Topics:
Method menu adds capabilities…Set the method to Lclk Center Green Here
and the behavior is the same as before. Placement of green ROI boxes
works the same, and blue conflict boxes work the same.
Set method to Lclk Where => Rclk What to
make a cyan box, then right-click the cyan box for a pop-up menu of
options:
Half- or Full-width cyan box
Smart fills, full-width only
Filling works from tip to top and observes the Rqd
maximum.
Load and view an existing file without applying.Default to {bank-0, ext ref, std gains, std filter}
without applying.Save as a file without applying.OK applies saved changes to new configuration.Cancel reverts to prior configuration.Apply saved changes to current run.Revert to current settings.Pix/pad box.A typical probe has 1000+ electrode sites, but, to keep the probe thin, compact, lightweight, and preserve high sample rate, you must select a smaller subset (typically 384) for readout.
The editor helps you visually select the sites you want: your region
of interest (ROI). The ROI, your differential referencing choice, and a
few other channel parameters are stored in an imro table
data structure, and these are made portable by storing them in
imro files.
The editor can be accessed from many situations:
You can use the included SpikeGLX_NISIM.exe to access the offline editor from any Windows PC. No need to install NI drivers or any additional environments or tool/library packages.
A strictly offline, Linux version of SpikeGLX_NISIM is available here.
How to choose sites?
Looking at overlays is best…
The best way is to (1) Do a survey run to sample activity everywhere on the probe. (2) Review the survey in the FileViewer which paints an activity heatmap on the probe. Use that context to select sites having desired levels of activity, or desired responses to stimuli. Learn about that here.
You can overlay the ShankViewer with anatomy data. Use that context to select sites in relevant brain regions. If using Pinpoint, anatomy can be applied in online or offline ShankViewers. Anatomy colors the space outside of shanks, so you can see anatomy and activity at the same time.
During an online run, before you start recording files, you can open the editor tab and try several different ROIs to hunt for desired activity. This affords some degree of feedback.
If you don’t have a clue yet, use a standard guess:
Default imro, which is random, but
super easy.In the editor you don’t need to click on 384 individual sites, though you can. Rather, you work with larger boxes of sites. There are several types of boxes:
Green: These are your selected ROI boxes. You’ll create as many green boxes as needed to lasso interesting clusters of sites. The editor guides you so you won’t select more than the required site count (usually 384), and you won’t put boxes in forbidden places.
Heavy Black: Every probe has selection rules: If you choose this site, you can’t select those. As you make green boxes, the corresponding excluded sites are automatically outlined with heavy black boxes. This shows you which areas of the probe remain available for new green boxes. When your required site count is reached all the black boxes disappear, meaning “you’re done.”
Cyan: The recently added Where/What
method uses cyan to indicate a potential action box. Right-click in a
cyan box to get the pop-up menu. Fill the available space with new green
boxes (several fill patterns available), or, delete the overlapped green
space, so you can make alternate green boxes elsewhere. The filling
actions work from tip toward the top and will not go over the
Rqd limit. The cyan box is erased when an action
completes.
Blue: These are visual aids that do not affect your site count. They help with conflict resolution. For example, you’ve created a number of green boxes and you see that a key activity hot spot is now in a forbidden area but you really want to include it…you’ll have to undo some of the green, but which green is involved? Control-click a blue box over the hot spot and all related sites are outlined with heavy blue boxes. You’ll be able to see what needs adjustment.
The Rqd readout reminds you how many total
channels/sites you must select to make a valid table. Most probes have
384 channels that are shared over the whole probe surface. Some probes
have fewer than 384 readout channels, NP3 probes have 912 or 1536
channels, and quad-probes have 384 channels on each of the four shanks.
In all cases, Rqd tells you the required total channel count.
Sum is the channel count summed over your current set of
boxes. You are done making a valid ROI when Sum =
Rqd.
When you click in an existing box Sel reads out its
size, in channels.
All Boxes
Nrows sets the height (in rows) of new boxes.Width either to full- or half-shank.You can left- or right-click to make the new box.
Green: Lclk Center Green Here
Clicking directly makes green boxes:
Cyan: Lclk Where => Rclk What
Clicking makes a cyan action box.
