bregma·lambda : mouse stereotaxic trajectory planner

/01 Inputs

Target · mm from bregma

AP + ant − post

ML + right − left

DV depth · sign ignored

DV reference where DV = 0

Probe anglesDegrees from vertical. 0 = straight down.

ML tilt tip toward + ML

AP tilt tip toward + AP

Bregma offset (µm in CCF)Tune if regions look off. If targets at AP=0 look ~0.3–0.5 mm anterior in your mouse, try AP = 5700–5800.

AP Chon 5400, alt 5739

ML Chon 5700

DV Chon 332

Probe geometry

Custom probe width µm

Show Allen region outlines

OptogeneticsPredicted light spread from a flat-cut fiber at the probe tip. Kubelka–Munk model (Aravanis 2007 / Yizhar 2011; equivalent to the Stanford Deisseroth-lab calculator).

Show light spread

Bilateral mirror across midline · sums in overlap

Wavelength sets scattering S

Scattering S mm⁻¹, gray matter

Fiber NA

Fiber core diameter is taken from Custom probe width above (defaults to 400 µm).

Output power mW at tip

Threshold iso-line mW/mm²

Axis conventions

AP anterior(+) / posterior(−). ML right(+) / left(−). DV depth into brain : sign ignored.

ML tilt: rotation in the coronal plane. Positive tilt sends the tip toward +ML, so the entry hole sits on the −ML side of the target.

AP tilt: rotation in the sagittal plane. Positive tilt sends the tip toward +AP, so the entry hole sits on the −AP side of the target.

/02 Atlas Views

Coronal ML horizontal · DV vertical

− ML left + ML right

Sagittal AP horizontal · DV vertical · anterior right

− AP posterior + AP anterior

Method: CCFv3 to stereotaxic corrections applied

Allen CCFv3 is not stereotaxic. Wang et al. Cell 2020 explicitly state it is "not suitable for determining stereotaxic coordinates." The atlas was built without skull fiducials, so bregma position, pitch, and absolute scale all need correction.

This coordinate planner applies the following corrections in order:

Pitch +5.0° rotation around bregma. The atlas brain sits tilted ~5° nose-up relative to a real mouse on a stereotaxic frame with bregma and lambda at the same DV. To compare apples to apples we rotate every atlas point around bregma onto the flat-skull plane. Effect: brain becomes shallower at posterior AP, deeper at anterior AP. Source: Pinpoint / Virtual Brain Lab in-vivo alignment docs.
Per-axis scale using the Pinpoint convention: in_vivo = (1.031·ap, 0.952·ml, 0.885·dv). The CCFv3 reference brain is roughly ~15% larger by volume, but the per-axis errors are not equal. DV is the biggest correction: atlas DV is ~11.5% too deep, so we multiply atlas DV by 0.885. ML is ~5% too wide (×0.952). AP is actually slightly too short in the atlas: ×1.031 expands it back. The previous version applied an isotropic 0.95 which is why DV was reading too deep until now.
Bregma offset (AP, ML, DV) in µm, tunable in the left panel. This sets which CCF voxel is treated as the bregma origin. Chon 2019 defaults are 5400 / 5700 / 332. Many labs find AP closer to 5700:5800. Calibration persists in localStorage.

Tweak CCF_PITCH_DEG, CCF_AP_SCALE, CCF_ML_SCALE, CCF_DV_SCALE or SKULL_THICKNESS_MM near the top of the JS block if your strain or age systematically differs.

Surfaces drawn on the canvas:
  solid amber: local outer skull (atlas pial minus 200 µm)
  faint cyan: atlas brain pial (rolling-min smoothed across midline fissure)
  dashed amber: bregma plane (stereotaxic DV = 0), tilted after pitch correction

Real mouse skulls still vary by ±0.5 mm even after all corrections. Trust your dura-touch over any atlas number.