Allen Brain Atlas

The Allen Brain Atlas is a free, publicly accessible resource from the Allen Institute for Brain Science. It offers:

• Anatomical reference plates: standardized coronal, sagittal, and horizontal sections with labeled brain regions at multiple anterior-posterior levels
• Gene expression data: in situ hybridization maps for thousands of genes across the entire mouse brain
• Connectivity data: projection mapping showing axonal connections between brain regions
• 3D reference space: a common coordinate framework (CCF) that enables comparison across experiments and labs

PanoBrain's Panolyzer software automatically registers each scanned brain section against the Allen Brain Atlas. The registration process:

1. Identifies the best-matching atlas plate based on tissue morphology
2. Applies non-rigid transformations to account for tissue deformation
3. Projects standardized region boundaries onto the experimental image
4. Assigns anatomical labels to every pixel in the section

Registration therefore allows region-specific quantification without manual ROI drawing, because the atlas defines every brain region automatically.