SpikeGLX
Highlights, hints and tips
UCL Course 10/14/2024
Resources (all free, open source)
•Download page, it’s all here: https://billkarsh.github.io/SpikeGLX/
•Get the latest version: bug fixes, richest metadata
•Quick-ref: tour all the main features
•Videos
•Manuals and help documents
•Metadata Guides, Latest items:
•GeomMaps
•Tip Length
•Anatomy
•Probe error flags
•Mux Table (helps 3rd-party software do multiplexing time-shift corrections)
Metadata complete: Everything you need to know about THIS probe is in there…
3rd-party processing tools don’t need tables of auxiliary data.
Probe Geometry (Metadata ~snsGeomMap)
Z=0
tip length
X=0
X=0
X=0
X=0
width
shank spacing
Z
X
•Replaces ~snsShankMap.
•Gives locations of all selected sites on
the probe surface in microns.
•Uses coordinate system shown here.
This is described in ‘Metadata_30’ guide
How to Run
•New Acquisition (Ctrl+N)
•Configure dialog ->
•Data flow: Follow the tabs:
•Which hardware
•Hardware parameters
•Synchronizing the hardware
•How/when files are written
•Where to save data, what to call it
•Context help at each step
Where I plugged my probes,
Which {slot port dock}. NEW:
Slots can be PXI, OneBox, Sim.
All NI devices are here Help on current tab
? in title bar = more help
OneBox ! ?
•8 x 8 X 1 inches
•USB 3.0
•2 probe ports
•12 Aux analog channels in
•12 analog out
•~ 3600 EUR
•Order: Neuropixels.org
Quickstart Guide:
•SpikeGLX/_Help
•Online
Assign slot to each OneBox!
1. Add…
2. Browse for run file
3. Assign { slot port dock }, double-click the cells
4. Click Enable
Devices Tab
IM Setup Tab
•Lower latency remote fetching NEW!!
•Survey mode
•Check box, secs/bank
•FileViewer to see survey
•Filtered buffers NEW!!
•Check box, bandpass
•Better SNR:
•Audio
•ShankViewer
•SpikeViewer
•IMRO editor
•Double-click cell
See, context sensitive
1. Set rows/box
2. Set width {full, half} shank
3. Click to place centers of boxes
4. Resize; shift-click to remove box
5. When sum = rqd, save as a file
But this is much cooler
when you can see the
activity on the shank…
And you can:
1. Online in ShankViewer
2. Offline in FileViewer
ShankViewer Edit tab!!
IMRO Editor
Green boxes
select sites
for readout
Right-click to see
more commands
Right-click menu
ColorTTL
Track up to 4 TTL channels
Each a different color
Note:
Anatomy simulated for
illustration purposes
Anatomy
stuff is on the
ShankViewer
‘View’ tab.
•Link
•Ctrl+click = zoom
•Shift+click = meas. span
•Open survey
•Integrate activity
•Select hotspots
Other SpikeGLX Features
•Windows::More Traces (ctrl+T) :
opens a second Graphs window
with two more streams and
ShankViewers.
•Windows::Run Metrics (ctrl+M) :
Monitors performance of
SpikeGLX.
•Graphs Window lower-right
menu : select layout of trace
viewers.
Near Term SpikeGLX Features
•Click-to-listen shortcut
•Waveform designer + triggered playback (OneBox, NI)
•PSTH for opto-tagging
•Support ONYX Commutator + IMU headstage
Scripting (‘SDKs’)
•C++
•C
•C#
•Python
•MATLAB
Control everything
Get real-time data, extend SpikeGLX feature set
Mean 4.8 Mean 3.6
SpikeGLX Ecosystem (all on download page)
•SpikeGLX Acquisition, Offline FileViewer
•Remote SDKs Remote control / scripting
The postprocessing tools are maintained alongside SpikeGLX, they are aware of
all the options and variety of data types and formats in SpikeGLX:
•CatGT Filter, Remove artifacts, Extract TTL evens, Join/split runs
•C_Waves Fast mean waveform calculator
•TPrime ‘Aligner’ = Translate event time from stream to stream
•ecephys Pipeline that runs the above and Kilosort in one package
Jennifer Colonell modified Allen Inst (Josh Siegle) version of ecephys for SpikeGLX data
