Agnes B. Fogo

35 papers B 4Journal 23Unranked 8
YearRankTypeTitle / Venue / Authors
2024 J jnl
Circle Representation for Medical Instance Object Segmentation.
CoRR
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
2023 J jnl
Omni-Seg: A Scale-Aware Dynamic Network for Renal Pathological Image Segmentation.
IEEE Trans. Biomed. Eng.
Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. Michael Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, Yuankai Huo
2023 J jnl
Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging.
CoRR
Ruining Deng, Can Cui, Quan Liu, Tianyuan Yao, Lucas W. Remedios, Shunxing Bao, Bennett A. Landman, Lee E. Wheless, Lori A. Coburn, Keith T. Wilson, Yaohong Wang, Shilin Zhao, Agnes B. Fogo, Haichun Yang, Yucheng Tang, Yuankai Huo
2023 J jnl
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology.
CoRR
Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B. Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo
2022 J jnl
Circle Representation for Medical Object Detection.
IEEE Trans. Medical Imaging
Ethan H. Nguyen, Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Joseph T. Roland, Le Lu, Bennett A. Landman, Agnes B. Fogo, Yuankai Huo
2022 — conf
CircleSnake: Instance Segmentation with Circle Representation.
MLMI@MICCAI
Ethan H. Nguyen, Haichun Yang, Zuhayr Asad, Ruining Deng, Agnes B. Fogo, Yuankai Huo
2022 J jnl
CircleSnake: Instance Segmentation with Circle Representation.
CoRR
Ethan H. Nguyen, Haichun Yang, Zuhayr Asad, Ruining Deng, Agnes B. Fogo, Yuankai Huo
2022 J jnl
Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning.
CoRR
Tianyuan Yao, Chang Qu, Jun Long, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Zuhayr Asad, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A. Landman, Haichun Yang, Catie Chang, Yuankai Huo
2022 — conf
Dense multi-object 3D glomerular reconstruction and quantification on 2D serial section whole slide images.
Digital and Computational Pathology
Ruining Deng, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Shiru Wang, Lee E. Wheless, Agnes B. Fogo, Yuankai Huo
2022 J jnl
Glo-In-One: Holistic Glomerular Detection, Segmentation, and Lesion Characterization with Large-scale Web Image Mining.
CoRR
Tianyuan Yao, Yuzhe Lu, Jun Long, Aadarsh Jha, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Agnes B. Fogo, Yuankai Huo
2022 J jnl
Holistic Fine-grained GGS Characterization: From Detection to Unbalanced Classification.
CoRR
Yuzhe Lu, Haichun Yang, Zuhayr Asad, Zheyu Zhu, Tianyuan Yao, Jiachen Xu, Agnes B. Fogo, Yuankai Huo
2022 J jnl
Multi-contrast computed tomography healthy kidney atlas.
Comput. Biol. Medicine
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
2022 J jnl
Omni-Seg+: A Scale-aware Dynamic Network for Pathological Image Segmentation.
CoRR
Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Jun Long, Zuhayr Asad, R. Michael Womick, Zheyu Zhu, Agnes B. Fogo, Shilin Zhao, Haichun Yang, Yuankai Huo
2022 — conf
Self-supervised learning with large-scale web image mining for characterizing glomerular lesions.
Digital and Computational Pathology
Tianyuan Yao, Yuzhe Lu, Ruining Deng, Zheyu Zhu, Zuhayr Asad, Haichun Yang, Lee E. Wheless, Agnes B. Fogo, Yuankai Huo
2022 B conf
Supervised deep generation of high-resolution arterial phase computed tomography kidney substructure atlas.
Image Processing
Ho Hin Lee, Yucheng Tang, Shunxing Bao, Yan Xu, Qi Yang, Xin Yu, Agnes B. Fogo, Raymond Harris, Mark P. de Caestecker, Jeffrey M. Spraggins, Mattias P. Heinrich, Yuankai Huo, Bennett A. Landman
2021 J jnl
BEDS: Bagging ensemble deep segmentation for nucleus segmentation with testing stage stain augmentation.
CoRR
Xing Li, Haichun Yang, Jiaxin He, Aadarsh Jha, Agnes B. Fogo, Lee E. Wheless, Shilin Zhao, Yuankai Huo
2021 — conf
Beds: Bagging Ensemble Deep Segmentation For Nucleus Segmentation With Testing Stage Stain Augmentation.
