Quantifying and Visualizing Hidden Preferential Aggregations Amid Heterogeneity (1708.08097v1)

Abstract: Biological systems often exhibit a heterogeneous arrangement of objects, such as assorted nuclear chromatin patterns in a tumor, assorted species of bacteria in biofilms, or assorted aggregates of subcellular particles. Principle Component Analysis (PCA) and Multiple Component Analysis (MCA) provide information about which features in multidimensional data aggregate, but do not provide in situ spatial information about these aggregations. This paper outlines the Numericized Histogram Score (NHS) algorithm, which converts the histogram distribution of shortest distances between objects into a continuous variable that can be represented as a spatial heatmap. A histogram can be transformed into an intensity value by assigning a weighting factor to each sequential bin. Each object in an image can be replaced by its NHS value, which when calibrated to a color scale results in a heatmap. These spatial heatmaps reveal regions of aggregation amid heterogeneity that would otherwise mask loco-regional spatial associations, which will be especially useful in the field of digital pathology. In addition to visualizing aggregations as heatmaps, the ability to calculate degrees of recurring patterns of aggregation allows investigators to stratify samples for further insights into clinical outcome, response to treatment, or omic subtypes (genomic, transcriptomic, proteomic, metabolomic, etc.).