Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

TLDR

The Allen Brain Atlas is an online public resource that integrates extensive gene expression, connectivity, and neuroanatomical data with powerful search and viewing tools for adult and developing mouse, human, and non‑human primate brains. This review describes the Atlas’s resources, detailing each product and data type—including in situ hybridization, supporting histology, microarray, RNA sequencing, reference atlases, projection mapping, and magnetic resonance imaging. The authors outline web‑application features that allow users to search and mine the datasets, such as gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of expression data, 3D navigation via Brain Explorer, an interactive reference atlas viewer, and cross‑dataset search capabilities. All Atlas resources are accessible through the Allen Brain Atlas data portal.

Abstract

The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.