SpikeGLX Tutorial
Probe and OneBox Basic Run
How to Run a Probe and OneBox XIO Stream
•Set parameters
•Run
•View traces
•View probe
•Record files
•Find files
•View files
In this example:
•I set the OneBox slot = 21.
•I only need 1 Dock/port for my 1.0 probe.
Check the ‘Enable’ box for the probe in
port 1 and the OneBox XIO (auxiliary I/O
stream).
Check ‘Include probe checks` which tests
for broken shanks and quality of probe-
headstage connection.
Click ‘Detect.’
Detect talks to the hardware to check that
selected items are present and working.
All device info and your settings will be
stored in run metadata.
Visit the tabs from left-to-right to
complete run setup. Settings from the last
run are retained; just review if that’s what
you want this time.
This is a good set of defaults for probes.
Two key features, though…
Double-click here to select electrodes
and other probe settings; covered in
another tutorial.
This button always opens help for
the current tab
Double-click here to name analog output
channels. These are controlled from SpikeGLX
remote SDK. Note that Waveplayer requires
channel-0.
Double-click here to name analog input
channels. These are recorded into data files
‘myrun.obx0.obx.bin.’
The twelve channels [0-11] can each be
used exclusively as input or output.
Select the OneBox (slot 21) as the sync
square wave source.
Sync will be recorded in the SY word of
the probe stream and the OneBox XIO
‘obx’ stream. No other wires required if
only device is a single OneBox.
These are good defaults for the Gates tab.
These settings:
•Control recording with Record button.
•Show the Record button (Graphs window).
•Wait until the button is clicked.
•Stop recording when clicked again.
This is simplest Triggers tab option.
These settings:
•Control recording with Record button.
•Wait until the button is clicked.
•Stop recording when clicked again.
Other options covered in another tutorial.
Here you set:
•Where to save run files.
•The run name.
•If each probe has its own subfolder.
Click ‘Update’ to see how long you can record
before you fill up the disk. It’s optional, just FYI.
Filling up the disk may corrupt your data files.
When happy with settings click either:
•Verify: Just check settings.
•Run: Check settings and start if all OK.
If any settings are out of range or conflict, you’ll
get a message about what to fix.
Verify and Run both save all settings; they are
preloaded so you can make an identical run
next time.
Type notes here to add to the recorded
metadata files
When you click ‘Run’
the hardware is
configured and data
acquisition starts.
This ‘Graphs’ window
pops up. You have a lot
of options here to look
at the quality of the
data; we cover that in
another tutorial.
When you’ve verified
data quality, click
‘Enable Recording’ to
start making files; click
again to stop recording.
Click ‘Stop Acquisition’
to stop the run and turn
off hardware (or click
Close box).
Click on the shanks icon
(highlighted) to open an
‘Online ShankViewer.’
On its View tab:
•Select activity heatmaps
•Navigate to channels
•Right-click for more ops
•View anatomy context
•Change views anytime
On its Edit tab:
•Change site selection
•Change referencing
•You can change probe
settings interactively
whenever file recording
is OFF.
Covered in another tutorial.
I recorded for a few seconds to create a set of output
files. This is Windows File Explorer. Our ‘data
directory’ where all runs are stored is named
‘Tutorial’ here. Inside is our run…
This recording created:
run1_g0 // run folder
….run1_g0_imec0 // probe-0 folder
……..run1_g0_t0.imec0.ap.bin // ap-band binary
……..run1_g0_t0.imec0.ap.meta // ap-band metadata
……..run1_g0_t0.imec0.lf.bin // lf-band binary
……..run1_g0_t0.imec0.lf.meta // lf-band metadata
….run1_g0_t0.obx0.obx.bin // obx binary
….run1_g0_t0.obx0.obx.meta // obx metadata
We cover file naming in another tutorial.
To view recorded data files, go to the SpikeGLX Console
window (Log window) and choose File::Open File Viewer.
A Windows File dialog will open. Navigate to any SpikeGLX .bin
file and select it.
Here I selected the ap-
band file from our run.
There’s a lot you can do
in this viewer, and we’ll
cover it in another
tutorial.
You can safely explore
the tools…nothing will
change the data in the
files.
Highlighted:
•Channel scrollbar
•Time scrollbar
•Help for window
•Offline ShankViewer
