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Mouse Brain Architecture Project

Brainwide maps of inter-regional neural connectivity specifying the inputs and outputs of every mouse brain region at a ����??mesoscopic����?? level of analysis corresponding to brain compartments defined in classical neuroanatomy. To determine the outputs of a brain region (i.e., the other regions it projects to), anterograde tracers are used which are taken up by neurons locally (����??the input����??), then transported actively down the axons to the ����??output regions����??. The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled����?? only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location (����??the input����??), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a ����??virtual microscope.����?? The images are integrated with other data sources from the web, and are fully accessible to the neuroscience community as well as interested members of the general public. Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range ����??mesoscopic����?? scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in ����??shotgun����?? fashion from the full dataset.

URL: http://brainarchitecture.org/mouse/about

Resource ID: nlx_146201     Resource Type: Resource     Version: Latest Version


brain, connectivity, neuroanatomy

Additional Resource Types

d spatial image, reference atlas

Old URLs





MBA, MBA Project


Mouse Brain Architecture

Parent Organization

Funding Information

Office of the Director, NIH, RC1MH088659, R01MH087988


Fully accessible to the neuroscience community as well as interested members of the general public.



Original Submitter


Version Status


Submitted On

12:00am June 11, 2012

Originated From


Changes from Previous Version

First Version

Version 1

Created 3 years ago by Anonymous