SimTriplet: Simple Triplet Representation Learning with a Single GPU. - Quan Liu 002; Peter C. Louis; Yuzhe Lu; Aadarsh Jha; Mengyang Zhao; Ruining Deng; Tianyuan Yao; Joseph T. Roland; Haichun Yang; Shilin Zhao; Lee E. Wheless; Yuankai Huo (MICCAI (2), 2021)

Compound Figure Separation of Biomedical Images with Side Loss. - Tianyuan Yao; Chang Qu; Quan Liu 002; Ruining Deng; Yuanhan Tian; Jiachen Xu; Aadarsh Jha; Shunxing Bao; Mengyang Zhao; Agnes B. Fogo; Bennett A. Landman; Catie Chang; et al. (DGM4MICCAI/DALI@MICCAI, 2021)

VoxelEmbed: 3D Instance Segmentation and Tracking with Voxel Embedding based Deep Learning. - Mengyang Zhao; Quan Liu 002; Aadarsh Jha; Ruining Deng; Tianyuan Yao; Anita Mahadevan-Jansen; Matthew J. Tyska; Bryan A. Millis; Yuankai Huo (MLMI@MICCAI, 2021)

Leverage Supervised and Self-supervised Pretrain Models for Pathological Survival Analysis via a Simple and Low-cost Joint Representation Tuning. - Quan Liu 002; Can Cui 006; Ruining Deng; Zuhayr Asad; Tianyuan Yao; Zheyu Zhu; Yuankai Huo (REMIA@MICCAI, 2022)

Self-supervised learning with large-scale web image mining for characterizing glomerular lesions. - Tianyuan Yao; Yuzhe Lu; Ruining Deng; Zheyu Zhu; Zuhayr Asad; Haichun Yang; Lee E. Wheless; Agnes B. Fogo; Yuankai Huo (Digital and Computational Pathology, 2022)

Large-Scale Patch-Wise Pathological Image Feature Dataset with a Hardware-agnostic Feature Extraction Tool. - Zheyu Zhu; Ruining Deng; Quan Liu 002; Zuhayr Asad; Can Cui 006; Tianyuan Yao; Yuankai Huo (MIUA, 2022)

Holistic Fine-grained GGS Characterization: From Detection to Unbalanced Classification. - Yuzhe Lu; Haichun Yang; Zuhayr Asad; Zheyu Zhu; Tianyuan Yao; Jiachen Xu; Agnes B. Fogo; Yuankai Huo (CoRR, 2022)

Glo-In-One: Holistic Glomerular Detection, Segmentation, and Lesion Characterization with Large-scale Web Image Mining. - Tianyuan Yao; Yuzhe Lu; Jun Long; Aadarsh Jha; Zheyu Zhu; Zuhayr Asad; Haichun Yang; Agnes B. Fogo; Yuankai Huo (CoRR, 2022)

Omni-Seg+: A Scale-aware Dynamic Network for Pathological Image Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jun Long; Zuhayr Asad; R. Michael Womick; Zheyu Zhu; Agnes B. Fogo; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2022)

Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning. - Tianyuan Yao; Chang Qu; Jun Long; Quan Liu 002; Ruining Deng; Yuanhan Tian; Jiachen Xu; Aadarsh Jha; Zuhayr Asad; Shunxing Bao; Mengyang Zhao; Agnes B. Fogo; et al. (CoRR, 2022)

A Unified Learning Model for Estimating Fiber Orientation Distribution Functions on Heterogeneous Multi-shell Diffusion-Weighted MRI. - Tianyuan Yao; Nancy Newlin; Praitayini Kanakaraj; Vishwesh Nath; Leon Y. Cai; Karthik Ramadass; Kurt Schilling; Bennett A. Landman; Yuankai Huo (CDMRI@MICCAI, 2023)

Comparing voxel- and feature-wise harmonization of complex graph measures from multiple sites for structural brain network investigation of aging. - Nancy R. Newlin; Leon Y. Cai; Tianyuan Yao; Derek B. Archer; Kurt G. Schilling; Timothy J. Hohman; Kimberly R. Pechman; Angela L. Jefferson; Andrea T. Shafer; Susan M. Resnick; Bennett A. Landman (Image Processing, 2023)

