Introduction

1. The gPRIME Software Oscilloscope The main scope interface to the program is designed to be user friendly and intuitive with soft colors and a moderate degree of flexibility. All of the classic functionality found on a modern hardware oscilloscope is available including trigger modes, channel selection/scaling, and data logging to disk. It is a simple process, for example, of clicking and dragging the channel name in the scope window to move the traces vertically for visualization. Data is streamed to the display in 100-200ms samples. Data streaming to disk supports all trigger modes of the scope and allows for pre-trigger buffering and storage and multiple trigger storage to a single file as well as DMA writing. The user may produce a variety of stimuli from an analog output (the computer speakers or DACs on a sampling board) including pulse trains or an arbitrary signal shape from a loaded file (such as a wave audio file). One channel is used for stimulus presentation and one channel is used for stimulus trigger. A pulse on channel 2 may be fed back into the hardware to trigger time correlated acquisition with the stimulus. The program automatically detects any interface supported by the Matlab data acquisition toolbox from your computer’s sound card to calibrated sampling boards (such as NIDAQ systems from National Instruments). Turn any Modern PC into a Physiology Teaching Tool or Research Environment for Free http://crawdad.cornell.edu/gprime/ gPRIME – Data Acquisition & Analysis Software for Physiology in Research and Education Gus K. Lott III1,2, Bruce R. Johnson1, Robert H. Bonow1, Bruce R. Land1, and Ronald R. Hoy11Department of Neurobiology and Behavior, Cornell Univ., Ithaca, NY2Howard Hughes Medical Institute – Janelia Farm Research Campus Introduction This software project grew out of a confluence of events at Cornell University in the Spring of 2007. The undergraduate neurophysiology lab course at Cornell needed an acquisition and analysis “tech refresh” and a PhD student biophysical & electrical engineer was brought on as a teaching assistant. The result was gPRIME (Physiology Recording & Identification of Multiple Events). This software package was developed week to week in the course as students moved from lab exercise to lab exercise. A new version of the software would be developed and deployed and the students would carry out the week’s exercise using new features and provide feedback about usability and bugs. This rapid design and feedback process was made possible by the Matlab (Mathworks Inc.) development environment. Matlab’s powerful engineering tools allow for rapid code development and testing while the Matlab Compiler toolbox allows for any code to be exported to a stand-alone executable file for deployment. As the software developed, researchers in the Neurobiology & Behavior department at Cornell began to take an interest. The tool transferred to active research projects and feedback from both researchers and students drove development. At the end of the spring semester, student projects in the physiology lab course where reproducing and exceeding published work from recent articles from a variety of well funded groups. For example, students were characterizing crayfish neuromuscular junction response to a variety of chemicals (including DDT and caffeine), and were characterizing nerve conduction velocity as a function of temperature in the crayfish. Other students explored network connectivity and synchrony in multiple nerves of the crayfish tail. Since its development, gPRIME has expanded to applications in multiple university level courses and enables global collaborative projects in high schools while still acting as a work-horse for several distinguished researchers around the world from behavioral physiology in invertebrates to deep brain recordings in mammalian systems. Developed for students & researchers in a collaborative feedback loop Data Grooming and Analysis of Clusters Clusters of spikes may be extracted from a 2 dimensional space using an arbitrary polygon or box. Resulting spike clusters may be groomed (click on an outlier and hit the delete key, see right) to make sure that your results accurately represent the data or simply to visualize where a certain event is located in the data space. This mode also allows for visualization of the rate behavior of a specific subset of events and the location of the events in the raw data channel. Real Time and Offline Correlations gPRIME allows the user to correlate a set of time points with any source in both real time and offline modes. The students auto-correlate a spike in real time to produce SNR enhancement of an otherwise noisy spike (top). In the bottom image, students have cross-correlated a spike in an innervating neuron with the post synaptic potential produced by that neuron in the muscle. This feature is a powerful tool to extract time correlated signals from otherwise uncorrelated background noise in any experiment where a triggering signal is available. Current Availability gPRIME is currently available from a Cornell University based web site associated with the neurophysiology lab course for which it was initially developed. http://crawdad.cornell.edu/gprime/ The software consists of a 180MB download and the web site contains documentation, application examples, real data from experiments, and step-by-step instructions on getting started with your applications Future Development & Status as Freeware The feedback driven development cycle that produced gPRIME is ongoing (physically) at the Howard Hughes Medical Institute’s Janelia Farm Research Campus in response to user needs around the world. Future versions of the software will have expanded hardware support and more powerful analysis tools and will be hosted by HHMI as freeware for Educational and University Based Research Applications. A licensing fee will be required for commercial applications of the software. Sorting by Peak Frequency of EOD in the Electric Fish When recording electric organ discharges from fish in a tank (or in a river), amplitude of spikes is not a reliable measure given the constant motion of the fish relative to the electrode. The peak frequency component of the discharge, however, is constant (unless intentionally modified by the fish) and may be used to visualize the location of distinct individuals. Shown here is a courtship display (provided by Carl Hopkins, Cornell University) Intracellular Study of Synaptic Plasticity in the Crayfish NMJ This study illustrates the ability of gPRIME to measure Post Synaptic Potential (PSP) amplitudes in an intracellular application. Note how the amplitude of the first PSP is smaller than the PSP at 6 seconds post tetanic stimulation, thus illustrating a form of short term potentiation. 6-Neuron Nerve Recordings (Extracellular) in the Crayfish gPRIME allows for clustering of detected events in a 2 parameter space. In this case, Action Potentials where threshold detected and sorted based on their signal energy density and maximum amplitude. Stretch Receptor (MRO) Adaptation in the Crayfish Here, the exponential adaptation rate of a stretch detecting proprioceptor neuron is evident in response to a stretch and hold of the muscle of interest. Students are able to visualize this adaptation in real-time for an immediate understanding of the underlying physiological mechanisms. Applications Around the World in Research and Education While we have not actively tracked the dissemination of this software to research groups and educational environments, we know that it has found application in labs in Spain, Venezuela, and in several places in the United States outside of Cornell University. One particular application which we are actively involved in is a High School collaboration between the Loudoun County (Virginia) High School Academy of Science (an HHMI Funded program) and a High School in Singapore. Students will use gPRIME to turn their laptop computers into data acquisition and analysis tools (using the native sound card and a microphone) to study the characteristics of cricket chirps from a variety of species on both sides of the globe. This free tool is currently enabling this international collaboration and connecting kids in a manner never before achieved. Signal Conditioning & Data Analysis in Real Time and Offline gPRIME offers several tools for signal conditioning and event detection. The user may access built-in high and low pass filters at a variety of frequencies between 10Hz and 40kHz as well as a 60Hz notch filter for line noise reduction. The user may also create their own FIR filter coefficients and load them into the program for application to the current signal trace. Resulting events are initially detected by amplitude thresholds and events may be rejected based on a second amplitude threshold or thresholds in energy density or peak frequency component (of the FFT) space. The resulting events are characterized in terms of Max Value, Minimum Value, Event Time, Interval/Rate since last event, window energy density, and signal peak frequency component. Publication Quality Graphics Production Any trace may be extracted from any graphics window in the program (see the small maroon box in the corner of each axis containing graphics). The user has the ability to overlay multiple traces in a single figure, scale the figure and the data, and control the properties of the resulting figure (line width, color, order, data markers, log/linear scale, etc with limited annotation features). The resulting figures may be saved in common graphics formats including TIFF and JPEG. In addition to the graphics outputs, gPRIME enables you to export results and raw data in a variety of formats including .wav and ASCII text files.