Computational methods for stitching, alignment, and artifact correction of serial section data

Abstract

Imaging large samples at the resolution offered by electron microscopy is typically achieved by sequentially recording overlapping tiles that are later combined to seamless mosaics. Mosaics of serial sections are aligned to reconstruct three-dimensional volumes. To achieve this, image distortions and artifacts as introduced during sample preparation or imaging need to be removed. In this chapter, we will discuss typical sources of artifacts and distortion, and we will learn how to use the open source software TrakEM2 to correct them.

Keywords: Alignment; Axial distortion correction; Contrast correction; Lens distortion correction; Montage; Serial section; Stitching.