General use

A video demo of usage (from the UCL Neuropixels 2021 course on a slightly older version) is here: https://www.youtube.com/watch?v=ZtiX0iunUTM

Overview of interface

Controls

Moving the probe: arrow keys Insert/retract the probe: alt + arrow keys Move probe tip independent from top (changes probe angle): shift + arrow keys Select probe (if more than one): click on probe, selected is blue

Menu descriptions:

• Probe controls
  • Display controls: pop up box with probe controls
  • Set entry: move probe to specific entry coordinates
  • Set endpoint: move probe to specific endpoint coordinates (NOTE: this uses the roughly approximated bregma DV position)
  • Add probe: add a new probe
  • Remove probe: remove selected probe (unless only 1 probe)
• Brain scaling
  • Set bregma-lambda distance: set to rescale brain (relative to standard average 4.1 mm)
• 3D areas
  • List areas: choose from list all areas in the CCF
  • Search areas: search CCF areas (e.g. search for "CA1" to find what the CCF calls "Field CA1")
  • Hierarchy areas: pick CCF area by regional hierarchy
  • Remove areas: select previously drawn 3D areas to remove
• Display
  • Trajectory areas: Areas to show in right-hand plot (areas along current probe position or full trajectory)
  • Region names: display full or abbreviated region names under right-hand areas plot
  • Slice: brain slice between anatomy (greyscale), CCF regions (with CCF-assigned colors), or off
  • Objects: visibility of objects (brain, probe, 3D areas, dark mode)
• Manipulator
  • New Scale MPM: sync with New Scale MPM manipulator
  • Scientifica Patchstar: sync with Scientifica Patchstar manipulator
• Save/load
  • Save: save current probe positions (in CCF coordinates)
  • Load: load previously saved probe positions
    • you can load in a manually created file containing the probe_positions_ccf cell array described below
  • NOTE: file format for save/load, this is a .mat file containing:
    • [N probes x 1] cell array probe_positions_ccf: each cell contains CCF coordinates in native order (AP,DV,ML) for top/bottom of probe as: [AP top, AP bottom; DV top, DV bottom; ML top, ML bottom]
    • [N probes x 1] cell array probe_areas: CCF structure tree entry for each area the probe passes through, with depth added as probe_depth (e.g. the areas on probe 2 is probe_areas{2}, the info for the first area on probe 2 is probe_areas{2}(1,:), and the depth along the probe for that area is probe areas{2}.probe_depth(1,:)).

Atlas

The atlas can be rotated by clicking and dragging (the slice updates when the mouse is released). The probe can be moved with the arrow keys (+SHIFT: rotation, +ALT: depth).

Probe areas

These are the regions that the probe (blue line) is passing through

Practical use of Neuropixels coordinates for experiments

The coordinates of the probe are displayed above the atlas relative to bregma (anterior/posterior and medial/lateral) and the brain surface (depth, axis along the probe)

The Probe insertion coordinate is the point at which the probe is inserted into the brain. The Recording top/tip are the coordinates for the top and tip of the recording sites. The Probe insertion does not change with depth (the insertion point is the same, regardless of how deep the probe is), while the Recording top/top change with depth (since these are the coordinates for the active sites), as illustrated here:

The angles of the manipulator are displayed as the azimuth (polar) relative to the line from tail to nose, where 0 degrees means the probe is coming straight from behind the mouse, and to the elevation (pitch) relative to the horizontal, where 90 degrees means the probe is going straight downward.

During the experiment:

• Position the manipulator angles in azimuth/polar and elevation/pitch
• Position the probe tip over bregma and zero the AP/ML coordinates
• Move the probe tip until it's lightly touching the brain at the desired AP/ML coordinates
• Zero the depth coordinate (along the probe-axis), then descend until the desired depth is reached