CircleNet: Anchor-Free Glomerulus Detection with Circle Representation. - Haichun Yang; Ruining Deng; Yuzhe Lu; Zheyu Zhu; Ye Chen; Joseph T. Roland; Le Lu 001; Bennett A. Landman; Agnes B. Fogo; Yuankai Huo (MICCAI (4), 2020)

EasierPath: An Open-Source Tool for Human-in-the-Loop Deep Learning of Renal Pathology. - Zheyu Zhu; Yuzhe Lu; Ruining Deng; Haichun Yang; Agnes B. Fogo; Yuankai Huo (iMIMIC/MIL3ID/LABELS@MICCAI, 2020)

CircleNet: Anchor-free Detection with Circle Representation. - Haichun Yang; Ruining Deng; Yuzhe Lu; Zheyu Zhu; Ye Chen; Joseph T. Roland; Le Lu 001; Bennett A. Landman; Agnes B. Fogo; Yuankai Huo (CoRR, 2020)

Instance Segmentation for Whole Slide Imaging: End-to-End or Detect-Then-Segment. - Aadarsh Jha; Haichun Yang; Ruining Deng; Meghan E. Kapp; Agnes B. Fogo; Yuankai Huo (CoRR, 2020)

Beds: Bagging Ensemble Deep Segmentation For Nucleus Segmentation With Testing Stage Stain Augmentation. - Xing Li; Haichun Yang; Jiaxin He; Aadarsh Jha; Agnes B. Fogo; Lee E. Wheless; Shilin Zhao; Yuankai Huo (ISBI, 2021)

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)

Improve global glomerulosclerosis classification with imbalanced data using CircleMix augmentation. - Yuzhe Lu; Haichun Yang; Zheyu Zhu; Ruining Deng; Agnes B. Fogo; Yuankai Huo (Image Processing, 2021)

Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data. - Ruining Deng; Quan Liu 002; Can Cui 006; Zuhayr Asad; Haichun Yang; Yuankai Huo (CoRR, 2021)

Map3D: Registration-Based Multi-Object Tracking on 3D Serial Whole Slide Images. - Ruining Deng; Haichun Yang; Aadarsh Jha; Yuzhe Lu; Peng Chu; Agnes B. Fogo; Yuankai Huo (IEEE Trans. Medical Imaging, 2021)

Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomic, and Demographic Data. - Can Cui 006; Han Liu; Quan Liu 002; Ruining Deng; Zuhayr Asad; Yaohong Wang; Shilin Zhao; Haichun Yang; Bennett A. Landman; Yuankai Huo (MICCAI (5), 2022)

CircleSnake: Instance Segmentation with Circle Representation. - Ethan H. Nguyen; Haichun Yang; Zuhayr Asad; Ruining Deng; Agnes B. Fogo; Yuankai Huo (MLMI@MICCAI, 2022)

Single Dynamic Network for Multi-label Renal Pathology Image Segmentation. - Ruining Deng; Quan Liu 002; Can Cui 006; Zuhayr Asad; Haichun Yang; Yuankai Huo (MIDL, 2022)

Dense multi-object 3D glomerular reconstruction and quantification on 2D serial section whole slide images. - Ruining Deng; Haichun Yang; Zuhayr Asad; Zheyu Zhu; Shiru Wang; Lee E. Wheless; Agnes B. Fogo; Yuankai Huo (Digital and Computational Pathology, 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)

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)

Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomics, and Demographic Data. - Can Cui 006; Han Liu; Quan Liu 002; Ruining Deng; Zuhayr Asad; Yaohong Wang; Shilin Zhao; Haichun Yang; Bennett A. Landman; Yuankai Huo (CoRR, 2022)

Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: A Review. - Can Cui 006; Haichun Yang; Yaohong Wang; Shilin Zhao; Zuhayr Asad; Lori A. Coburn; Keith T. Wilson; Bennett A. Landman; 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)

Circle Representation for Medical Object Detection. - Ethan H. Nguyen; Haichun Yang; Ruining Deng; Yuzhe Lu; Zheyu Zhu; Joseph T. Roland; Le Lu 001; Bennett A. Landman; Agnes B. Fogo; Yuankai Huo (IEEE Trans. Medical Imaging, 2022)

