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Brain Atlas Region Explorer

Search brain regions, look up stereotaxic coordinates, and plan injection volumes using Allen CCF reference data.

Stereotaxic SystemsAtlas ReferenceClient-Side
Tool details, related tools, and citation

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Load example Brain Atlas Region Explorer data to see the full workflow

Search Regions

Search for a region and select it to view details

  • Plan stereotaxic injection coordinates for mouse brain surgery
  • Look up brain region locations, volumes, and parent structures quickly
  • Estimate injection volumes and flow rates for viral vector delivery
  • Find the closest brain regions to a given set of stereotaxic coordinates
  • Export region data for inclusion in methods sections or lab protocols

Don't use for

  • As a substitute for a full stereotaxic atlas — verify coordinates against Paxinos & Franklin or Allen CCF
  • For rat, primate, or human brain coordinates — this tool is mouse-specific
  • For precise injection volume optimization — volumes are starting estimates that require empirical validation

Stereotaxic Coordinate Systems

Stereotaxic surgery in rodents uses a standardized coordinate system anchored to skull landmarks. The three axes are:

Anterior-Posterior (AP): Distance from bregma along the midline. Positive values are anterior (toward the nose), negative values are posterior (toward the cerebellum).
Medial-Lateral (ML): Distance from the midline. Positive values are lateral (away from midline). Most coordinates are given for one hemisphere; mirror for the contralateral side.
Dorsal-Ventral (DV): Depth from the brain surface (or skull surface, depending on convention). Negative values indicate deeper (more ventral) targets. DV coordinates are the most variable between animals and require careful zeroing at the brain surface.

Common Pitfalls in Stereotaxic Targeting

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

Frequently Asked Questions

Next Steps

Stereotaxic Systems

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