Allen Mouse Atlas

Cover imageFull brain coverage mouse connectivity atlas.

Automated pipeline algorithms for signal detection and registration.

Web application tools for search and visualization.

The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database. Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.


  • 2D, two dimensional;
  • 3D, three dimensional;
  • EGFP, enhanced green fluorescent protein;
  • IDP, informatics data pipeline;
  • INCF, International Informatics Coordinating Facility;
  • MIP, maximum intensity projection;
  • MRI, magnetic resonance imaging;
  • R, G, B, red, green, blue;
  • STP, serial two-photon;
  • WHS, Waxholm Space;
  • ZAP, zoom-and-pan


  • Mouse connectivity atlas;
  • Image registration;
  • Signal detection;
  • Digital atlas;
  • Neuronal projection

1. Introduction

Modern neuroscience is increasingly exploiting three-dimensional digital brain atlases as a means for understanding complex brain anatomy, localizing experimental data, and planning experiments. Such atlases are critical to integrating diverse information in a topographically meaningful fashion . Several recent studies and atlases of brain connectivity have become available, spanning scales from micro through meso to macro, that pose new challenges for data mapping and organization, , and . Beyond conventional structure-based atlases, large scale atlases of connectivity of the brain pose special demands on informatics and quantitative processing of the data. In addition to issues of data preprocessing, image registration, and signal quantification, there are substantial challenges in tracing neuronal connections and proper interpretation of the data.

High-resolution image series of a coronally sectioned brain specimen from the ...The Allen Mouse Brain Connectivity Atlas is a comprehensive database of high-resolution images of axonal projections originating from distinct anatomical regions of wild-type mouse brains or from various genetically labeled cell populations in individual brain regions of Cre-driver mice . Briefly, to create the atlas, each mouse brain was injected with an enhanced green fluorescent protein (EGFP)-expressing adeno-associated virus (AAV) as an anterograde viral tracer into a particular brain region. EGFP labeled axonal projections throughout the brain were systematically imaged using a customized TissueCyte 1000 serial two-photon (STP) tomography system, which couples high-speed two-photon microscopy with automated vibratome sectioning . By imaging serially at 75 μm below the tissue surface of the brain, STP tomography reduces tissue distortions that occur in conventional section-based histological methods, yielding a series of high resolution, inherently pre-aligned images amenable to more precise 3D spatial mapping.

The three dimensional geometry of projections is obtained by sequentially sampling high resolution 2D imagery. For each brain specimen, 140 coronal plane high resolution (0.35 μm) images were obtained at a -sampling interval of 100 μm. This procedure spans the entire brain during a continuous 18.5 h scanning period, resulting in an approximately 750 gigabyte data set per brain. The GFP signals from the injection site and axonal projections were collected in the green channel, while background fluorescence recorded in the red channel provides basic anatomy of brain structures.

Fig. 1.

High-resolution image series of a coronally sectioned brain specimen from the Allen Mouse Brain Connectivity Atlas with EGFP viral tracer injected into the primary visual area (blue arrow). The injection site and major projection targets are visible in green. Sequential imaging at 100 μm intervals generates inherently pre-aligned images amenable to precise 3D reconstruction and mapping. The coronal images on the middle and left side of this figure are displayed from a medial to a caudal plane of section through an adult mouse brain. The inset at the upper right shows a detail of EGFP-labeled axonal projections, terminating in the lateral geniculate nucleus. The sagittal and horizontal planes are virtual extrapolations derived from reconstruction of the coronal image series.

Each image series was processed through a high-throughput informatics data pipeline (IDP) to obtain spatially mapped and quantified projection information. To do this, key algorithms were developed to reliably extract labeled axons from the digitized images and to bring data from different brains into registration to allow computational comparison. The output of the data generation and processing pipeline supports the creation of whole-brain connectivity matrices and analysis of connectional strength distribution, symmetry, and other network properties . Through an online web application, informatics results support key features that allow easier navigation of this large database, such as an interactive projection summary graph for each specimen; an image synchronization feature to browse images from multiple injections, reference data, and atlases in a coordinated manner; and on-the-fly search service to identify specimens with specific projection profiles. Here we report the detailed methodologies in developing this informatics pipeline and web product.

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