Glo-In-One-v2: holistic identification of glomerular cells, tissues, and lesions in human and mouse histopathology.
Academic Article
Overview
abstract
PURPOSE: Segmenting intraglomerular tissue and glomerular 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 glomerulus detection and segmentation. We leverage the Glo-In-One toolkit to version 2 (Glo-In-One-v2), which adds fine-grained segmentation capabilities. We curated 14 distinct labels spanning tissue regions, cells, and lesions across 23,529 annotated glomeruli from human and mouse histopathology data. To our knowledge, this dataset is among the largest of its kind to date. APPROACH: We present a single dynamic-head deep learning architecture for segmenting 14 classes within partially labeled images from human and mouse kidney pathology. The model was trained on data derived from 368 annotated kidney whole-slide images with five key intraglomerular tissue types and nine glomerular lesion types. RESULTS: The glomerulus segmentation model achieved a decent performance compared with baselines and achieved a 76.5% average Dice similarity coefficient. In addition, transfer learning from rodent to human for the glomerular lesion segmentation model has enhanced the average segmentation accuracy across different types of lesions by more than 3%, as measured by Dice scores. CONCLUSIONS: We introduce a convolutional neural network for multiclass segmentation of intraglomerular tissue and lesions. The Glo-In-One-v2 model and pretrained weight are publicly available at https://github.com/hrlblab/Glo-In-One_v2.
