Beyond the microscope: interpreting renal biopsy findings in the era of precision medicine

Semi-Supervised Segmentation of Renal Pathology: An Alternative to Manual Segmentation and Input to Deep Learning Training

Kidney biopsy interpretation is the gold standard for the diagnosis and prognosis for kidney disease. Pathognomonic diagnosis hinges on the correct assessment of different structures within a biopsy that is manually visualized and interpreted by a renal pathologist. This laborious undertaking has spurred attempts to automate the process, offloading the consumption of temporal resources. Segmentation of kidney structures, specifically, the glomeruli, tubules, and interstitium, is a precursory step for disease classification problems. Translating renal disease decision making into a deep learning model for diagnostic and prognostic classification also relies on adequate segmentation of structures within the kidney biopsy. This study showcases a semi-automated segmentation technique where the user defines starting points for glomeruli in kidney biopsy images of both healthy normal and diabetic kidney disease stained with Nile Red that are subsequently partitioned into four areas: background, glomeruli, tubules and interstitium. Five of 30 biopsies that were segmented using the semi-automated method were randomly selected and the regions of interest were compared to the manual segmentation of the same images. Dice Similarity Coefficients (DSC) between the methods showed excellent agreement; Healthy (glomeruli: 0.92, tubules: 0.86, intersititium: 0.78) and diabetic nephropathy: (glomeruli: 0.94, tubules: 0.80, intersititium: 0.80). To our knowledge this is the first semi-automated segmentation algorithm performed with human renal biopsies stained with Nile Red. Utility of this methodology includes further image processing within structures across disease states based on biological morphological structures. It can also be used as input into a deep learning network to train semantic segmentation and input into a deep learning algorithm for classification of disease states.