Software for Extracellular Neurophysiology
OpenEx Suite—Multi-Channel Data Acquisition
OpenEx is a user extensible software platform that taps into the speed, flexibility, and real-time control of our System 3 hardware. An open architecture and customizable, visual interface make it flexible enough to address a wide range of research applications, ranging from behavioral training paradigms to multi-channel neurophysiology.
The core suite of programs includes configuration, control, display, and analysis applications. Because OpenEx is built on a distributed client/server architecture, all OpenEx applications can run in parallel, organized under a single workspace manager. This allows you to configure any number of custom client windows for your specific application, each able to access data as it’s acquired and stored.
OpenEx Suite includes:
TTank Engine
TTank is a data server that operates behind the scenes to provide fast, reliable data storage and retrieval. Response waveforms as well as behavioral and stimulus events can be time stamped with microsecond accuracy and stored to our unique DataTank format. This format allows TTank to save large amounts of data and efficiently serve data up to client applications for real-time display and analysis.
OpenWorkbench
OpenWorkbench is the interface between OpenEx applications and the System 3 hardware. Through OpenWorkbench’s graphical user interface, you can select which devices will be used in an experiment, specify which functions each will perform, select which data to store, and control the general flow of the experiment.
OpenController
OpenController gives you real-time control of your experiment. Parameters such as filter settings, single-unit thresholds, and stimulus variables, can all be modified on the fly. You can combine built-in components to create your own visual interfaces for parameter control and data display. OpenController includes over twenty customizable controls including gauges, switches, sliders, manual and automated spike sorting controls, and data displays.
OpenScope
OpenScope is a user-customizable application developed to visualize neural spike data and other bioelectric waveforms (e.g. EEGs or local field potentials) in real-time and offline. A number of plot types allow viewing of raw data in several ways including: continuous time base, spike shape overlay and feature space, PSTH and raster plots.
OpenBrowser
OpenBrowser is a data export and viewing application that accesses data through the TTank data server. Data from one or more data tanks can be selected, filtered, previewed, and exported. OpenBrowser supports Neuroshare, and a variety of export formats including a standard ASCII file and formats for NeuroExplorer® or Plexon’s Offline Sorter. 
OpenProject
OpenProject acts as the essential environment integration tool, greatly simplifying the system’s ease of use. With OpenProject, all OpenEx programs are brought under the control of a single management tool and all of the files related to a given experiment are managed automatically under a single directory structure.
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More OpenEx Software:
SpikePac—Online Multi-channel Neural Recordings *NEW*
SpikePac is a powerful extension package for TDT’s OpenEx software suite designed specifically for researchers doing multi-channel neural recordings. The software package includes a group of easy-to-use RPvdsEx components and paired OpenController interfaces that provide the foundation needed to build powerful recording paradigms. These building blocks handle all OpenEx integration details automatically. Most importantly, SpikePac offers this new level of integration without compromising the flexibility essential to TDT customers.
SpikePac includes:
- Principal Component Feature Space Spike Sorting
- Real-Time, Time-Voltage Spike Sorting
- Filtering
- Signal Monitoring with Noise Gating
- Signal Denoising
- Electrode Site Remapping
Building on existing OpenEx functionality, SpikePac simplifies experiment configuration and incorporates a broader range of spike sorting techniques and performance enhancing tools.
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OpenExplorer—Data Mining
OpenExplorer is a powerful data mining tool for the OpenEx software suite. Flexible plotting features allow you to explore the relationships between recorded data, stimulus parameters, and other defined events. With OpenExplorer you can quickly sort through complex data sets and display these relationships dynamically. A graphical interface makes it easy to select the data and plot type for each cell in a grid display. Simply drag any stored parameter to the control area to plot it or filter other data based on that parameter. After your plots are configured, OpenExplorer allows you to view snap shots of activity or an animated display across an array of data over time. With OpenExplorer you’ll be able to explore a single data set using virtually any combination of stimulus, behavioral, or environmental data stored to the data tank.
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OpenDeveloper—Development Tools
OpenDeveloper is a application program interface that can be used with programming languages such as MATLAB, Visual Basic, and Visual C++ to generate client applications that access the OpenEx servers. OpenDeveloper provides access to the same set of server interfaces used by OpenEx applications such as OpenScope and OpenController.
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OpenSorter—Spike Sorting
OpenSorter is a stand-alone package for sorting neural spike data and is the latest addition to TDT’s OpenEx software suite. OpenSorter offers a number of powerful sorting methods including Bayesian expectation-maximization, k-means, and closest-centers algorithms in addition to manual cluster cutting and waveform selection.
Capabilities include manual, semi-automated, and fully automated processing. Spikes can be sorted as individual channels, batched for fast processing of groups of datasets, or combined across blocks or channels and sorted as a pooled superset.
Data are displayed and can be sorted in principal components feature space, waveform parameter feature space, an event timeline, or piled waveform shape windows. Sorting results can be edited and spikes re-assigned using feature or waveform space editors. Post-hoc analyses including Pseudo-F, isolation distances, L-ratios, and silhouette indices indicate sort quality and help to guide manual resorting and editing.
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BrainWare—Extracellular Recording and Data Analysis
BrainWare software is a versatile package for stimulus presentation, extracellular recording, and analysis. BrainWare plots neural responses versus stimulus parameters online, providing immediate feedback about the responsiveness of cells. With BrainWare you can acquire data on up to 16 channels, sort spikes, view data online, and use built-in analysis tools. A “feature space” representation of action potential candidates allows you to “cut clusters” in a visual interface and PSTHs are automatically generated for each cluster. Once clusters are defined, cross-correlation, auto-correlation, ISI, and period histograms can be generated to provide further analysis.
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