ISBI
Xing Li, Haichun Yang, Jiaxin He, Aadarsh Jha, Agnes B. Fogo, Lee E. Wheless, Shilin Zhao, Yuankai Huo
2021 J jnl
Circle Representation for Medical Object Detection.
CoRR
Ethan H. Nguyen, Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Joseph T. Roland, Le Lu, Bennett A. Landman, Agnes B. Fogo, Yuankai Huo
2021 — conf
Compound Figure Separation of Biomedical Images with Side Loss.
DGM4MICCAI/DALI@MICCAI
Tianyuan Yao, Chang Qu, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A. Landman, Catie Chang, Haichun Yang, Yuankai Huo
2021 J jnl
Compound Figure Separation of Biomedical Images with Side Loss.
CoRR
Tianyuan Yao, Chang Qu, Quan Liu, Ruining Deng, Yuanhan Tian, Jiachen Xu, Aadarsh Jha, Shunxing Bao, Mengyang Zhao, Agnes B. Fogo, Bennett A. Landman, Catie Chang, Haichun Yang, Yuankai Huo
2021 B conf
Construction of a multi-phase contrast computed tomography kidney atlas.
Image Processing
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
2021 J jnl
Improve Global Glomerulosclerosis Classification with Imbalanced Data using CircleMix Augmentation.
CoRR
Yuzhe Lu, Haichun Yang, Zheyu Zhu, Ruining Deng, Agnes B. Fogo, Yuankai Huo
2021 B conf
Improve global glomerulosclerosis classification with imbalanced data using CircleMix augmentation.
Image Processing
Yuzhe Lu, Haichun Yang, Zheyu Zhu, Ruining Deng, Agnes B. Fogo, Yuankai Huo
2021 J jnl
Map3D: Registration-Based Multi-Object Tracking on 3D Serial Whole Slide Images.
IEEE Trans. Medical Imaging
Ruining Deng, Haichun Yang, Aadarsh Jha, Yuzhe Lu, Peng Chu, Agnes B. Fogo, Yuankai Huo
2021 B conf
Renal cortex, medulla and pelvicaliceal system segmentation on arterial phase CT images with random patch-based networks.
Image Processing
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
2020 — conf
CircleNet: Anchor-Free Glomerulus Detection with Circle Representation.
MICCAI (4)
Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Ye Chen, Joseph T. Roland, Le Lu, Bennett A. Landman, Agnes B. Fogo, Yuankai Huo
2020 J jnl
CircleNet: Anchor-free Detection with Circle Representation.
CoRR
Haichun Yang, Ruining Deng, Yuzhe Lu, Zheyu Zhu, Ye Chen, Joseph T. Roland, Le Lu, Bennett A. Landman, Agnes B. Fogo, Yuankai Huo
2020 — conf
EasierPath: An Open-Source Tool for Human-in-the-Loop Deep Learning of Renal Pathology.
iMIMIC/MIL3ID/LABELS@MICCAI
Zheyu Zhu, Yuzhe Lu, Ruining Deng, Haichun Yang, Agnes B. Fogo, Yuankai Huo
2020 J jnl
EasierPath: An Open-source Tool for Human-in-the-loop Deep Learning of Renal Pathology.
CoRR
Zheyu Zhu, Yuzhe Lu, Ruining Deng, Haichun Yang, Agnes B. Fogo, Yuankai Huo
2020 J jnl
Instance Segmentation for Whole Slide Imaging: End-to-End or Detect-Then-Segment.
CoRR
Aadarsh Jha, Haichun Yang, Ruining Deng, Meghan E. Kapp, Agnes B. Fogo, Yuankai Huo
2020 J jnl
Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images.
CoRR
Ruining Deng, Haichun Yang, Aadarsh Jha, Yuzhe Lu, Peng Chu, Agnes B. Fogo, Yuankai Huo
2020 J jnl
Multi-Contrast Computed Tomography Healthy Kidney Atlas.
CoRR
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
2020 J jnl
Neural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies.
CoRR
Brandon Ginley, Kuang-Yu Jen, Avi Rosenberg, Felicia Yen, Sanjay Jain, Agnes B. Fogo, Pinaki Sarder
2019 J jnl
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
Nat.
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, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson
2018 — conf
Computational analysis of the structural progression of human glomeruli in diabetic nephropathy.
Digital Pathology
Brandon G. Ginley, John Tomaszewski, Kuang-Yu Jen, Agnes B. Fogo, Sanjay Jain, Pinaki Sarder