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 Rotate the probe: ctrl + 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
  • Add probe: add a new probe (select probe type)
    • Neuropixels: select 1.0 (1 shank) or 2.0 (4-shank)
    • Cambridge Neurotech: load JSON file containing geometry for your probe (e.g. from this database)
  • Remove selected probe: remove selected probe (unless only 1 probe)
  • 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)
• 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)
• Connect
  • Manipulator
    • New Scale MPM: sync with New Scale MPM manipulator
    • Scientifica Patchstar: sync with Scientifica Patchstar manipulator
  • Recording
    • OpenEphys: send probe areas to OpenEphys
    • SpikeGLX: send probe areas to SpikeGLX
    • Set recording slot: set recording slot for each probe (if not in order, e.g. probe 1 in slot 1)
• Save/load
  • Save: save current probe positions (in CCF coordinates)
  • Load: load previously saved probe positions
  • NOTE: file format for save/load, this is a .mat file containing:
    • probe_positions_ccf: [N probes x 1] cell array, the cell for each probe is [3 x 2 x N shanks] with CCF coordinates as [AP(start,end);DV(start,end);ML(start,end)] x N shanks
    • probe_areas: [N probes x 1] cell array probe_areas: CCF structure tree entry for each area along the probe trajectory, with distance of area borders from shank tip in probe_areas{x}.tip_distance, and probe shank number as probe_areas{x}.probe_shank

Moving the probe

The probe can be moved with the arrow keys (+SHIFT: probe tip - changes rotation, +ALT: depth, +CTRL: rotation). Note that holding SHIFT+arrow keys changes the AP/ML position of the probe tip independently from the rest of the probe, which effectively changes the angle. This allows the user to precisely position both the top (arrow keys) and bottom (shift+arrow keys) of the probe:

Atlas

The atlas can be rotated by clicking and dragging (the slice updates when the mouse is released).

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 Probe tip changes 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