PathFlow-MixMatch for Whole Slide Image Registration: An Investigation of a Segment-Based Scalable Image Registration Method

Image registration involves finding the best alignment between different images of the same object. In these tasks, the object in question is viewed differently in each of the images (e.g. different rotation or light conditions, etc.). In digital pathology, image registration aligns correspondent regions of tissue from different stereotactic viewpoints (e.g. subsequent deeper sections of the same tissue). These comparisons are important for histological analysis and can facilitate previously unavailable manipulations, such as 3D tissue reconstruction and cell-level alignment of immunohistochemical (IHC) and special stains. Several benchmarks have been established for evaluating image registration techniques for histological tissue; however, little work has evaluated the impact of scaling registration techniques to Giga-Pixel Whole Slide Images (WSI), which are large enough for significant memory limitations, and contain recurrent patterns and deformations that hinder traditional alignment algorithms. Furthermore, as tissue sections often contain multiple, discrete, smaller tissue fragments, it is unnecessary to align an entire image when the bulk of the image is background whitespace and tissue fragments orientations are often agnostic of each other. We present a methodology for circumventing large-scale image registration issues in histopathology and accompanying software. By removing background pixels, parsing the slide into discrete tissue segments, and matching, orienting and registering smaller segment pairs, we recovered registrations with lower Target Registration Error (TRE) when compared to utilizing the unmanipulated WSI. We tested our technique by having a pathologist annotate landmarks from 13 pairs of differently stained liver biopsy slides, performing WSI and segment-based registration techniques, and comparing overall TRE. Preliminary results demonstrate superior performance of registering segment pairs versus registering WSI (difference of median TRE of 44 pixels, p<0.001). Segment matching within WSI is an effective solution for histology image registration but requires further testing and validation to ensure its viability for stain translation and 3D histology analysis.