Data Analysis

Summary of analysis features

• Toolbars for convenient access to analysis features
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• Flexible analysis of graphs with multiple traces, or groups of traces
• • simultaneously analyze every trace in a group, or all traces in a graph
  • rapidly analyze data from multiple graphs by first combining them into a new graph
  • focus on a selected x-axis region, or analyze the whole graph
  • temporarily 'mask' selected traces to exclude them from an analysis
  • ensemble average groups of traces with optional error bars or confidence limits
    
  
  
• Numerical results accumulate as tab-delimited tables in the 'log' window
• • instantly graph a results table
  • combine, transpose and clean up tables
  • compute basic statistics (mean, standard error) for each column of a table
  • copy and paste tables into a spreadsheet application for further analysis
  
  
• Click the mouse at one or two points in a graph window and measure...
• • x- and y-axis location of each click
  • distance between a pair of clicks
  • trace amplitude at each click
  • amplitude difference between a pair of clicks
  
  
• Place two vertical cursors on a graph and between them measure...
• • average amplitude, area, minimum and maximum amplitude
  • variance, standard deviation, standard error of the mean
  
  
• Automatically find peaks and measure their amplitudes and shape parameters
• • find the largest peak in a trace, or all peaks greater than a threshold amplitude
  • measure peak amplitude and location, rise-time, width and onset
  • a sophisticated 'Event Detection Package' is included with 'Electrophysiology Tools' (below)
  
  
• Linear, exponential and general curve fit
• • optionally append the fitted curve to the graph
  • standard linear regression with correlation coefficient and uncorrelated probability
  • fast multi-exponential fits using the Chebyshev algorithm
  • fit any equation using the general curve fit
  • • type in an equation, or select from a list of standard equations
  
  
• Scale and offset traces
• • type in the scale and offset factors to be applied to every trace in a group
  • 'peak' or 'region' amplitude normalization
  • • 'peak' scales every trace to have a peak amplitude of 1
    • 'region' scales every trace to have a mean amplitude of 1 over a selected region
  
  
• Subtract a baseline from every trace
• • flat: subtract the average amplitude of the baseline region
  • sloping: subtract the regression line fit to the baseline region
  • two region: subtract the line interpolated between two separate baseline regions
    
  
  
• Adjust x-axis zero
  
• • useful when measuring locations relative to a start point, or when fitting exponentials
  
  
• Select specific events from an episodic data file
• • pick a single event by clicking on it
  • mask misshaped events by testing onset time, rise-time, half-width, etc.
  • mask large events
  • mask even episodes
  • swap in masked events
  
  
• Statistics (Chi Sq., T-test, KS, F-test)
• • Chi Squared test: asses how well a fitted curve describes the data
  • T test: compare the means of two data sets
  • K-S test: compare two distributions (also known as Kolmogorov-Smirnov test)
  • F test: compare the quality of two different fits to the same data set
  
  
• Amplitude histogram
• • zero-centered or zero-aligned bins
  • results displayed as a traditional binned histogram or a probability density function
  
  
• Power spectrum displayed with log-log axes
• Reduce noise using an optimal Gaussian filter
• Filter out line noise using a notch filter at 50 or 60 Hz
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• Align traces at event onset
• • slide each trace to the left until the events they contain are aligned
  
  
• Transform traces
• • differentiate, delta-y, integrate, invert, rectify, raise to power, log, reciprocal
  • decimate with averaging: reduce the noise on a trace and the number of data points
  
  
• Trace and group math
• • add, subtract, multiply or divide traces, or groups of traces
  
  
• List all files in a folder
• Select a list of file names and open them simultaneously
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• AxoGraph is extensible and programmable
• • automate analysis, or add new analysis features by writing plug-in programs
  • supports C, Basic, Pascal or Fortran
    
  • add new menu items and menus, pose dialogs
  • precompiled plug-ins can be created for number-crunching
  
  

Additional features included with Electrophysiology Tools

• Chemical-Kinetic model of voltage- and ligand-gated channels (Markov model)
• • a channel's states and the reactions rates between those states are entered
  • some reaction rates are dependent on drug concentration or membrane voltage
  • the model is driven by a drug time-course, or voltage time-course
  • calculates the evolution of state occupancy and predicts the time-course of the channel current
  
  
• Event detection package
• • used by neuroscientists for analyzing spike-trains or miniature postsynaptic currents (mPSCs)
  • state-of-the-art sliding template event detection
  • alternatively detect events using an amplitude or first derivative threshold
  • automatically measure and graph event amplitudes, shape parameters, frequency, etc.
  • post-detection filters eliminate false-positives based on event rise-time, width, etc.
  
  
• Population spike analysis
• • used by neuroscientists for analyzing extracellular field recordings
  • commonly used in long-term potentiation (LTP) studies
  • maximum slope measures EPSP amplitude
  • population spike area measures evoked action potentials
  
  
• Current-Voltage (I-V) analysis
• • used by neuroscientists for analyzing voltage dependence of a membrane conductance
  • package includes automatic subtraction of leak currents
  
  
• Vesicle release model
• • models the synaptic release process incorporating several vesicle release pools and subsequent endocytocis of released vesicles