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Data Analysis

Summary of analysis features

  • Toolbars for convenient access to analysis features

  • 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

  • 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

  • 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