Search brain regions, look up stereotaxic coordinates, and plan injection volumes using Allen CCF reference data.
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Load example Brain Atlas Region Explorer data to see the full workflow
Search for a region and select it to view details
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No atlas coordinate guarantees accurate targeting in every animal. Post-hoc histological verification (e.g., DAPI staining, reporter expression) is essential to confirm injection placement and should be reported in publications.
Measure bregma-lambda distance in each animal. If it differs from the atlas reference (4.21 mm for C57BL/6J), scale AP coordinates: adjusted_AP = atlas_AP (measured_BL / 4.21). This single correction can significantly improve targeting accuracy.
DV coordinates in this tool are referenced from the brain surface. Some protocols reference from skull surface or dura. Document your reference point and be consistent. Brain surface reference is generally more reproducible for cortical and hippocampal targets.
Faster injection rates cause more backflow and irregular spread patterns. For small nuclei (< 1 ), use the lower end of the flow rate range (50 nL/min) and the longer wait time (10 min) to maximize on-target delivery.
Region coordinates are approximate centers of mass derived from the Allen Common Coordinate Framework v3 (Wang et al., 2020) for the adult C57BL/6J mouse brain. Injection volumes calculated as 3% of region volume, clamped to 50–500 nL range. Flow rates (50–100 nL/min) and wait times (5–10 min) follow published best practices for viral vector delivery. Coordinate lookup uses Euclidean distance to region centers.
Last validated 2026-04-08. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
ConductScience Brain Atlas Region Explorer (v1.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/brain-atlas-region-explorer
Wang Q et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell. 2020;181(4):936–953.
Paxinos G, Franklin KBJ. The Mouse Brain in Stereotaxic Coordinates. 5th ed. Academic Press; 2019.
Stereotaxic surgery in rodents uses a standardized coordinate system anchored to skull landmarks. The three axes are:
Several factors can cause missed targets in stereotaxic surgery:
• Bregma-lambda distance variation: Individual animals vary in skull size. If bregma-lambda distance differs from the atlas reference (4.21 mm for C57BL/6J), scale AP coordinates proportionally • DV zeroing errors: Whether DV is measured from skull surface, dura, or brain surface changes the effective depth by 0.1–0.3 mm • Age and sex differences: Atlas coordinates are typically for 8–12 week male mice. Younger, older, or female mice may require adjustments • Needle angle: Angled approaches (necessary for some deep targets) require trigonometric correction of AP and ML coordinates • Brain shift: Removing bone and dura can cause the brain to shift, particularly for superficial cortical targets • Injection spread: Viral vectors spread beyond the injection site. AAV serotypes, promoter, and titer all affect the effective transduction volume
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