Riffle Shuffle: A Supervised, Symmetry-Driven, GUI Toolkit for Mouse Brain Stack Registration and Plane Assignment

Immunostaining of brain slices is a ubiquitous technique used throughout neuroscience for the purposes of understanding the anatomical and molecular characteristics of brain circuits. Yet the variety of distortions introduced, and the manual nature of the preparation, hinder the use of the generated images from being rigorously quantified; instead most registration of brain slices is done laboriously by hand. Existing automated registration methods rarely make use of geometric shape information. When registering anterior-posterior brain slices, for example, small errors between consecutive planes accumulate, causing the symmetry axis of a plane to drift away from its starting position as depth increases. Furthermore, planes with imaging artifacts - e.g. one half of the slice is missing - can cause large errors, which are difficult to fix by changing global parameters. In this work we describe a method in which we register a set of consecutive brain slices enforcing all slices to have a vertical axis of symmetry, and then pair these slices optimally to planes from the Allen Mouse Brain Atlas via Dynamic Programming. The pipeline offers multiple human-in-the-loop opportunities, allowing users to fix algorithmic errors in various stages, including symmetry detection and pairwise assignment, via custom graphical interfaces. This pipeline enables large-scale analysis of brain slices, allowing this common technique to be used to generate quantitative datasets.