Publications (85)
Weighted Circle Fusion: Ensembling Circle Representation from Different Object Detection Results
Jialin Yue, Tianyuan Yao, Ruining Deng +5
How Close Are We? Limitations and Progress of AI Models in Banff Lesion Scoring
Yanfan Zhu, Juming Xiong, Ruining Deng +7
Compound Figure Separation of Biomedical Images with Side Loss
Tianyuan Yao, Chang Qu, Quan Liu +11
VoxelEmbed: 3D Instance Segmentation and Tracking with Voxel Embedding based Deep Learning
Mengyang Zhao, Quan Liu, Aadarsh Jha +6
Expanding Training Data for Endoscopic Phenotyping of Eosinophilic Esophagitis
Juming Xiong, Hou Xiong, Quan Liu +4
Democratizing Pathological Image Segmentation with Lay Annotators via Molecular-empowered Learning
Ruining Deng, Yanwei Li, Peize Li +11
Assessment of Cell Nuclei AI Foundation Models in Kidney Pathology
Junlin Guo, Siqi Lu, Can Cui +14
Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology
Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios +16
Circle Representation for Medical Instance Object Segmentation
Juming Xiong, Ethan H. Nguyen, Yilin Liu +8
Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers
Muhao Liu, Chenyang Qi, Shunxing Bao +6
High-performance Data Management for Whole Slide Image Analysis in Digital Pathology
Haoju Leng, Ruining Deng, Shunxing Bao +8
Multi-scale Multi-site Renal Microvascular Structures Segmentation for Whole Slide Imaging in Renal Pathology
Franklin Hu, Ruining Deng, Shunxing Bao +2
mTREE: Multi-Level Text-Guided Representation End-to-End Learning for Whole Slide Image Analysis
Quan Liu, Ruining Deng, Can Cui +4
DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction
Junchao Zhu, Ruining Deng, Junlin Guo +11
HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis
Ruining Deng, Quan Liu, Can Cui +10
All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning
Can Cui, Ruining Deng, Quan Liu +5
DeepAndes: A Self-Supervised Vision Foundation Model for Multi-Spectral Remote Sensing Imagery of the Andes
Junlin Guo, James R. Zimmer-Dauphinee, Jordan M. Nieusma +16
Glo-VLMs: Leveraging Vision-Language Models for Fine-Grained Diseased Glomerulus Classification
Zhenhao Guo, Rachit Saluja, Tianyuan Yao +8
MORI-Seg: Learning Morphological Geometry for Instance Segmentation without Instance Annotations
Leiyue Zhao, Tianyu Shi, Daniel Reisenbuchler +12
Fine-grained Multi-class Nuclei Segmentation with Molecular-empowered All-in-SAM Model
Xueyuan Li, Can Cui, Ruining Deng +7
PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation
Ruining Deng, Quan Liu, Can Cui +11
CASC-AI: Consensus-aware Self-corrective Learning for Noise Cell Segmentation
Ruining Deng, Yihe Yang, David J. Pisapia +15
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 +10
Cross-modality Attention-based Multimodal Fusion for Non-small Cell Lung Cancer (NSCLC) Patient Survival Prediction
Ruining Deng, Nazim Shaikh, Gareth Shannon +1
Instance Segmentation for Whole Slide Imaging: End-to-End or Detect-Then-Segment
Aadarsh Jha, Haichun Yang, Ruining Deng +3
From Classification to Cross-Modal Understanding: Leveraging Vision-Language Models for Fine-Grained Renal Pathology
Zhenhao Guo, Rachit Saluja, Tianyuan Yao +13
Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology
Lining Yu, Mengmeng Yin, Ruining Deng +9
PFPs: Prompt-guided Flexible Pathological Segmentation for Diverse Potential Outcomes Using Large Vision and Language Models
Can Cui, Ruining Deng, Junlin Guo +4
GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation
Jialin Yue, Tianyuan Yao, Ruining Deng +7
HoloHisto: End-to-end Gigapixel WSI Segmentation with 4K Resolution Sequential Tokenization
Yucheng Tang, Yufan He, Vishwesh Nath +11
Map3D: Registration Based Multi-Object Tracking on 3D Serial Whole Slide Images
Ruining Deng, Haichun Yang, Aadarsh Jha +4
MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics
Junchao Zhu, Ruining Deng, Tianyuan Yao +12
BackSplit: The Importance of Sub-dividing the Background in Biomedical Lesion Segmentation
Rachit Saluja, Asli Cihangir, Ruining Deng +3
Omni-Seg: A Scale-aware Dynamic Network for Renal Pathological Image Segmentation
Ruining Deng, Quan Liu, Can Cui +9
Towards Fine-grained Renal Vasculature Segmentation: Full-Scale Hierarchical Learning with FH-Seg
Yitian Long, Zhongze Wu, Xiu Su +4
Improve Global Glomerulosclerosis Classification with Imbalanced Data using CircleMix Augmentation
Yuzhe Lu, Haichun Yang, Zheyu Zhu +3
Explainable Pathomics Feature Visualization via Correlation-aware Conditional Feature Editing
Yuechen Yang, Junlin Guo, Ruining Deng +9
An Accelerated Pipeline for Multi-label Renal Pathology Image Segmentation at the Whole Slide Image Level
Haoju Leng, Ruining Deng, Zuhayr Asad +4
CircleSnake: Instance Segmentation with Circle Representation
Ethan H. Nguyen, Haichun Yang, Zuhayr Asad +3
ASIST: Annotation-free Synthetic Instance Segmentation and Tracking by Adversarial Simulations
Quan Liu, Isabella M. Gaeta, Mengyang Zhao +6
GLAM: Glomeruli Segmentation for Human Pathological Lesions using Adapted Mouse Model
Lining Yu, Mengmeng Yin, Ruining Deng +9
ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics
Junchao Zhu, Ruining Deng, Tianyuan Yao +9
IRS: Incremental Relationship-guided Segmentation for Digital Pathology
Ruining Deng, Junchao Zhu, Juming Xiong +14
False Negative/Positive Control for SAM on Noisy Medical Images
Xing Yao, Han Liu, Dewei Hu +9
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology
Jiayuan Chen, Yu Wang, Ruining Deng +9
SimTriplet: Simple Triplet Representation Learning with a Single GPU
Quan Liu, Peter C. Louis, Yuzhe Lu +9
Quantitative Benchmarking of Anomaly Detection Methods in Digital Pathology
Can Cui, Xindong Zheng, Ruining Deng +8
Cross-organ Deployment of EOS Detection AI without Retraining: Feasibility and Limitation
Yifei Wu, Juming Xiong, Tianyuan Yao +5
MAdam: Metric-Aware Multi-Objective Adam
Fengbei Liu, Rachit Saluja, Sunwoo Kwak +5
Omni-Seg: A Single Dynamic Network for Multi-label Renal Pathology Image Segmentation using Partially Labeled Data
Ruining Deng, Quan Liu, Can Cui +3
DyMorph-B2I: Dynamic and Morphology-Guided Binary-to-Instance Segmentation for Renal Pathology
Leiyue Zhao, Yuechen Yang, Yanfan Zhu +7
Enhanced Feature-based Image Stitching for Endoscopic Videos in Pediatric Eosinophilic Esophagitis
Juming Xiong, Muyang Li, Ruining Deng +5
Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging
Ruining Deng, Can Cui, Quan Liu +13
Deep Learning-Based Open Source Toolkit for Eosinophil Detection in Pediatric Eosinophilic Esophagitis
Juming Xiong, Yilin Liu, Ruining Deng +5
Cross-scale Multi-instance Learning for Pathological Image Diagnosis
Ruining Deng, Can Cui, Lucas W. Remedios +12
Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images
Ruining Deng, Can Cui, Lucas W. Remedios +12
SCR2-ST: Combine Single Cell with Spatial Transcriptomics for Efficient Active Sampling via Reinforcement Learning
