Glomerulosclerosis identification in whole slide images using semantic segmentation

Comput Methods Programs Biomed. 2020 Feb:184:105273. doi: 10.1016/j.cmpb.2019.105273. Epub 2019 Dec 19.


Background and objective: 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.

Methods: 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.

Results: 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.

Conclusion: 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.

Keywords: Consecutive segmentation-classification CNN; Deep learning; Digital pathology; Glomeruli detection; Sclerotic glomeruli; Segnet; Semantic segmentation; U-Net.

MeSH terms

  • Datasets as Topic
  • Humans
  • Image Processing, Computer-Assisted
  • Kidney Diseases / diagnosis*
  • Kidney Diseases / pathology
  • Kidney Glomerulus / pathology*
  • Neural Networks, Computer
  • Semantics*