Question 1

What angle conventions does this planner use?

Accepted Answer

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.

Question 2

Which atlas edition are the presets based on?

Accepted Answer

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.

Question 3

How is craniotomy diameter calculated?

Accepted Answer

Craniotomy diameter = probe diameter (0.5 mm default) + 2 $	imes$ tan(elevation angle) $	imes$ 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.

Question 4

Does this planner support different probe types?

Accepted Answer

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.

Question 5

How should I plan bilateral surgeries?

Accepted Answer

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.

Question 6

How do I correct for bregma-lambda distance differences?

Accepted Answer

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 $	imes$ (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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