Example trajectory planning

Neuropixels trajectory explorer

On opening, the explorer looks like this:

Display regions of interest

1. Turn off the brain slice view (this can get in the way when trying to see 3D structures): Display > Slice > Anatomical (uncheck)

2. Add V1: 3D areas > Search areas > enter “primary vis” > select “Primary visual area” and hit “OK”

3. Add LGN: 3D areas > Search areas > enter “lateral gen” > select “Dorsal part of the lateral geniculate complex”

Set trajectory

4. Move the probe to intersect these two areas. One way to do this is:

• Press “Sagittal” button in lower left and set the AP coordinates:

• Place top of probe in V1: press down arrow (move probe posterior) until the top of the probe is in V1

• Move the probe pitch angle until the tip is in LGN: hold shift and press the up arrow (move probe tip anterior) until the tip is in LGN

• Press “Horizontal” button in lower left and set ML coordinates:

• Place top of probe in V1: press left arrow (move probe left) until the top of the probe is in the center of V1

• Move the probe polar angle until the tip is in LGN: hold shift and press the right arrow (move probe tip rightwards) until the probe tip is in LGN

• Press “Coronal” button in lower left and set depth coordinate:

• Move the top of the probe slightly out of the brain while keeping the tip in LGN (this gives a landmark at the top: the data should have a small region with no spikes, then the first spikes are at the top of V1): hold alt and press the up arrow (move the probe upward in the Z-axis)

Your final trajectory goes through all layers of primary visual cortex (~0.5-1.4mm) and the LGN (~3-3.5mm). To see the names displayed in full, go to Display > Region names > Full:

Using the trajectory

To use this coordinate during an experiment, note the probe coordinates in the top left:

How to use these numbers:

• Probe angle: set your manipulator azimuth/polar angle at 15 (relative to 0 = tail-to-nose) and elevation/pitch angle at 61 degrees (relative to 0 = horizontal)
• Probe insertion: these AP/ML coordinates (-3.37 mm AP, -2.59 mm ML) is where you will center your craniotomy, and where you will touch the brain before inserting the probe. Once the probe is touching the brain at this coordinate, insert the probe along the probe-axis to a depth of 3.38 mm
• Recording top: this is an FYI of the coordinate of the top of the probe
• Recording tip: this is an FYI coordinate of the tip of the probe
• Bregma-Lambda distance: this is the current scaling of the axis, and coordinates will change with a larger or smaller mouse. To manually set this, go to Brain scaling > set bregma-lambda distance: