97 citations · 119 across the 28 of their papers we have counts for
29 papers
DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction
Junchao Zhu, Ruining Deng, Junlin Guo +11
Inferring spatially resolved gene expression from histology images offers a cost-effective complement to spatial transcriptomics (ST). However, existing methods reduce this task to…
Explainable Pathomics Feature Visualization via Correlation-aware Conditional Feature Editing
Yuechen Yang, Junlin Guo, Ruining Deng +9
Pathomics is a recent approach that offers rich quantitative features beyond what black-box deep learning can provide, supporting more reproducible and explainable biomarkers in di…
SCR2-ST: Combine Single Cell with Spatial Transcriptomics for Efficient Active Sampling via Reinforcement Learning
Junchao Zhu, Ruining Deng, Junlin Guo +13
Spatial transcriptomics (ST) is an emerging technology that enables researchers to investigate the molecular relationships underlying tissue morphology. However, acquiring ST data…
HistoWAS: A Pathomics Framework for Large-Scale Feature-Wide Association Studies of Tissue Topology and Patient Outcomes
Yuechen Yang, Junlin Guo, Yanfan Zhu +10
High-throughput "pathomic" analysis of Whole Slide Images (WSIs) offers new opportunities to study tissue characteristics and for biomarker discovery. However, the clinical relevan…
How Close Are We? Limitations and Progress of AI Models in Banff Lesion Scoring
Yanfan Zhu, Juming Xiong, Ruining Deng +7
The Banff Classification provides the global standard for evaluating renal transplant biopsies, yet its semi-quantitative nature, complex criteria, and inter-observer variability p…
Evaluating New AI Cell Foundation Models on Challenging Kidney Pathology Cases Unaddressed by Previous Foundation Models
Runchen Wang, Junlin Guo, Siqi Lu +12
Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of r…
MedFoundationHub: A Lightweight and Secure Toolkit for Deploying Medical Vision Language Foundation Models
Xiao Li, Yanfan Zhu, Ruining Deng +6
Recent advances in medical vision-language models (VLMs) open up remarkable opportunities for clinical applications such as automated report generation, copilots for physicians, an…
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
Recent advances in multi-modal AI have demonstrated promising potential for generating the currently expensive spatial transcriptomics (ST) data directly from routine histology ima…
IRS: Incremental Relationship-guided Segmentation for Digital Pathology
Ruining Deng, Junchao Zhu, Juming Xiong +14
Continual learning is rapidly emerging as a key focus in computer vision, aiming to develop AI systems capable of continuous improvement, thereby enhancing their value and practica…
MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics
Junchao Zhu, Ruining Deng, Tianyuan Yao +12
The rapid development of spatial transcriptomics (ST) offers new opportunities to explore the gene expression patterns within the spatial microenvironment. Current research integra…
KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level
Ruining Deng, Tianyuan Yao, Yucheng Tang +44
Chronic kidney disease (CKD) is a major global health issue, affecting over 10% of the population and causing significant mortality. While kidney biopsy remains the gold standard f…
PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit
Yuechen Yang, Yu Wang, Tianyuan Yao +5
Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples. However, traditional feature extract…
ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics
Junchao Zhu, Ruining Deng, Tianyuan Yao +9
Spatial transcriptomics (ST) is an emerging technology that enables medical computer vision scientists to automatically interpret the molecular profiles underlying morphological fe…
Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology
Lining Yu, Mengmeng Yin, Ruining Deng +9
Segmenting glomerular intraglomerular tissue and lesions traditionally depends on detailed morphological evaluations by expert nephropathologists, a labor-intensive process suscept…
Evaluating Cell AI Foundation Models in Kidney Pathology with Human-in-the-Loop Enrichment
Junlin Guo, Siqi Lu, Can Cui +14
Training AI foundation models has emerged as a promising large-scale learning approach for addressing real-world healthcare challenges, including digital pathology. While many of t…
Cross-Species Data Integration for Enhanced Layer Segmentation in Kidney Pathology
Junchao Zhu, Mengmeng Yin, Ruining Deng +6
Accurate delineation of the boundaries between the renal cortex and medulla is crucial for subsequent functional structural analysis and disease diagnosis. Training high-quality de…
GLAM: Glomeruli Segmentation for Human Pathological Lesions using Adapted Mouse Model
Lining Yu, Mengmeng Yin, Ruining Deng +9
Moving from animal models to human applications in preclinical research encompasses a broad spectrum of disciplines in medical science. A fundamental element in the development of…
HATs: Hierarchical Adaptive Taxonomy Segmentation for Panoramic Pathology Image Analysis
Ruining Deng, Quan Liu, Can Cui +10
Panoramic image segmentation in computational pathology presents a remarkable challenge due to the morphologically complex and variably scaled anatomy. For instance, the intricate…
PrPSeg: Universal Proposition Learning for Panoramic Renal Pathology Segmentation
Ruining Deng, Quan Liu, Can Cui +11
Understanding the anatomy of renal pathology is crucial for advancing disease diagnostics, treatment evaluation, and clinical research. The complex kidney system comprises various…
Evaluation Kidney Layer Segmentation on Whole Slide Imaging using Convolutional Neural Networks and Transformers
Muhao Liu, Chenyang Qi, Shunxing Bao +6
The segmentation of kidney layer structures, including cortex, outer stripe, inner stripe, and inner medulla within human kidney whole slide images (WSI) plays an essential role in…
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
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of feat…
Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging
Ruining Deng, Can Cui, Quan Liu +13
The segment anything model (SAM) was released as a foundation model for image segmentation. The promptable segmentation model was trained by over 1 billion masks on 11M licensed an…
Omni-Seg: A Scale-aware Dynamic Network for Renal Pathological Image Segmentation
Ruining Deng, Quan Liu, Can Cui +9
Comprehensive semantic segmentation on renal pathological images is challenging due to the heterogeneous scales of the objects. For example, on a whole slide image (WSI), the cross…
Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: A Review
Can Cui, Haichun Yang, Yaohong Wang +6
The rapid development of diagnostic technologies in healthcare is leading to higher requirements for physicians to handle and integrate the heterogeneous, yet complementary data th…