Neuropixels Planner
An interactive 3D tool for planning Neuropixels probe trajectories on the Allen Mouse Brain atlas. Aim your probe, read out bregma-relative coordinates and arm angles, and see every brain region the track passes through — before you ever pick up a drill.
What it does
Planning a Neuropixels insertion means choosing where the probe enters the brain, what angle to set on the stereotaxic arm, and how deep to go — while making sure the track hits your target and avoids the wrong structures. The Neuropixels Planner lets you do all of this visually on a 3D mouse brain built from the Allen CCFv3 atlas, with a live-brain (Qiu 2018) coordinate correction, and hands you the exact numbers to dial into your rig.
How to use it
Set the entry
Click the brain surface to drop the probe entry point, or drag the cyan ball to slide it.
Aim & set depth
Drag the orange tip to aim the probe and set insertion depth in one motion.
Read the numbers
Get entry & target AP/ML/DV, ML/AP tilt, and a plain-language "set the arm" instruction.
Check the track
Review the ordered list of brain regions the probe crosses, with depth spans.
Highlights
Quick start
Click Launch Neuropixels Planner. Orbit with a drag, zoom with the wheel, then click the brain to drop your entry point and drag the orange tip to aim. The left panel updates live with the coordinates and arm angles to set on your stereotaxic rig. Numbers are planning estimates — always cross-check against your stereotaxic atlas.