Allen Mouse Brain Atlas · drag-to-place trajectory
Coordinate frame
Surgery readout (from bregma)
Entry AP–
Entry ML–
Target AP–
Target ML–
Target DV–
Target region–
Depth (along probe)–
ML tilt–
AP tilt–
Angle from vertical–
Depth fine‑tune
3.00
Or drag the orange tip ball in 3D to aim & set depth at once.
Regions along track
Place a probe to see traversed regions.
View
Structures · 316 fine regions
Regions the probe crosses are highlighted automatically. Click any region in the lists to pin/zoom it.
How to use
• Drag empty space = orbit · wheel = zoom · Shift‑drag = pan.
• Click the brain to set the entry point on the surface.
• Drag the orange tip ball to aim the probe & set depth.
• Drag the cyan entry ball to slide the entry across the surface.
• Numbers update live in both Qiu2018 in‑vivo and raw CCF stereotaxic frames.
Geometry: Allen Institute CCFv3 structure meshes (decimated). Bregma at CCF
(AP 5400, DV 440, ML 5700 µm). Qiu2018 live‑brain scaling AP×1.031, ML×0.952,
DV×0.885 with −5° pitch. Estimates only — verify against your stereotaxic atlas.
Click the brain to drop the entry, then drag the orange tip to aim.