CASC-AI: Consensus-aware Self-corrective AI Agents for Noise Cell Segmentation

Multi-class cell segmentation in high-resolution gigapixel whole slide images (WSI) is crucial for various clinical applications. However, training such models typically requires labor-intensive, pixel-wise annotations by domain experts. Recent efforts have democratized this process by involving lay annotators without medical expertise. However, conventional non-agent-based approaches struggle to handle annotation noise adaptively, as they lack mechanisms to mitigate false positives (FP) and false negatives (FN) at both the image-feature and pixel levels. In this paper, we propose a consensus-aware self-corrective AI agent that leverages the Consensus Matrix to guide its learning process. The Consensus Matrix defines regions where both the AI and annotators agree on cell and non-cell annotations, which are prioritized with stronger supervision. Conversely, areas of disagreement are adaptively weighted based on their feature similarity to high-confidence agreement regions, with more similar regions receiving greater attention. Additionally, contrastive learning is employed to separate features of noisy regions from those of reliable agreement regions by maximizing their dissimilarity. This paradigm enables the AI to iteratively refine noisy labels, enhancing its robustness. Validated on one real-world lay-annotated cell dataset and two simulated noisy datasets, our method demonstrates improved segmentation performance, effectively correcting FP and FN errors and showcasing its potential for training robust models on noisy datasets. The official implementation and cell annotations are publicly available at https://github.com/ddrrnn123/CASC-AI.

KPIs 2024 Challenge: Advancing Glomerular Segmentation from Patch- to Slide-Level

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 for CKD diagnosis and treatment, the lack of comprehensive benchmarks for kidney pathology segmentation hinders progress in the field. To address this, we organized the Kidney Pathology Image Segmentation (KPIs) Challenge, introducing a dataset that incorporates preclinical rodent models of CKD with over 10,000 annotated glomeruli from 60+ Periodic Acid Schiff (PAS)-stained whole slide images. The challenge includes two tasks, patch-level segmentation and whole slide image segmentation and detection, evaluated using the Dice Similarity Coefficient (DSC) and F1-score. By encouraging innovative segmentation methods that adapt to diverse CKD models and tissue conditions, the KPIs Challenge aims to advance kidney pathology analysis, establish new benchmarks, and enable precise, large-scale quantification for disease research and diagnosis.

Towards Fine-grained Renal Vasculature Segmentation: Full-Scale Hierarchical Learning with FH-Seg

Accurate fine-grained segmentation of the renal vasculature is critical for nephrological analysis, yet it faces challenges due to diverse and insufficiently annotated images. Existing methods struggle to accurately segment intricate regions of the renal vasculature, such as the inner and outer walls, arteries and lesions. In this paper, we introduce FH-Seg, a Full-scale Hierarchical Learning Framework designed for comprehensive segmentation of the renal vasculature. Specifically, FH-Seg employs full-scale skip connections that merge detailed anatomical information with contextual semantics across scales, effectively bridging the gap between structural and pathological contexts. Additionally, we implement a learnable hierarchical soft attention gates to adaptively reduce interference from non-core information, enhancing the focus on critical vascular features. To advance research on renal pathology segmentation, we also developed a Large Renal Vasculature (LRV) dataset, which contains 16,212 fine-grained annotated images of 5,600 renal arteries. Extensive experiments on the LRV dataset demonstrate FH-Seg's superior accuracies (71.23% Dice, 73.06% F1), outperforming Omni-Seg by 2.67 and 2.13 percentage points respectively. Code is available at: https://github.com/hrlblab/FH-seg.

Expanding Training Data for Endoscopic Phenotyping of Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic esophageal disorder marked by eosinophil-dominated inflammation. Diagnosing EoE usually involves endoscopic inspection of the esophageal mucosa and obtaining esophageal biopsies for histologic confirmation. Recent advances have seen AI-assisted endoscopic imaging, guided by the EREFS system, emerge as a potential alternative to reduce reliance on invasive histological assessments. Despite these advancements, significant challenges persist due to the limited availability of data for training AI models - a common issue even in the development of AI for more prevalent diseases. This study seeks to improve the performance of deep learning-based EoE phenotype classification by augmenting our training data with a diverse set of images from online platforms, public datasets, and electronic textbooks increasing our dataset from 435 to 7050 images. We utilized the Data-efficient Image Transformer for image classification and incorporated attention map visualizations to boost interpretability. The findings show that our expanded dataset and model enhancements improved diagnostic accuracy, robustness, and comprehensive analysis, enhancing patient outcomes.

