Glomerulosclerosis identification in whole slide images using semantic segmentation.
Bueno, Gloria;Fernandez-Carrobles, M Milagro;Gonzalez-Lopez, Lucia;Deniz, Oscar;
computer methods and programs in biomedicine2019Vol. 184pp. 105273
198
bueno2019glomerulosclerosiscomputer
Abstract
Glomeruli identification, i.e., detection and characterization, is a key procedure in many nephropathology studies. In this paper, semantic segmentation based on convolutional neural networks (CNN) is proposed to detect glomeruli using Whole Slide Imaging (WSI) follows by a classification CNN to divide the glomeruli into normal and sclerosed.Comparison between U-Net and SegNet CNNs is performed for pixel-level segmentation considering both a two and three class problem, that is, a) non-glomerular and glomerular structures and b) non-glomerular normal glomerular and sclerotic structures. The two class semantic segmentation result is then used for a CNN classification where glomerular regions are divided into normal and global sclerosed glomeruli.These methods were tested on a dataset composed of 47 WSIs belonging to human kidney sections stained with Periodic Acid Schiff (PAS). The best approach was the SegNet for two class segmentation follows by a fine-tuned AlexNet network to characterize the glomeruli. 98.16% of accuracy was obtained with this process of consecutive CNNs (SegNet-AlexNet) for segmentation and classification.The results obtained demonstrate that the sequential CNN segmentation-classification strategy achieves higher accuracy reducing misclassified cases and therefore being the methodology proposed for glomerulosclerosis detection.