SmartBox 2.0: Mapping for Spike Identification

February 29, 2016

The long-awaited SmartBox version 2 software is almost finished, and we are in the midst of testing it out in live experiments. As part of an NIH program, we recently brought the SmartBox out to a lab in California and did some exciting experiments in both pigs and mice, recording signals ranging from EMG to neural.

One of the new features of SmartBox 2.0 that immediately came in handy was the new mapping feature. Because NeuroNexus produces all the components from electrode through data acquisition, we are able to provide a user interface in which the map of every probe is readily accessible through the recording software. We think this is a game-changing feature that will allow users to take full advantage of the spatial benefits of multi-channel microelectrode arrays with maximum convenience.

One way in which this benefit plays out is in trying to determine whether a given signal is physiological, or whether it is noise. With extracellular recordings, there is a certain radius around the recording site in which a single action potential could realistically be recorded. This range can vary, but generally it is somewhere in the range of 50 µm to 100 µm. NeuroNexus offers many microelectrode arrays with site spacings such that a single action potential might show up on multiple sites simultaneously. However, it is also possible for some noise signals to roughly resemble a neural signal. If the same signal is showing up on multiple channels, one of the first “sanity checks” for whether that signal is neural is whether it only shows up on channels that are reasonably close to each other (more likely neural) or if it shows up on channels that are far apart (almost certainly noise/artifact).

However, most (if not all) currently available acquisition systems aren’t equipped to help answer this sanity check question. And the reason is because of the complexity of probe mapping.

When a probe is made, the way that the sites are bonded to the package will produce a certain map of how the sites are arranged that is called a site/package map. Often that probe will be connected directly with a headstage, and the headstage will also have a map that could re-arrange where the sites are represented on the headstage. Sometimes, an adapter is required between the probe and the headstage, and adapters also have their own maps. Finally, some acquisition software does another level of re-mapping after the headstage before displaying it on the screen. The only way to know how one data channel relates to another, spatially, is to account for all of these potential levels of mapping.

Usually, this mapping is done off-line as part of the analysis process. But this doesn’t help live-action, when you might be seeing signals on more than one channel and wondering if they are realistically from the same unit. To answer that question you can either look up all of the different map components and create your spreadsheet to do the mapping during the experiment…which isn’t very convenient...or, if you are using the new NeuroNexus SmartBox V2 software, all you have to do is click on your signals of interest and the software will tell you where they are. Then, if you want to re-map your image so that those sites are together, you can so with the touch of a button. Here’s an example of us doing just that, during our California experiment.

SmartBox 01 Mapping Cropped

Figure 1: One signal showing up on two channels. Using the SmartBox 2 software and automatic re-mapping feature, we identified that this waveform showed up only on two sites that were directly next to each other.

The SmartBox 2.0 software is designed to make life easier for those during neural recordings. This is just one example, but it helps illustrate that using the SmartBox to record from NeuroNexus probes will allow users to maximize the convenience, utility, and power of their neural data acquisition experiments.

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On the Blog:

SmartBox 2.0: Mapping for Spike Identification

SmartBox 01 Mapping Cropped

The SmartBox 2.0 software integrates probe mapping into the recording user interface, providing extremely convenient spike identification during recording.

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