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Mouse Brain Atlas Coordinate Viewer

Look up brain regions from stereotaxic coordinates and plan multi-target experiments with AP/ML and AP/DV scatter-plot visualization.

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Coordinate Lookup

AP -2.0, ML +2.0, DV -1.5

Region Search

Add to Target List

Uses current coordinates: AP -2.0, ML +2.0, DV -1.5

Add targets to see scatter-plot visualizations

All Regions (20)

  • Planning stereotaxic injection or recording coordinates
  • Identifying which brain region a coordinate falls within
  • Building a multi-target experiment coordinate list
  • Quick reference for common target AP/ML/DV ranges

Don't use for

  • As a replacement for the full Allen Brain Atlas plate viewer
  • For rat brain coordinates (use a rat-specific atlas)
  • For surgical navigation without independent atlas verification

The Stereotaxic Coordinate System

Mouse brain coordinates use bregma (the junction of coronal and sagittal sutures) as the origin.

Three axes: - AP (Anterior-Posterior): Positive = toward nose, negative = toward cerebellum - ML (Medial-Lateral): Distance from midline, typically reported for one hemisphere - DV (Dorsal-Ventral): Measured from skull surface, negative = deeper into brain

Common Injection & Recording Targets

The most frequently targeted regions in mouse neuroscience:

  • Hippocampus (CA1/CA3/DG): Memory, spatial navigation, epilepsy models
  • VTA/SNc: Dopamine circuits, reward, Parkinson's models
  • mPFC: Decision-making, working memory, psychiatric models
  • Amygdala (BLA): Fear conditioning, anxiety models
  • Striatum (CPu/NAc): Motor control, addiction models

Frequently Asked Questions

Next Steps

Stereotaxic Instruments

Frames, manipulators, and accessories for mouse surgery

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Injection Systems

Syringe pumps and microinjection equipment

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