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SmartBox 2.0: Full-screen Data Streaming Option

March 22, 2016

As detailed in the last two entries, a lot of time and planning has gone into designing the probe-centric aspects of the new SmartBox 2.0 software. The software is able to map NeuroNexus probes in real-time, and can do so for multiple probes recording simultaneously in different locations. This is all done to allow users to take full advantage of the spatial benefits of mult-channel microelectrode arrays with maximum convenience during experiments.

But when doing recordings, there are times when the focus needs to be purely on the streaming data. Do the waveforms look correct? Does the spike timing match-up with external cues? What does the activity look like over a longer time period?

For situations like this, the SmartBox 2.0 software allows the user to clear all status, configuration, and/or mapping information off the screen to more wholly focus on the streaming data itself. Consider the following screen shots:

In Figure 1, an example is shown in which two probes are connected into the first two ports on the SmartBox. The user has selected one channel from probe A and two channels from probe B as worthy of further interest. There are also two digital inputs plugged in as part of this experiment. One digital input might be the TTL pulse controlling a laser for optogenetics, and the other a TTL pulse generated by the animal accessing a feeder for a reward. Those two signals are shown in the central panel at the top of the screen, labeled as “DIN-00x,” where the “x” corresponds to the input channel on the SmartBox.

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Figure 1: SmartBox 2.0 software with two probes implanted, displaying shared information from the probes in ports A and B.

In Figure 2, the same data is displayed, but with the configuration panel (left) minimized such that the data streams can take up both the center and left portions of the screen.

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Figure 2: SmartBox 2.0 software with two probes implanted, displaying shared information from the probes in ports A and B across the full screen.

In Figure 3, we see the alternative approach, where the Probe Mapping Display panel (right) is minimized but the configuration panel is left open.

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Figure 3: SmartBox 2.0 software with two probes implanted, displaying shared information from the probes in ports A and B across the full screen.

Finally, in Figure 4, we see the data streams in full screen mode, with both the configuration and the probe mapping panels minimized.

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Figure 4: SmartBox 2.0 software with two probes implanted, displaying shared information from the probes in ports A and B across the full screen.

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.

SmartBox 2.0: Displaying Multiple Probes

March 16, 2016

The long-awaited version 2.0 SmartBox software is almost available. As detailed in the last entry, one of the useful new features of the Version 2.0 software is that it is equipped to automatically map any NeuroNexus probe, allowing users to take full advantage of the spatial benefits of multi-channel microelectrode arrays with maximum convenience during experiments.

But what if you want to record using more than one electrode at the same time? The SmartBox has four entry ports for different headstages, meaning that you could record from up to four probes simultaneously using a single SmartBox. For example, you might want to do penetrating recordings down into a particular brain area while simultaneously doing ECOG recordings at the surface. Alternatively, it might be of interest to place multiple penetrating probes into different structures (Figure 1).

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Figure 1: Two microelectrode arrays implanted in different structures for simultaneous recordings.

This type of multi-level, multi-area recording could potentially yield key information about brain interaction mechanisms that aren’t readily apparent when recording from only one location. But while much of the analysis for such an experiment may be done offline after the fact, one still needs some feedback during the actual experiment.

The SmartBox 2.0 software is equipped to handle these types of recordings in an elegant way, displaying the detailed mapping information on different panels with the option to concentrate pertinent information into a single display. Let’s walk through an example, where simultaneous recordings are being done through a 4x8 penetrating array and a 32-channel surface array.

In Figure 2 we see a screenshot from the SmartBox 2.0 software with two probes implanted, displaying information from the probe in port A. The first place to look is in the upper-left corner, which shows a graphical display of the front of a SmartBox with a blue circle and two of the four entry ports lit up. The blue circle indicates that the SmartBox is on, and the two lit entry ports indicate where two headstages are plugged in. Directly below that display is a status box, which confirms that the SmartBox status is “Connected” and that there is a 32-channel probe in each of ports A and B. On the opposite side of the screen, in the upper right corner, the letter ‘A’ indicates that the probe in port A is currently being displayed. To the left of that ‘A’ is the box indicating that the probe on display is an A4x8 probe, and below that is the graphical representation of that probe with the sites shown in the correctly mapped orientation. Finally, in the central panel, the streaming waveforms are labeled “AMP-A1-0xx” where ‘xx’ is the channel number from the probe in port A.

