Computational analysis of the structural progression of human glomeruli in diabetic nephropathy. - Brandon G. Ginley; John Tomaszewski 001; Kuang-Yu Jen; Agnes B. Fogo; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2018)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

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)

Neural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies. - Brandon Ginley; Kuang-Yu Jen; Avi Rosenberg; Felicia Yen; Sanjay Jain 006; Agnes B. Fogo; Pinaki Sarder (CoRR, 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)

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)

Construction of a multi-phase contrast computed tomography kidney atlas. - Ho Hin Lee; Yucheng Tang; Kaiwen Xu; Shunxing Bao; Agnes B. Fogo; Raymond Harris; Mark P. de Caestecker; Mattias P. Heinrich; Jeffrey M. Spraggins; Yuankai Huo; Bennett A. Landman (Image Processing, 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)

Renal cortex, medulla and pelvicaliceal system segmentation on arterial phase CT images with random patch-based networks. - Yucheng Tang; Riqiang Gao; Ho Hin Lee; Zhoubing Xu; Brent V. Savoie; Shunxing Bao; Yuankai Huo; Agnes B. Fogo; Raymond Harris; Mark P. de Caestecker; Jeffrey M. Spraggins; Bennett A. Landman (Image Processing, 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)

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

Supervised deep generation of high-resolution arterial phase computed tomography kidney substructure atlas. - Ho Hin Lee; Yucheng Tang; Shunxing Bao; Yan Xu; Qi Yang 004; Xin Yu 010; Agnes B. Fogo; Raymond Harris; Mark P. de Caestecker; Jeffrey M. Spraggins; Mattias P. Heinrich; Yuankai Huo; et al. (Image Processing, 2022)

Multi-contrast computed tomography healthy kidney atlas. - Ho Hin Lee; Yucheng Tang; Kaiwen Xu; Shunxing Bao; Agnes B. Fogo; Raymond Harris; Mark P. de Caestecker; Mattias P. Heinrich; Jeffrey M. Spraggins; Yuankai Huo; Bennett A. Landman (Comput. Biol. Medicine, 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)

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)

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)

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)

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)

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)