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Stereotaxic SystemsFree in-browser calculator

Stereotaxic Trajectory Planner.

Plan probe trajectories with 12 Paxinos & Watson atlas presets, multi-probe clearance checking, and craniotomy sizing for stereotaxic surgery.

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When to use

  • Plan single or multi-probe stereotaxic insertions with atlas-based target coordinates
  • Calculate skull-surface entry points for angled probe approaches
  • Size craniotomy diameter based on insertion angle and skull thickness
  • Check clearance between multiple simultaneous probe insertions
  • Generate surgical checklists with coordinates, depths, and verification steps

Do not use for

  • As a substitute for atlas verification — always confirm coordinates in the printed atlas or digital atlas software
  • For species other than rat without manually entering species-specific coordinates
  • When skull is not properly leveled — angle calculations assume a flat skull reference

Always level the skull before taking coordinates

Stereotaxic calculations assume bregma and lambda are in the same horizontal plane. A tilted skull introduces systematic AP and DV errors that compound with depth. Verify that the bregma-lambda DV difference is < 0.1 mm and check bilateral ML symmetry.

DV coordinates are measured from skull surface, not brain surface

Atlas DV coordinates reference the skull surface at bregma. After craniotomy, the brain surface may be 0.5–1.0 mm below the skull. Some protocols measure from dura or brain surface — confirm which convention your coordinates use before entering values.

Angled approaches shift the entry point significantly

Even a 10° elevation angle shifts the skull entry point by ~1.5 mm for a typical 8.5 mm insertion. Use this planner to calculate exact entry coordinates and avoid accidentally drilling over a sinus or suture line.

Skull thickness varies by region and age

The default skull thickness of 0.5 mm is typical for adult rats at the parietal bone. Frontal bone and occipital regions may be thicker (0.8–1.2 mm). Younger animals have thinner skulls. Measure at the craniotomy site with a depth gauge when possible.

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Method

Entry-point coordinates are computed by projecting the probe shaft vector from the target back to the skull surface: AP_entry = AP_target + depth ×\times sin(elevation) ×\times cos(azimuth), ML_entry = ML_target + depth ×\times sin(elevation) ×\times sin(azimuth). Insertion depth = (|DV_target| + skull_thickness) / cos(elevation). Clearance is evaluated by sampling 20 points along each shaft and computing pairwise Euclidean distances. Atlas presets sourced from Paxinos & Watson, The Rat Brain in Stereotaxic Coordinates, 6th ed.

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Published

Published 2026-04-08. Calculations support planning and documentation; verify procurement decisions against manufacturer specifications or institutional SOPs.

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How to cite

How to Cite

ConductScience Stereotaxic Trajectory Planner. ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/stereotaxic-trajectory-planner

Paxinos G, Watson C. The Rat Brain in Stereotaxic Coordinates. 6th ed. Academic Press; 2007.

Cetin A, Komai S, Eliava M, Seeburg PH, Osten P. Stereotaxic gene delivery in the rodent brain. Nature Protocols. 2006;1(6):3166-3173. doi:10.1038/nprot.2006.450

Frequently asked

What angle conventions does this planner use?
Elevation is measured in degrees from vertical (0° = straight down). Azimuth is measured in degrees from the anterior direction (0° = anterior, 90° = lateral). This matches the convention used by most digital stereotaxic instruments. All angles are entered in degrees and converted internally to radians for trigonometric calculations.
Which atlas edition are the presets based on?
The 12 built-in presets use coordinates from the Paxinos & Watson rat brain atlas (6th edition). All coordinates are in millimeters relative to bregma (AP and ML) and the skull surface (DV). For mouse coordinates, you can enter custom values from the Paxinos & Franklin mouse brain atlas or the Allen Brain Atlas. Always verify coordinates against the atlas edition that matches your animal’s strain and weight.
How is craniotomy diameter calculated?
Craniotomy diameter = probe diameter (0.5 mm default) + 2 ×\times tan(elevation angle) ×\times skull thickness + 0.5 mm safety margin. For vertical insertions, this gives a 1.0 mm diameter. Angled insertions require wider craniotomies because the probe crosses more of the skull at an oblique angle. The safety margin accounts for drill tolerance and dural deflection.
Does this planner support different probe types?
The calculator uses a default probe diameter of 0.5 mm, which is typical for standard cannulas and electrode probes. The probe length input (default 10 mm) sets the maximum insertion depth warning threshold. For fiber optic cannulas (typically 200–400 µm core), tetrodes, or silicon probes, the trajectory math is identical — the key parameters are target coordinates and insertion angle.
How should I plan bilateral surgeries?
Add two probes with identical AP and DV coordinates but mirrored ML coordinates (e.g., ML +2.0 and ML −2.0). The clearance checker will verify that the two probes do not conflict. For bilateral angled approaches, you may need to angle each probe laterally (azimuth 90° or 270°) to avoid the sagittal sinus. Always check clearance with the multi-probe view before drilling.
How do I correct for bregma-lambda distance differences?
The Paxinos & Watson atlas assumes a standard bregma-lambda distance of approximately 9.0 mm for adult rats. If your animal’s measured distance differs, apply a linear scaling factor: adjusted coordinate = atlas coordinate ×\times (measured distance / 9.0). This is especially important for AP coordinates in younger or smaller animals. Measure bregma-lambda after leveling the skull.
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