When to use
- 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
ToolsConductScience tool
NeuroscienceFree in-browser calculator
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.
PrivateData stays in your browser
LiveNo sign-up required
Validated2026-04-08
CitableMethods and citation included
Calculator
Results update in placeCoordinate 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)
Do not 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
Always verify with atlas plates
Bounding boxes are approximate. Confirm targets on the coronal section at your specific AP level.
ML is absolute distance
ML values are reported as absolute distance from midline. For left hemisphere injections, the coordinate is the same; just position the manipulator to the left.
DV depends on skull angle
DV is measured from skull surface with a level skull. Use the Bregma-Lambda Helper to correct for tilt before targeting.
Strain matters
Coordinate atlases are based on C57BL/6. Other strains may need proportional scaling based on bregma-lambda distance.
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Method
Region bounding boxes derived from the Allen Mouse Brain Atlas (C57BL/6J reference) and Paxinos & Franklin Mouse Brain in Stereotaxic Coordinates (4th ed.). Coordinates are approximate for planning purposes.
2
Validated
Last validated 2026-04-08. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
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How to cite
How to Cite
ConductScience Mouse Brain Atlas Coordinate Viewer (v1.0). ConductScience, Inc. 2026. https://conductscience.com/tools/mouse-brain-atlas-coordinate-viewer
Paxinos G, Franklin KBJ. The Mouse Brain in Stereotaxic Coordinates. 4th ed. Academic Press; 2019.
Lein ES et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007;445:168-176.
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
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