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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.

SmartBox Workflow Web

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.

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