File Viewer


Run Anywhere

Compiled SpikeGLX releases contain two executables:

    SpikeGLX.exe        Full function, but needs NI-DAQmx software
    SpikeGLX-NISIM.exe  Full Imec function, simulated NI

SpikeGLX-NISIM.exe is provided so you can:


Opening a File Viewer

From main Console window, choose File/Open File Viewer then select any SpikeGLX bin file.

You can open several files, one Viewer for each.

You can view files from different runs at the same time. Linking is smart and only connects files within the same run.


File Viewer Titlebar

This shows the name of the open file, its channel count, the sampling rate, and some useful time information:

Note: Each Viewer is listed in the console Window menu. Select a window here to bring it front.


Shank Viewer

Click the Shank Viewer button in the upper-left corner of the File Viewer.

The Shank Viewer averages over the data currently visible in the File Viewer.


Linking (Time Axes)

Linked viewers send messages to each other so actions in one automatically update the others. These messages are passed:

To turn linking on, choose Viewer menu item File::Link (Ctrl+L). The link options dialog is shown. The currrent Viewer's context will be propagated to the other windows belonging to this run.

You can only link files of the same run. You can only link them if their bin and meta files are all stored in the same directory. Said another way, the path and file base name myRun_gXXX_tYYY are the association keys.


The Link command always opens a dialog in which you can select which streams from the current run you want opened. You can independently specify a list of imec AP files and imec LF files. When the dialog is closed, all the files (from this run) that are on screen will be linked.

Note 1: You can open and link 30 files at the same time BUT IT WILL BE SLOW AND NOT VERY USEFUL. Try a modest number of files.

Note 2: All the windows that are opened will get the current settings for filters and so on. Before linking, turn off all unneeded filters, and set a modest time range so that opening and arranging the new files will happen reasonably quickly.


Unlinking

When linking is on, scrolling in one window causes scrolling in other windows which is normally what you want, but if you're mostly looking at a particular file it will certainly slow you down. You can scroll faster like this:

  1. Turn linking off (Ctrl+U).
  2. Navigate manually (the windows are now independent).
  3. Make sure the view of interest is the frontmost window.
  4. Turn linking back on (Ctrl+L) in that window; the others will sync up to it.

Exporting a Subset of the Data

Open the Export dialog by: choosing File::Export, or pressing Ctrl+E, or right-clicking anywhere in the graph area.

The dialog offers several choices for the range of graphs (channels) to include and for the time span to include.

The next two sections explain how to graphically specify these selections before opening the Export dialog.


Selecting Channels to Show or Export

You can remove uninteresting channels from the view in two ways:

  1. In the Channels menu, toggle that channel off (uncheck it).
  2. Hover the cursor (mouse) over the right edge of the desired graph at its baseline (y=0). A red X will appear. Click this to remove the channel.
Close box

Close box

Channels can be restored in the Channels menu by toggling them on or choosing Show All.


Selecting Time Ranges

You can use click-and-drag to graphically select a time range either to zoom the current view, or to set a range for the export function.

For either type of drag operation the window will automatically scroll if you move the mouse beyond the right or left edge of the window.


Measuring Time Spans

Shift key + left-click & drag.

This sweeps out a colored bar that vertically spans across all channels. The Status area at the bottom reads out the width (time span). Use this as a straight-edge to see how events line up, or to measure time offsets between channels.

As above, it's also the way to select a time range for export.


Right-Clicking

Right-click anywhere in the graph area to get a menu of additional features.

ShankMap Operators

Only spiking channels have an associated entry in the stream's shankMap. The shankMap describes the location of the sensing electrode that's connected to each channel, and if that channel should be included in spatial averaging -<S> operations. Bad channels diminish the effectiveness of spatial averaging...

Note: None of these shankMap editing operations permanently alter the on-disk metadata.

Export


Performance Tips

Navigating is faster if less work is needed to update the view(s).

fin