Connectivity Atlas: How to

This is the online help for the Allen Mouse Connectivity web application.

The Allen Mouse Brain Connectivity Atlas is a high-resolution map of neural connections in the mouse brain. Built on an array of transgenic mice genetically engineered to target specific cell types, the Atlas comprises a unique compendium of projections from selected neuronal populations throughout the brain.


Projection Mapping image data detailing axonal projections labeled by viral tracers

  • Specific anatomic regions throughout the brain
  • Intrinsic Signal Imaging for detailed Visual Area projection mapping
  • Numerous defined neuronal populations
  • Stacks of two-dimensional images obtained by serial two-photon tomography
  • BDA vs. AAV for direct comparison of data derived from both conventional and viral tracing methods

Transgenic Characterization data detailing transgene expression in Cre or other driver lines

  • Adult and developing brain
  • Colorimetric in situ hybridization
  • Fluorescent in situ hybridization
  • Other histological methods

Anatomic Reference

  • Histology
  • Immunohistochemistry