Enhanced Feature-based Image Stitching for Endoscopic Videos in Pediatric Eosinophilic Esophagitis

Video endoscopy represents a major advance in the investigation of gastrointestinal diseases. Reviewing endoscopy videos often involves frequent adjustments and reorientations to piece together a complete view, which can be both time-consuming and prone to errors. Image stitching techniques address this issue by providing a continuous and complete visualization of the examined area. However, endoscopic images, particularly those of the esophagus, present unique challenges. The smooth surface, lack of distinct feature points, and non-horizontal orientation complicate the stitching process, rendering traditional feature-based methods often ineffective for these types of images. In this paper, we propose a novel preprocessing pipeline designed to enhance endoscopic image stitching through advanced computational techniques. Our approach converts endoscopic video data into continuous 2D images by following four key steps: (1) keyframe selection, (2) image rotation adjustment to correct distortions, (3) surface unwrapping using polar coordinate transformation to generate a flat image, and (4) feature point matching enhanced by Adaptive Histogram Equalization for improved feature detection. We evaluate stitching quality through the assessment of valid feature point match pairs. Experiments conducted on 20 pediatric endoscopy videos demonstrate that our method significantly improves image alignment and stitching quality compared to traditional techniques, laying a robust foundation for more effective panoramic image creation.

PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit

Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples. However, traditional feature extraction pipelines based on tools like CellProfiler often involve lengthy workflows, requiring WSI segmentation into patches, feature extraction at the patch level, and subsequent mapping back to the original WSI. To address these challenges, we present PySpatial, a high-speed pathomics toolkit specifically designed for WSI-level analysis. PySpatial streamlines the conventional pipeline by directly operating on computational regions of interest, reducing redundant processing steps. Utilizing rtree-based spatial indexing and matrix-based computation, PySpatial efficiently maps and processes computational regions, significantly accelerating feature extraction while maintaining high accuracy. Our experiments on two datasets-Perivascular Epithelioid Cell (PEC) and data from the Kidney Precision Medicine Project (KPMP)-demonstrate substantial performance improvements. For smaller and sparse objects in PEC datasets, PySpatial achieves nearly a 10-fold speedup compared to standard CellProfiler pipelines. For larger objects, such as glomeruli and arteries in KPMP datasets, PySpatial achieves a 2-fold speedup. These results highlight PySpatial's potential to handle large-scale WSI analysis with enhanced efficiency and accuracy, paving the way for broader applications in digital pathology.

ASIGN: An Anatomy-aware Spatial Imputation Graphic Network for 3D Spatial Transcriptomics

Spatial transcriptomics (ST) is an emerging technology that enables medical computer vision scientists to automatically interpret the molecular profiles underlying morphological features. Currently, however, most deep learning-based ST analyses are limited to two-dimensional (2D) sections, which can introduce diagnostic errors due to the heterogeneity of pathological tissues across 3D sections. Expanding ST to three-dimensional (3D) volumes is challenging due to the prohibitive costs; a 2D ST acquisition already costs over 50 times more than whole slide imaging (WSI), and a full 3D volume with 10 sections can be an order of magnitude more expensive. To reduce costs, scientists have attempted to predict ST data directly from WSI without performing actual ST acquisition. However, these methods typically yield unsatisfying results. To address this, we introduce a novel problem setting: 3D ST imputation using 3D WSI histology sections combined with a single 2D ST slide. To do so, we present the Anatomy-aware Spatial Imputation Graph Network (ASIGN) for more precise, yet affordable, 3D ST modeling. The ASIGN architecture extends existing 2D spatial relationships into 3D by leveraging cross-layer overlap and similarity-based expansion. Moreover, a multi-level spatial attention graph network integrates features comprehensively across different data sources. We evaluated ASIGN on three public spatial transcriptomics datasets, with experimental results demonstrating that ASIGN achieves state-of-the-art performance on both 2D and 3D scenarios. Code is available at https://github.com/hrlblab/ASIGN.

