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

TL;DR

GloFinder is an AI-powered QuPath plugin that automates glomeruli detection in whole slide images, offering high accuracy, visualization, and editing capabilities to improve kidney pathology analysis for clinicians.

Contribution

It introduces GloFinder, a user-friendly QuPath plugin utilizing CircleNet and ensemble methods for accurate, flexible, and accessible glomeruli detection in WSIs, addressing limitations of existing tools.

Findings

Achieved superior detection accuracy with ensemble CircleNet models.

Enabled seamless visualization and editing within QuPath.

Demonstrated effectiveness on large, manually annotated datasets.

Abstract

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. Code and the QuPath plugin are available at https://github.com/hrlblab/GloFinder