Registration and Composition of Stacks of Serial Optical Slices Captured by a Confocal Microscope

Abstract

This article deals with image and volume registration of stacks of serial optical slices from a large biological tissue specimen captured by a confocal microscope. Due to the limited depth of observation and the restricted field of view of the confocal microscope the oversized specimen has to be sliced into smaller physical sections and scanned individually. The composition of the stacks of optical slices, which is based on data registration, is achieved in two steps. First, sub-volumes are created by volume registration of overlapping stacks of optical slices (volumes) captured from individual physical section. Second, image registration of peripheral images of sub-volumes of neighboring physical slices makes possible to compose 3D image of the whole specimen. Both registrations are based on similarity measures, such as the sum of absolute valued differences, normalized correlation coefficient, and mutual information. Data registration requires optimization of the search for the global extreme of a similarity measure over a parametrical space. Therefore, optimization strategies—n-step search, adaptive simulated annealing and stochastic approach—are used, and their optimal set-up is presented. The composition of stacks enables us to visualize and study a large biological specimen in 3D in high resolution.