Mouse Brain Architecture Project Technical White Paper

Download a PDF version of the Mouse Brain Architecture Project technical white paper (June, 2012).

Project Overview

The Brain Architecture Project is an ongoing effort to assemble and integrate information about connectivity in the vertebrate brain. As part of this effort, we previously prepared a position paper [1] that argues for a systematic effort to map neural connectivity brainwide, starting with the mouse. The paper called for comprehensive connectivity assessment using light microscopy, and argues for the use of existing methods rooted in classical neuroanatomy, scaled up, standardized, and modernized for high throughput usage in an experimental and data analysis pipeline. We stressed the importance of integration with existing resources including the Allen Brain Atlas (ABA) [2], and open access to project data, following the model of genome projects. Based on these principles, the Mouse Brain Architecture (MBA) project was started in Fall of 2009.

The technical goal of the MBA project is to generate brain-wide maps of neural connectivity in the mouse, which will specify the inputs and outputs of major brain regions. Our approach uses standardized methods to label neuronal projections, followed by light microscopic visualization, and finally computational methods to integrate the results. These steps are integrated into a pipeline for performing experiments with high throughput and fidelity, including quality control steps at each stage.


The planning stage of the project, including meetings at the Banbury conference center at CSHL as well as initial informatics work, was made possible by an award from the Keck Foundation. Major funding for the Mouse Brain Architecture project comes from a Challenge Grant from the National Institutes of Health (RC1MH088659) and a Transformative Award from the Office of the NIH Director (R01MH087988). Additional sources of funding include internal funding at Cold Spring Harbor Laboratory.

Process Overview

To determine the outputs of a brain region (i.e., the other regions it projects to), it is injected with a small amount of anterograde tracer [3] that is taken up by neurons locally and transported down the axons to the “target” (output) regions. After an appropriate transport period, the brain is perfused, sectioned, suitably stained, and each section digitally imaged. These 2-D images are co-registered into a 3-D computer stack that is subsequently registered to a common reference atlas. The resulting 3-D brain image is largely unlabeled (i.e., contains no signal of interest), except for the connections between the injected region and its target regions. Thus the labeled connections are clearly identifiable. A given region is injected in multiple animals to account for individual variability.

To determine the inputs to the same brain region as above, a retrograde tracer (taken up by axonal terminals and transported to neuronal cell bodies [3]) is injected in the same stereotaxic location, and the process is repeated.

A systematic grid of injections spanning the brain is used to generate a brainwide connectivity map. Each injection is placed in a different individual mouse and the resulting 3D image volumes co-registered in order to obtain the connectivity atlas.