Junchao Zhu, Ruining Deng, Junlin Guo +13
Cross-Species Data Integration for Enhanced Layer Segmentation in Kidney Pathology
Junchao Zhu, Mengmeng Yin, Ruining Deng +6
An End-to-end Pipeline for 3D Slide-wise Multi-stain Renal Pathology Registration
Peize Li, Ruining Deng, Yuankai Huo
M^3-GloDets: Multi-Region and Multi-Scale Analysis of Fine-Grained Diseased Glomerular Detection
Tianyu Shi, Xinzi He, Kenji Ikemura +3
CircleNet: Anchor-free Detection with Circle Representation
Haichun Yang, Ruining Deng, Yuzhe Lu +7
Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images
Can Cui, Yaohong Wang, Shunxing Bao +11
ZeroReg3D: A Zero-shot Registration Pipeline for 3D Consecutive Histopathology Image Reconstruction
Juming Xiong, Ruining Deng, Jialin Yue +10
PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit
Yuechen Yang, Yu Wang, Tianyuan Yao +5
Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment
Junlin Guo, Siqi Lu, Can Cui +14
Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures
Shunxing Bao, Sichen Zhu, Vasantha L Kolachala +16
CoFi: A Fast Coarse-to-Fine Few-Shot Pipeline for Glomerular Basement Membrane Segmentation
Hongjin Fang, Daniel Reisenbüchler, Kenji Ikemura +3
Circle Representation for Medical Object Detection
Ethan H. Nguyen, Haichun Yang, Ruining Deng +7
Automatic Image Unfolding and Stitching Framework for Esophageal Lining Video Based on Density-Weighted Feature Matching
Muyang Li, Juming Xiong, Ruining Deng +4
CaCL: Class-aware Codebook Learning for Weakly Supervised Segmentation on Diffuse Image Patterns
Ruining Deng, Quan Liu, Shunxing Bao +5
ShapKO: Shapley-Adaptive Modality Knockout for Robust Multimodal Learning
Nusrat Binta Nizam, Fengbei Liu, Sunwoo Kwak +3
Dataset Distillation in Medical Imaging: A Feasibility Study
Muyang Li, Can Cui, Quan Liu +4
Eosinophils Instance Object Segmentation on Whole Slide Imaging Using Multi-label Circle Representation
Yilin Liu, Ruining Deng, Juming Xiong +5
Robust Fiber Orientation Distribution Function Estimation Using Deep Constrained Spherical Deconvolution for Diffusion MRI
Tianyuan Yao, Francois Rheault, Leon Y Cai +11
KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level
Ruining Deng, Tianyuan Yao, Yucheng Tang +44
Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning
Xueyuan Li, Ruining Deng, Yucheng Tang +3
Nucleus subtype classification using inter-modality learning
Lucas W. Remedios, Shunxing Bao, Samuel W. Remedios +14
EasierPath: An Open-source Tool for Human-in-the-loop Deep Learning of Renal Pathology
Zheyu Zhu, Yuzhe Lu, Ruining Deng +3
Compound Figure Separation of Biomedical Images: Mining Large Datasets for Self-supervised Learning
Tianyuan Yao, Chang Qu, Jun Long +13
Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models
Runchen Wang, Junlin Guo, Siqi Lu +12
Exploring shared memory architectures for end-to-end gigapixel deep learning
Lucas W. Remedios, Leon Y. Cai, Samuel W. Remedios +8
Survival Prediction of Brain Cancer with Incomplete Radiology, Pathology, Genomics, and Demographic Data
Can Cui, Han Liu, Quan Liu +6
ASIST: Annotation-free synthetic instance segmentation and tracking for microscope video analysis
Quan Liu, Isabella M. Gaeta, Mengyang Zhao +6
Patient-Conditioned Adaptive Offsets for Reliable Diagnosis across Subgroups
Gelei Xu, Yuying Duan, Jun Xia +3
MedFoundationHub: A Lightweight and Secure Toolkit for Deploying Medical Vision Language Foundation Models
Xiao Li, Yanfan Zhu, Ruining Deng +6