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

TL;DR

Glo-In-One-v2 is a deep learning toolkit that accurately segments glomerular tissues and lesions in human and mouse kidney histopathology images, facilitating faster and more consistent diagnoses.

Contribution

This study introduces a novel deep learning model with fine-grained segmentation of 14 classes in histopathology images, trained on a large annotated dataset, and demonstrates improved accuracy through transfer learning.

Findings

Achieved 76.5% average Dice score for glomerulus segmentation.

Enhanced lesion segmentation accuracy by over 3% using transfer learning.

Provided publicly available model and weights for community use.

Abstract

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.