Democratizing Pathological Image Segmentation with Lay Annotators via Molecular-Empowered Learning. - Ruining Deng; Yanwei Li; Peize Li; Jiacheng Wang; Lucas W. Remedios; Saydolimkhon Agzamkhodjaev; Zuhayr Asad; Quan Liu 002; Can Cui 006; Yaohong Wang; Yihan Wang; Yucheng Tang; et al. (MICCAI (6), 2023)

An accelerated pipeline for multi-label renal pathology image segmentation at the whole slide image level. - Haoju Leng; Ruining Deng; Zuhayr Asad; R. Michael Womick; Haichun Yang; Lipeng Wan; Yuankai Huo (Digital and Computational Pathology, 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)

Democratizing Pathological Image Segmentation with Lay Annotators via Molecular-empowered Learning. - Ruining Deng; Yanwei Li; Peize Li; Jiacheng Wang; Lucas W. Remedios; Saydolimkhon Agzamkhodjaev; Zuhayr Asad; Quan Liu 002; Can Cui 006; Yucheng Tang; Haichun Yang; Yuankai Huo (CoRR, 2023)

Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology. - Franklin Hu; Ruining Deng; Shunxing Bao; Haichun Yang; Yuankai Huo (CoRR, 2023)

High-performance Data Management for Whole Slide Image Analysis in Digital Pathology. - Haoju Leng; Ruining Deng; Shunxing Bao; Dazheng Fang; Bryan A. Millis; Yucheng Tang; Haichun Yang; Xiao Wang 004; Yifan Peng 002; Lipeng Wan; Yuankai Huo (CoRR, 2023)

Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning. - Xueyuan Li; Ruining Deng; Yucheng Tang; Shunxing Bao; Haichun Yang; 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)

Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers. - Muhao Liu; Chenyang Qi; Shunxing Bao; Quan Liu 002; Ruining Deng; Yu Wang; Shilin Zhao; Haichun Yang; Yuankai Huo (CoRR, 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)

Circle Representation for Medical Instance Object Segmentation. - Juming Xiong; Ethan H. Nguyen; Yilin Liu; Ruining Deng; Regina N. Tyree; Hernán Correa; Girish Hiremath; Yaohong Wang; Haichun Yang; Agnes B. Fogo; 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)

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)

Cross-Species Data Integration for Enhanced Layer Segmentation in Kidney Pathology. - Junchao Zhu; Mengmeng Yin; Ruining Deng; Yitian Long; Yu Wang; Yaohong Wang; Shilin Zhao; Haichun Yang; 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)

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)

Efficient MedSAMs: Segment Anything in Medical Images on Laptop. - Jun Ma 016; Feifei Li 010; Sumin Kim; Reza Asakereh; Bao-Hiep Le; Dang-Khoa Nguyen-Vu; Alexander Pfefferle; Muxin Wei; Ruochen Gao; Donghang Lyu; Songxiao Yang; Lennart Purucker; et al. (CoRR, 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)

stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration. - Yu Wang; Haichun Yang; Ruining Deng; Yuankai Huo; Qi Liu 024; Yu Shyr; Shilin Zhao (Briefings Bioinform., 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)

Towards Fine-grained Renal Vasculature Segmentation: Full-Scale Hierarchical Learning with FH-Seg. - Yitian Long; Zhongze Wu; Xiu Su; Lining Yu; Ruining Deng; Haichun Yang; 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)

CASC-AI: Consensus-aware Self-corrective AI Agents for Noise Cell Segmentation. - Ruining Deng; Yihe Yang; David J. Pisapia; Benjamin Liechty; Junchao Zhu; Juming Xiong; Junlin Guo; Zhengyi Lu; Jiacheng Wang; Xing Yao; Runxuan Yu; Rendong Zhang; 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)

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)

DyMorph-B2I: Dynamic and Morphology-Guided Binary-to-Instance Segmentation for Renal Pathology. - Leiyue Zhao; Yuechen Yang; Yanfan Zhu; Haichun Yang; Yuankai Huo; Paul Dennis Simonson; Kenji Ikemura; Mert R. Sabuncu; Yihe Yang; Ruining Deng (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)