Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

Norio Takata,Hideyuki Okano,Kenji F Tanaka,Yuji Komaki,Nobuhiko Sato

doi:10.1038/s41598-021-85807-0

Abstract

A brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher’s necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.

Highlights

A brain atlas is necessary for analyzing structure and function in neuroimaging research
Destructive nodes exist in the original annotation ontology (AO), which might impair the structure of the anatomical hierarchy in the AO and which might break consistency between AO and annotation volumes (AVs) upon combining or dividing nodes
The absence of a de facto standard annotation atlas for the mouse brain in magnetic resonance imaging (MRI) studies might engender inconsistent ROI definitions for brain structures, making it difficult to compare, replicate, and validate results obtained from other laboratories[19]

Summary

Introduction

A brain atlas is necessary for analyzing structure and function in neuroimaging research. For nodes with collapsed letters, see the zoomable HTML version of this plot at https://github.com/ntakata/flexible-annotation-atlas/tree/master/FAAs. The color code for the brain structure follows that of AIBS, and is applicable to Figs. The original AV by AIBS per se is not perfectly suited for MRI analysis because (1) a considerable number of brain structures defined in it are too small or large for MRI analysis, (2) the original AV is single-sided; Corresponding brain structures in the right and left brain hemisphere are treated as a single structure, and (3) there is inconsistency between an annotation ontology file and AVs provided by AIBS, leading to destructive nodes (defined in the first section of “Results” section)

Methods

Results

Conclusion