Deep constrained spherical deconvolution for robust harmonization. - Tianyuan Yao; Francois Rheault; Leon Y. Cai; Vishwesh Nath; Zuhayr Asad; Nancy Newlin; Can Cui 006; Ruining Deng; Karthik Ramadass; Kurt Schilling; Bennett A. Landman; Yuankai Huo (Image Processing, 2023)

A Unified Single-stage Learning Model for Estimating Fiber Orientation Distribution Functions on Heterogeneous Multi-shell Diffusion-weighted MRI. - Tianyuan Yao; Nancy Newlin; Praitayini Kanakaraj; Vishwesh Nath; Leon Y. Cai; Karthik Ramadass; Kurt Schilling; Bennett A. Landman; Yuankai Huo (CoRR, 2023)

Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging. - Ruining Deng; Can Cui 006; Quan Liu 002; Tianyuan Yao; Lucas W. Remedios; Shunxing Bao; Bennett A. Landman; Lee E. Wheless; Lori A. Coburn; Keith T. Wilson; Yaohong Wang; Shilin Zhao; et al. (CoRR, 2023)

Robust Fiber ODF Estimation Using Deep Constrained Spherical Deconvolution for Diffusion MRI. - Tianyuan Yao; Francois Rheault; Leon Y. Cai; Vishwesh Nath; Zuhayr Asad; Nancy Newlin; Can Cui 006; Ruining Deng; Karthik Ramadass; Andrea T. Shafer; Susan M. Resnick; Kurt Schilling; et al. (CoRR, 2023)

All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning. - Can Cui 006; Ruining Deng; Quan Liu 002; Tianyuan Yao; Shunxing Bao; Lucas W. Remedios; Yucheng Tang; Yuankai Huo (CoRR, 2023)

Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology. - Jiayuan Chen 003; Yu Wang; Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Yilin Liu; Jianyong Zhong; Agnes B. Fogo; Haichun Yang; Shilin Zhao; Yuankai Huo (CoRR, 2023)

Enhancing thoracic disease detection using chest X-rays from PubMed Central Open Access. - Mingquan Lin; Bo-Jian Hou; Swati Mishra 006; Tianyuan Yao; Yuankai Huo; Qian Yang 004; Fei Wang 001; George Shih; Yifan Peng 002 (Comput. Biol. Medicine, 2023)

Omni-Seg: A Scale-Aware Dynamic Network for Renal Pathological Image Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jun Long; Zuhayr Asad; R. Michael Womick; Zheyu Zhu; Agnes B. Fogo; Shilin Zhao; Haichun Yang; Yuankai Huo (IEEE Trans. Biomed. Eng., 2023)

Enhancing Physician Flexibility: Prompt-Guided Multi-class Pathological Segmentation for Diverse Outcomes. - Can Cui 006; Ruining Deng; Junlin Guo; Quan Liu 002; Tianyuan Yao; Haichun Yang; Yuankai Huo (BHI, 2024)

PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Jialin Yue; Juming Xiong; Lining Yu; Yifei Wu; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; et al. (CVPR, 2024)

HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis. - Ruining Deng; Quan Liu 002; Can Cui 006; Tianyuan Yao; Juming Xiong; Shunxing Bao; Hao Li; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; Haichun Yang; et al. (MICCAI (4), 2024)

Ts-FWE: Token-Aware Single-Shell Free Water Estimation for Brain Diffusion MRI. - Tianyuan Yao; Derek B. Archer; Zhiyuan Li 012; Leon Y. Cai; Praitayini Kanakaraj; Nancy Newlin; Quan Liu 002; Ruining Deng; Can Cui 006; Shunxing Bao; Kurt Schilling; Bennett A. Landman; et al. (CDMRI@MICCAI, 2024)

Field-of-View Extension for Diffusion MRI via Deep Generative Models. - Chenyu Gao; Shunxing Bao; Michael E. Kim; Nancy Newlin; Praitayini Kanakaraj; Tianyuan Yao; Gaurav Rudravaram; Yuankai Huo; Daniel Moyer; Kurt Schilling; Walter Kukull; Arthur W. Toga; et al. (CoRR, 2024)

mTREE: Multi-Level Text-Guided Representation End-to-End Learning for Whole Slide Image Analysis. - Quan Liu 002; Ruining Deng; Can Cui 006; Tianyuan Yao; Vishwesh Nath; Yucheng Tang; Yuankai Huo (CoRR, 2024)