Left-click to make a box (handy for resizing), right-click to make the box and immediately show the menu (fewer steps).
Blue: Control-click
All Boxes
Click-and-drag in the upper-half of a box to adjust its
top edge.Click-and-drag in the lower-half of a box to adjust its
bottom edge.Green: Lclk Center Green Here
Cyan: Lclk Where => Rclk What
Max Box Length extends the box to the full
shank height.Clear All button erases green and cyan boxes; not
blue.Shift-click in any box to clear it.Note: Blue boxes only go away when you manually shift-click in them. Otherwise they stay put even if you load alternative IMRO files.
Sum is
nonzero.IM Setup tab, but the current list of channels reflects
your current boxes.Recently, other developers are making imro editor tools:
We do not test, endorse, or attest to the fitness of third party tools.
Pixels/pad box.For dual-band probes, like NP 1.0, shift+click on a
viewer pad to select LF.T and antibounce
Stay low settings only apply to spike detection.Update (s) interval to
visualize infrequent activity.Raw data -> Fetcher -> Graphs -> Shank
Every tenth of a second a process thread called the ‘graph fetcher’ grabs the next chunk of raw data from the main data stream and pushes it to the Graphs window. The stepping of the visible time cursor across the screen heralds these events.
If the corresponding Shank Viewer is visible, the Graphs window pushes a copy of the unmodified raw data chunk to the Shank Viewer. Importantly, the filter choices in the Graphs window do not affect the Shank Viewer; each does its own filtering/processing.
Note that clicking Pause in the Graphs window
pauses/resumes both the graphs and the shank activity mapping.
When data are drawn from the raw streams, the Shank Viewers apply a
300Hz high-pass filter to AP-band data, and a
0.2Hz - 300Hz bandpass to LF-band data. No CAR filtering is
done on raw online streams.
Use the Configuration dialog/IM Setup tab to enable
prefiltered AP-band streams that run in parallel with the raw streams.
You can select the AP-bandpass edges. Global demux is always applied.
Using this filtered stream improves signal-to-background in both audio
output and Shank Viewers (for {spike, AP pk-pk} calculations). There is
a checkbox to disable this feature just in case you are running out of
RAM or CPU, but we don’t think this will be necessary unless you are
running 12 probes or more at the same time.
Colorizing by spike rate or AP peak-to-peak voltage first applies a
300Hz high-pass filter then optionally applies a global CAR filer. Turn
the CAR filter on or off using the Gbl dmx checkbox.
Turning CAR off can make it much easier to visually identify the
boundary between tissue and outside. Point the cursor at the boundary to
read out the row. Enter that row in the Max row box to
exclude electrodes outside the brain when ‘Gbl Dmx’ is on. Setting
-1 turns the Max-row feature off (‘Gbl Dmx’ uses all
channels when it is on).
Average current window applies a 300Hz high-pass and
optional global CAR filter, then counts spikes and tallies peak-to-peak
voltages over the data currently displayed in the File Viewer window.
The Shank Viewer updates as you scroll.
Sample whole survey is specifically for viewing survey
result files. It averages up to four half-second time chunks drawn from
each of the banks on the probe to build a whole-probe activity map. You
have to click Update whole survey to trigger the
calculation. If you change {Gbl dmx, Max row,
T(-uV), Stay low} you need to click
Update again.
You can read an appropriate threshold level from a graph:
300 - INF (approximates
Shank View filtering).This value gives you a rough spike width filter. Our spike detection logic requires that the signal cross the threshold (from high to low) and continuously stay low for at least this many samples.
Unfortunately, if you’ve got a lot of electrical noise, the signal could cross back and forth rapidly across the threshold. The detector thinks such spikes are narrow and they are rejected if ‘stay low’ is too high.
If your spike rates seem too low, try lowering ‘Stay low’.
To directly examine the noise in a selected graph:
Pause button to freeze the display for a better
look.This item group interacts with the Pinpoint and Trajectory Explorer real-time anatomy programs. The box receives a list of color-coded region labels. The checkboxes let you apply anatomy color separately to the shanks and to the traces in the Graphs Window.
Right-click on a viewer pad to select more channel-specific options.
fin