SpikeGLX Tutorial
IM Setup Tab
IM Setup Tab Features
•Low latency
•Filtered IM streams
•LED
•IMRO editor
•Site selection tips
•Bad channels
•Channel map
•Save channels
These settings are per probe.
Double-click in the highlighted areas to
activate editors:
•LED: Enables blinking LED on headstage
for animal tracking.
•IMRO: Graphical editor to select
electrodes, referencing and more.
•Bad: Disable listed amplifiers. They will
appear as zero volts and be marked in
metadata, excluding them from CAR in
SpikeGLX and CatGT.
•Chan Map: Use this to alter the order
that channels are displayed in the
Graphs window.
•Save: This determines which channels
are saved in files.
This is the graphical IMRO editor for site selection, and other settings.
Here the non-site controls are highlighted. The choices here apply to all
channels:
•Which type of reference
•AP and LF band gains
•Whether the AP-file data are AP-filtered, or full-band.
Any settings other than default must be saved in a file. Saved files can be
loaded. Press ‘Default’ at any time to revert to all default settings.
To select sites, use the ‘Boxes’ group of controls. Set how many rows tall
and how wide you want the boxes to be…then just click on the shank to
place a box. Keep placing boxes until 384 sites are enclosed.
•Boxes can be different sizes
•You can drag an existing box top/bottom edge to resize it
•Shift-click a box to erase it
Click ‘Boxes => file chans’ to turn your current boxes into a save channel list
Sites Selection Tips
Edit/Save an IMRO file while looking at activity heatmaps and anatomy
data overlaid onto the probe. You can do that here:
•Online Graphs window : ShankViewer : Edit tab.
•Offline FileViewer : ShankViewer : Edit tab (any run).
•Offline FileViewer : ShankViewer : Edit tab (survey run).
On IM Setup tab, click IMRO Editor : Load, to use file for a new run.
This orders Graphs window
traces when you click ‘Usr Order’
there. For any non-default order
you need to save a file.
You can edit the order column on
the left which is cumbersome.
Better, you can select {base-to-
tip, tip-to-base} using the ‘Auto-
arrange’ box.
Or ‘Arrange by list.’ A handy way
to use this is to first apply tip-to-
base using Auto-arrange. Then if
you want that order but want to
move channel 100 to the
beginning, enter ‘100’ in the
Arrange box and ‘Apply.’
Right-click on Graph window
traces to get this tool at run time.
You don’t have to save all channels in your files.
Use ‘Autofill’ to just save channels in the tissue, given
by row # or distance from tip.
Or, explicitly list channels to save.
For probes with an LF-band, use the ‘Force LF’ box to
automatically save the LF channels that match the AP
channels you list.
SY is always saved.
Right-click on Graph window traces to get this tool at
run time if you are not currently writing files.
Alternatively, the IMRO editor also lets you graphically
select save channels by drawing boxes around them.
