Siqi Lu

Juming Xiong, Ruining Deng, Jialin Yue et al.

Histological analysis plays a crucial role in understanding tissue structure and pathology. While recent advancements in registration methods have improved 2D histological analysis, they often struggle to preserve critical 3D spatial relationships, limiting their utility in both clinical and research applications. Specifically, constructing accurate 3D models from 2D slices remains challenging due to tissue deformation, sectioning artifacts, variability in imaging techniques, and inconsistent illumination. Deep learning-based registration methods have demonstrated improved performance but suffer from limited generalizability and require large-scale training data. In contrast, non-deep-learning approaches offer better generalizability but often compromise on accuracy. In this study, we introduced ZeroReg3D, a novel zero-shot registration pipeline tailored for accurate 3D reconstruction from serial histological sections. By combining zero-shot deep learning-based keypoint matching with optimization-based affine and non-rigid registration techniques, ZeroReg3D effectively addresses critical challenges such as tissue deformation, sectioning artifacts, staining variability, and inconsistent illumination without requiring retraining or fine-tuning. The code has been made publicly available at https://github.com/hrlblab/ZeroReg3D

Jialin Yue, Tianyuan Yao, Ruining Deng et al.

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