Weighted Circle Fusion: Ensembling Circle Representation from Different Object Detection Results. - Jialin Yue; Tianyuan Yao; Ruining Deng; Quan Liu 002; Juming Xiong; Haichun Yang; Yuankai Huo (CoRR, 2024)

HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization. - Yucheng Tang; Yufan He; Vishwesh Nath; Pengfei Guo; Ruining Deng; Tianyuan Yao; Quan Liu 002; Can Cui 006; Mengmeng Yin; Ziyue Xu 001; Holger Roth; Daguang Xu; et al. (CoRR, 2024)

PFPs: Prompt-guided Flexible Pathological Segmentation for Diverse Potential Outcomes Using Large Vision and Language Models. - Can Cui 006; Ruining Deng; Junlin Guo; Quan Liu 002; Tianyuan Yao; Haichun Yang; Yuankai Huo (CoRR, 2024)

Dataset Distillation in Medical Imaging: A Feasibility Study. - Muyang Li; Can Cui 006; Quan Liu 002; Ruining Deng; Tianyuan Yao; Marilyn Lionts; Yuankai Huo (CoRR, 2024)

Adapting Mouse Pathological Model to Human Glomerular Lesion Segmentation. - Lining Yu; Mengmeng Yin; Ruining Deng; Quan Liu 002; Tianyuan Yao; Can Cui 006; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2024)

Assessment of Cell Nuclei AI Foundation Models in Kidney Pathology. - Junlin Guo; Siqi Lu; Can Cui 006; Ruining Deng; Tianyuan Yao; Zhewen Tao; Yizhe Lin; Marilyn Lionts; Quan Liu 002; Juming Xiong; Catie Chang; Mitchell Wilkes; et al. (CoRR, 2024)

Multi-Modality Conditioned Variational U-Net for Field-of-View Extension in Brain Diffusion MRI. - Zhiyuan Li 012; Tianyuan Yao; Praitayini Kanakaraj; Chenyu Gao; Shunxing Bao; Lianrui Zuo; Michael E. Kim; Nancy R. Newlin; Gaurav Rudravaram; Nazirah Mohd Khairi; Yuankai Huo; Kurt G. Schilling; et al. (CoRR, 2024)

Automatic Image Unfolding and Stitching Framework for Esophageal Lining Video Based on Density-Weighted Feature Matching. - Muyang Li; Juming Xiong; Ruining Deng; Tianyuan Yao; Regina N. Tyree; Girish Hiremath; Yuankai Huo (CoRR, 2024)

How Good Are We? Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment. - Junlin Guo; Siqi Lu; Can Cui 006; Ruining Deng; Tianyuan Yao; Zhewen Tao; Yizhe Lin; Marilyn Lionts; Quan Liu 002; Juming Xiong; Yu Wang; Shilin Zhao; et al. (CoRR, 2024)

Cross-organ Deployment of EOS Detection AI without Retraining: Feasibility and Limitation. - Yifei Wu; Juming Xiong; Tianyuan Yao; Ruining Deng; Junlin Guo; Jialin Yue; Naweed Chowdhury; Yuankai Huo (CoRR, 2024)

Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology. - Lining Yu; Mengmeng Yin; Ruining Deng; Quan Liu 002; Tianyuan Yao; Can Cui 006; Junlin Guo; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2024)

GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation. - Jialin Yue; Tianyuan Yao; Ruining Deng; Siqi Lu; Junlin Guo; Quan Liu 002; Mengmeng Yin; Juming Xiong; Haichun Yang; Yuankai Huo (CoRR, 2024)

DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images. - Praitayini Kanakaraj; Tianyuan Yao; Leon Y. Cai; Ho Hin Lee; Nancy R. Newlin; Michael E. Kim; Chenyu Gao; Kimberly R. Pechman; Derek B. Archer; Timothy J. Hohman; Angela L. Jefferson; Lori L. Beason-Held; et al. (Neuroinformatics, 2024)