GloFinder: AI-empowered QuPath Plugin for WSI-level Glomerular Detection, Visualization, and Curation

Artificial intelligence (AI) has demonstrated significant success in automating the detection of glomeruli, the key functional units of the kidney, from whole slide images (WSIs) in kidney pathology. However, existing open-source tools are often distributed as source code or Docker containers, requiring advanced programming skills that hinder accessibility for non-programmers, such as clinicians. Additionally, current models are typically trained on a single dataset and lack flexibility in adjusting confidence levels for predictions. To overcome these challenges, we introduce GloFinder, a QuPath plugin designed for single-click automated glomeruli detection across entire WSIs with online editing through the graphical user interface (GUI). GloFinder employs CircleNet, an anchor-free detection framework utilizing circle representations for precise object localization, with models trained on approximately 160,000 manually annotated glomeruli. To further enhance accuracy, the plugin incorporates Weighted Circle Fusion (WCF), an ensemble method that combines confidence scores from multiple CircleNet models to produce refined predictions, achieving superior performance in glomerular detection. GloFinder enables direct visualization and editing of results in QuPath, facilitating seamless interaction for clinicians and providing a powerful tool for nephropathology research and clinical practice.

Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology

Segmenting glomerular intraglomerular tissue and lesions traditionally depends on detailed morphological evaluations by expert nephropathologists, a labor-intensive process susceptible to interobserver variability. Our group previously developed the Glo-In-One toolkit for integrated detection and segmentation of glomeruli. In this study, we leverage the Glo-In-One toolkit to version 2 with fine-grained segmentation capabilities, curating 14 distinct labels for tissue regions, cells, and lesions across a dataset of 23,529 annotated glomeruli across human and mouse histopathology data. To our knowledge, this dataset is among the largest of its kind to date.In this study, we present a single dynamic head deep learning architecture designed to segment 14 classes within partially labeled images of human and mouse pathology data. Our model was trained using a training set derived from 368 annotated kidney whole-slide images (WSIs) to identify 5 key intraglomerular tissues covering Bowman's capsule, glomerular tuft, mesangium, mesangial cells, and podocytes. Additionally, the network segments 9 glomerular lesion classes including adhesion, capsular drop, global sclerosis, hyalinosis, mesangial lysis, microaneurysm, nodular sclerosis, mesangial expansion, and segmental sclerosis. The glomerulus segmentation model achieved a decent performance compared with baselines, and achieved a 76.5 % average Dice Similarity Coefficient (DSC). Additional, transfer learning from rodent to human for glomerular lesion segmentation model has enhanced the average segmentation accuracy across different types of lesions by more than 3 %, as measured by Dice scores. The Glo-In-One-v2 model and trained weight have been made publicly available at https: //github.com/hrlblab/Glo-In-One_v2.

Cross-organ Deployment of EOS Detection AI without Retraining: Feasibility and Limitation

Chronic rhinosinusitis (CRS) is characterized by persistent inflammation in the paranasal sinuses, leading to typical symptoms of nasal congestion, facial pressure, olfactory dysfunction, and discolored nasal drainage, which can significantly impact quality-of-life. Eosinophils (Eos), a crucial component in the mucosal immune response, have been linked to disease severity in CRS. The diagnosis of eosinophilic CRS typically uses a threshold of 10-20 eos per high-power field (HPF). However, manually counting Eos in histological samples is laborious and time-intensive, making the use of AI-driven methods for automated evaluations highly desirable. Interestingly, eosinophils are predominantly located in the gastrointestinal (GI) tract, which has prompted the release of numerous deep learning models trained on GI data. This study leverages a CircleSnake model initially trained on upper-GI data to segment Eos cells in whole slide images (WSIs) of nasal tissues. It aims to determine the extent to which Eos segmentation models developed for the GI tract can be adapted to nasal applications without retraining. The experimental results show promising accuracy in some WSIs, although, unsurprisingly, the performance varies across cases. This paper details these performance outcomes, delves into the reasons for such variations, and aims to provide insights that could guide future development of deep learning models for eosinophilic CRS.