Tissue Cytometry With Machine Learning in Kidney: From Small Specimens to Big Data

Abstract

Advances in cellular and molecular interrogation of kidney tissue have ushered a new era of understanding the pathogenesis of kidney disease and potentially identifying molecular targets for therapeutic intervention. Classifying cells in situ and identifying subtypes and states induced by injury is a foundational task in this context. High resolution Imaging-based approaches such as large-scale fluorescence 3D imaging offer significant advantages because they allow preservation of tissue architecture and provide a definition of the spatial context of each cell. We recently described the Volumetric Tissue Exploration and Analysis cytometry tool which enables an interactive analysis, quantitation and semiautomated classification of labeled cells in 3D image volumes. We also established and demonstrated an imaging-based classification using deep learning of cells in intact tissue using 3D nuclear staining with 4′,6-diamidino-2-phenylindole (DAPI). In this mini-review, we will discuss recent advancements in analyzing 3D imaging of kidney tissue, and how combining machine learning with cytometry is a powerful approach to leverage the depth of content provided by high resolution imaging into a highly informative analytical output. Therefore, imaging a small tissue specimen will yield big scale data that will enable cell classification in a spatial context and provide novel insights on pathological changes induced by kidney disease.

High-throughput image analysis with deep learning captures heterogeneity and spatial relationships after kidney injury

“…There are relatively few techniques 7 – 9 available to extract spatial data from stained kidney tissue that can study 10 4 cells or more per sample, as is routinely achieved with single cell approaches. More commonly, IF analyses require time-consuming scoring or counting procedures or semi-automated thresholding approaches.…”

High-throughput image analysis with deep learning captures heterogeneity and spatial relationships after kidney injury

“…There are relatively few techniques [7][8][9] available to extract spatial data from stained kidney tissue that can study 10 4 cells or more per sample, as is routinely achieved with single cell approaches. More commonly, IF analyses require time-consuming scoring or counting procedures or semi-automated thresholding approaches.…”