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics. - Junchao Zhu; Ruining Deng; Tianyuan Yao; Juming Xiong; Chongyu Qu; Junlin Guo; Siqi Lu; Mengmeng Yin; Yu Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CVPR, 2025)

PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit. - Yuechen Yang; Yu Wang; Tianyuan Yao; Ruining Deng; Mengmeng Yin; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 2025)

Polyhedra Encoding Transformers: Enhancing Diffusion MRI Analysis Beyond Voxel and Volumetric Embedding. - Tianyuan Yao; Zhiyuan Li 012; Praitayini Kanakaraj; Derek B. Archer; Kurt Schilling; Lori L. Beason-Held; Susan M. Resnick; Bennett A. Landman; Yuankai Huo (CoRR, 2025)

Post-Training Quantization for 3D Medical Image Segmentation: A Practical Study on Real Inference Engines. - Chongyu Qu; Ritchie Zhao; Ye Yu; Bin Liu; Tianyuan Yao; Junchao Zhu; Bennett A. Landman; Yucheng Tang; Yuankai Huo (CoRR, 2025)

Enhanced Feature-based Image Stitching for Endoscopic Videos in Pediatric Eosinophilic Esophagitis. - Juming Xiong; Muyang Li; Ruining Deng; Tianyuan Yao; Shunxing Bao; Regina N. Tyree; Girish Hiremath; Yuankai Huo (CoRR, 2025)

KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level. - Ruining Deng; Tianyuan Yao; Yucheng Tang; Junlin Guo; Siqi Lu; Juming Xiong; Lining Yu; Quan Huu Cap; Pengzhou Cai; Libin Lan; Ze Zhao; Adrian Galdran; et al. (CoRR, 2025)

MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics. - Junchao Zhu; Ruining Deng; Tianyuan Yao; Juming Xiong; Chongyu Qu; Junlin Guo; Siqi Lu; Yucheng Tang; Daguang Xu; Mengmeng Yin; Yu Wang; Shilin Zhao; et al. (CoRR, 2025)

DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes. - Junlin Guo; James Zimmer-Dauphinee; Jordan M. Nieusma; Siqi Lu; Quan Liu 002; Ruining Deng; Can Cui 006; Jialin Yue; Yizhe Lin; Tianyuan Yao; Juming Xiong; Junchao Zhu; et al. (CoRR, 2025)

IRS: Incremental Relationship-guided Segmentation for Digital Pathology. - Ruining Deng; Junchao Zhu; Juming Xiong; Can Cui 006; Tianyuan Yao; Junlin Guo; Siqi Lu; Marilyn Lionts; Mengmeng Yin; Yu Wang; Shilin Zhao; Yucheng Tang; et al. (CoRR, 2025)

Quantitative Benchmarking of Anomaly Detection Methods in Digital Pathology. - Can Cui 006; Xindong Zheng; Ruining Deng; Quan Liu 002; Tianyuan Yao; Keith T. Wilson; Lori A. Coburn; Bennett A. Landman; Haichun Yang; Yaohong Wang; Yuankai Huo (CoRR, 2025)

ZeroReg3D: A Zero-shot Registration Pipeline for 3D Consecutive Histopathology Image Reconstruction. - Juming Xiong; Ruining Deng; Jialin Yue; Siqi Lu; Junlin Guo; Marilyn Lionts; Tianyuan Yao; Can Cui 006; Junchao Zhu; Chongyu Qu; Mengmeng Yin; Haichun Yang; et al. (CoRR, 2025)

Img2ST-Net: Efficient High-Resolution Spatial Omics Prediction from Whole Slide Histology Images via Fully Convolutional Image-to-Image Learning. - Junchao Zhu; Ruining Deng; Junlin Guo; Tianyuan Yao; Juming Xiong; Chongyu Qu; Mengmeng Yin; Yu Wang; Shilin Zhao; Haichun Yang; Daguang Xu; Yucheng Tang; et al. (CoRR, 2025)

Fine-grained Multi-class Nuclei Segmentation with Molecular-empowered All-in-SAM Model. - Xueyuan Li; Can Cui 006; Ruining Deng; Yucheng Tang; Quan Liu 002; Tianyuan Yao; Shunxing Bao; Naweed Chowdhury; Haichun Yang; Yuankai Huo (CoRR, 2025)