3D Cursor

Move cursor to the injection location you are interested in

3D Cursor Search: Move cursor to desired injection location

*Allen Mouse Atlas version 3

Tree Search

Tree Search: Select desired injection brain compartment


Data Navigation

– Cursor Search: Click on a point to find the coordinates to view injected datasets
– Directory Tree: Use grouping to search for specific regions and areas to access injected dataset information

About the Data

Datasets include mouse information, tracer location, and image details to visualize projections
Specified regions and areas throughout the brain
Projection patterns and defined neuronal populations


The goal of the Mouse Brain Architecture Project is to understand brain-wide connectivity in the mouse brain at the mesoscopic scale (Mitra 2014).

The primary data presented on this portal for wild-type connectivity consists of a comprehensive set of anterograde and retrograde tracer injections placed on a systematic grid spanning the whole mouse brain. The data was generated using a high throughput neuro-histological pipeline for doing injection-based tractography and is being processed using an integrated data analysis and web-posting pipeline for petabyte-scale histological image data.

The project was initiated with workshops in 2007-08, leading to a position paper (Bohland et al. 2009) proposing brain-wide mesoscale connectivity mapping in vertebrate brains. This original proposal also inspired corresponding efforts elsewhere including the Allen Institute mouse wildtype connectivity mapping project.