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Figure 2: Screenshot of SmartBox 2.0 software with two probes implanted, displaying information from the probe in port A.

In Figure 3, we see a screen capture of the same recording set-up, showing the probe in port B. The information on the right side of the screen is the same, but in the upper right corner the display is now labeled ‘B’, and the probe box displays that the probe being shown is an E32-600-10-100 surface probe. And in the central panel, the waveforms are now labeled “Amp-B1-0yy” where the ‘yy’ is the channel number of the probe in port B.

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Figure 3: SmartBox 2.0 software with two probes implanted, displaying information from the probe in port B.

Finally, in Figure 4 we see a screen capture showing shared information across the two probes. The central panel is still showing streamed data, but the top-3, colored traces were selected by the user as of interest. One of the chosen traces (red) came from the probe in port A, while the other two (green) were from the probe in port B and are labeled as such. The probe in port B is still shown in this display, with the user selected sites highlighted, and with a quick push of the left arrow in the upper right portion of the screen the display would shift to the probe in port A with the red site highlighted.

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Figure 4: SmartBox 2.0 software with two probes implanted, displaying shared information from the probes in ports A and B.

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.

SmartBox: Converting Data to MATLAB and NEX formats for analysis

Updated June 9, 2015

The 256-channel SmartBox is a control and data streaming system designed to interface with all NeuroNexus probes, as well as other commonly used electrodes. The SmartBox also has analog and digital I/O ports for synchronizing the data with external or physiological events. In use, a real-time display shows the experiment in progress, and data is streamed to file for offline analysis.

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Figure 1: Example workflow for an optogenetics experiment. The neural data is recorded through a probe, transferred along the SmartLink headstage into the SmartBox, synchronized with the laser system and waveform generator through the I/O ports, and then saved to files on the PC.

 

Once data is saved to the PC, the next step in the workflow involves classifying, analyzing and/or displaying the data. The typical output file for the SmartBox is the RHD file, which records a period of time across multiple/all channels. While NeuroNexus does not currently recommend a particular method to perform analysis, we provide two options for converting these files into a format that is compatible with standard analysis software options on the market.

The first method is a MATLAB script that reads RHD files and unpacks them such that all pertinent data is represented as variables in MATLAB. From there, the spike sorting analysis can be performed in MATLAB with the proper scripts. Alternatively, you can export the data from MATLAB in a form that a different analysis program can read. For example, data can be exported as text (.TXT) files, which can be read into a program such as Spike2.

The second method converts RHD files into NEX files. NEX files are the direct purview of NeuroExplorer, which can be used for analyzing and displaying data after spike/event sorting. (NeuroExplorer does not do the actual sorting.) Converting RHD to NEX allows analysis programs capable of spike sorting to read your data. For example, Offline Sorter can use NEX files, and the spike sorting can be done within Offline Sorter and then re-saved as a NEX file for further post-spike-sorting analysis.

Recent upgrades to the conversion software

NeuroNexus has included NEX conversion software with SmartBox purchases since 2014. The software was recently upgraded in two key ways to increase its utility:

  1. It can now handle files over 3 GB. NEX has a hard limit of 3 GB for the data files that it can handle. Depending on the recording parameters used, the SmartBox can produce files that are larger than 3 GB. The NEX converter now breaks extra-long data files down into several temporally sequential files for analysis. For example, a 9-minute recording with 64 channels may be broken down into three 3-minute NEX files.
  2. I/O data is now included. Event data recorded through the I/O ports on the SmartBox is also converted and included in the NEX file output.

NeuroNexus is committed to making the SmartBox powerful and convenient through software development. We highly value feedback from researchers, so if there are any software upgrades that you would like to see, please let us know.

SmartBox file conversion software can be downloaded here.

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.

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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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SmartBox 2.0: Mapping for Spike Identification

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

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