedios, Blake E. Dewey, Yuan Xue, Lianrui Zuo, Sandra D. Cassard, Carolyn Koch, Ann Fishman, Jerry L. Prince, Ellen M. Mowry, and Scott D. Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  3. Compliance with CMSC MRI Guidelines in a Multi-Center, Pragmatic, Randomized Clinical Trial: Improvements over Time
    Blake E. Dewey, Lianrui Zuo, Samuel W. Remedios, Yuan Xue, Sandra D. Cassard, Carolyn Koch, Ann Fishman, Aaron Carass, Jerry L. Prince, Ellen M. Mowry, and Scott D. Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  4. Inconsistent MR Acquisition in Longitudinal Volumetric Analysis: Impacts and Solutions
    Lianrui Zuo, Savannah P Hays, Blake E Dewey, Samuel W Remedios, Yuan Xue, Sandra D Cassard, Carolyn Koch, Ann Fishman, Aaron Carass, Jerry L Prince, Ellen M. Mowry, and Scott D Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  5. Quantifying contrast differences among MR images used in clinical studies
    Savannah P. Hays, Lianrui Zuo, Blake E. Dewey, Samuel W. Remedios, Yuan Xue, Sandra D. Cassard, Carolyn Koch, Ann Fishman, Aaron Carass, Peter A. Calabresi, Jerry L. Prince, Ellen M. Mowry, and Scott D. Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  6. Measuring MRIs Differences Between Sites: Design of a Traveling Subject Study in MS
    Blake E. Dewey, Ann Fishman, Sandra D. Cassard, Lianrui Zuo, Samuel W. Remedios, Yuan Xue, Carolyn Koch, Aaron Carass, Jerry L. Prince, Ellen M. Mowry, and Scott D. Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  7. Synthesizing Missing MRI Sequences to Improve Processing Images in Multiple Sclerosis
    Yuan Xue, Blake E. Dewey, Lianrui Zuo, Samuel W. Remedios, Savannah P. Hays, Sandra D. Cassard, Carolyn Koch, Ann Fishman, Aaron Carass, Peter A. Calabresi, Jerry L. Prince, Ellen M. Mowry, and Scott D. Newsome
    In International Journal of Multiple Sclerosis Care, Sep 2023
  8. A deep generative prior for high-resolution isotropic MR head slices
    Samuel W. Remedios, Blake E. Dewey, Aaron Carass, Dzung L. Pham, and Jerry L. Prince
    In Medical Imaging 2023: Image Processing, Sep 2023
  9. Unsupervised quality assurance for brain MR image rigid registration using latent shape representation
    Yuan Xue, Lianrui Zuo, Samuel W. Remedios, Blake E. Dewey, Peiyu Duan, Yihao Liu, Rendong Zhang, Scott D. Newsome, Ellen M. Mowry, Aaron Carass, and Jerry L. Prince
    In Medical Imaging 2023: Image Processing, Sep 2023

2022

  1. Deep filter bank regression for super-resolution of anisotropic MR brain images
    Samuel W Remedios, Shuo Han, Yuan Xue, Aaron Carass, Trac D Tran, Dzung L Pham, and Jerry L Prince
    In International Conference on Medical Image Computing and Computer-Assisted Intervention, Sep 2022
  2. Bi-directional Synthesis of Pre-and Post-contrast MRI via Guided Feature Disentanglement
    Yuan Xue, Blake E Dewey, Lianrui Zuo, Shuo Han, Aaron Carass, Peiyu Duan, Samuel W Remedios, Dzung L Pham, Shiv Saidha, Peter A Calabresi, and others
    In International Workshop on Simulation and Synthesis in Medical Imaging, Sep 2022
  3. Efficient quality control with mixed CT and CTA datasets
    Lucas W. Remedios, Leon Y. Cai, Colin B. Hansen, Samuel W. Remedios, and Bennett Landman
    In Medical Imaging 2022: Image Processing, Sep 2022
  4. Automatic classification of MRI contrasts using a deep Siamese network and one-shot learning
    Yiyu Chou, Samuel W. Remedios, John A. Butman, and Dzung L. Pham
    In Medical Imaging 2022: Image Processing, Sep 2022
  5. Multiple Sclerosis brain lesion segmentation with different architecture ensembles
    Pouria Tohidi, Samuel W. Remedios, Danielle L. Greenman, Muhan Shao, Shuo Han, Blake E. Dewey, Jacob C. Reinhold, Yi-Yu Chou, Dzung L. Pham, Jerry L. Prince, and Aaron Carass
    In Medical Imaging 2022: Biomedical Applications in Molecular, Structural, and Functional Imaging, Sep 2022

2021

  1. Joint Image and Label Self-super-Resolution
    Samuel W. Remedios, Shuo Han, Blake E. Dewey, Dzung L. Pham, Jerry L. Prince, and Aaron Carass
    In Simulation and Synthesis in Medical Imaging, Sep 2021
  2. MR Slice Profile Estimation by Learning to Match Internal Patch Distributions
    Shuo Han, Samuel W Remedios, Aaron Carass, Michael Schär, and Jerry L Prince
    In Information Processing in Medical Imaging, Sep 2021
  3. Perivascular space volumes relate to arterial stiffness and cognition
    Corey W Bown, Omair A Khan, Dandan Liu, Samuel Remedios, Kimberly R Pechman, Matthew Schrag, L Taylor Davis, James G Terry, Sangeeta Nair, J Jeffrey Carr, and others
    In 2021 Alzheimer’s Association International Conference, Sep 2021

2020

  1. Federated gradient averaging for multi-site training with momentum-based optimizers
    Samuel W Remedios, John A Butman, Bennett A Landman, and Dzung L Pham
    In Domain Adaptation and Representation Transfer, and Distributed and Collaborative Learning, Sep 2020
  2. Generalizing deep whole brain segmentation for pediatric and post-contrast MRI with augmented transfer learning
    Camilo Bermudez, Justin Blaber, Samuel W. Remedios, Jess E. Reynolds, Catherine Lebel, Maureen McHugo, Stephan Heckers, Yuankai Huo, and Bennett A. Landman
    In Medical Imaging 2020: Image Processing, Sep 2020
  3. Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection
    Samuel Remedios, Zihao Wu, Camilo Bermudez, Cailey I. Kerley, Snehashis Roy, Mayur B. Patel, John A. Butman, Bennett A. Landman, and Dzung L. Pham
    In Medical Imaging 2020: Image Processing, Sep 2020

2019

  1. Learning 3D White Matter Microstructure from 2D Histology
    V. Nath, K. G. Schilling, S. Remedios, R. G. Bayrak, Y. Gao, J. A. Blaber, Y. Huo, B. A. Landman, and A. W. Anderson
    In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Sep 2019
  2. Inter-scanner harmonization of high angular resolution DW-MRI using null space deep learning
    Vishwesh Nath, Prasanna Parvathaneni, Colin B Hansen, Allison E Hainline, Camilo Bermudez, Samuel Remedios, Justin A Blaber, Kurt G Schilling, Ilwoo Lyu, Vaibhav Janve, Yurui Gao, Iwona Stepniewska, Baxter P. Rogers, Allen T. Newton, L. Taylor Davis, Jeff Luci, Adam W. Anderson, and Landman Bennett A.
    In International Conference on Medical Image Computing and Computer-Assisted Intervention, Sep 2019
  3. Distributed deep learning for robust multi-site segmentation of CT imaging after traumatic brain injury
    Samuel Remedios, Snehashis Roy, Justin Blaber, Camilo Bermudez, Vishwesh Nath, Mayur B. Patel, John A. Butman, Bennett A. Landman, and Dzung L. Pham
    In Medical Imaging 2019: Image Processing, Sep 2019
  4. Harmonizing 1.5T/3T diffusion weighted MRI through development of deep learning stabilized microarchitecture estimators
    Vishwesh Nath, Samuel Remedios, Prasanna Parvathaneni, Colin B. Hansen, Roza G. Bayrak, Camilo Bermudez, Justin A. Blaber, Kurt G. Schilling, Vaibhav A. Janve, Yurui Gao, Yuankai Huo, Ilwoo Lyu, Owen Williams, Susan Resnick, Lori Beason-Held, Baxter P. Rogers, Iwona Stepniewska, Adam W. Anderson, and Bennett A. Landman
    In Medical Imaging 2019: Image Processing, Sep 2019

2018

  1. Classifying magnetic resonance image modalities with convolutional neural networks
    Samuel Remedios, Dzung L. Pham, John A. Butman, and Snehashis Roy
    In Medical Imaging 2018: Computer-Aided Diagnosis, Sep 2018