

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 xaxis 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 tabdelimited 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 yaxis 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, risetime, 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 multiexponential 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 xaxis 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, risetime, halfwidth, etc.
 mask large events
 mask even episodes
 swap in masked events
 Statistics (Chi Sq., Ttest, KS, Ftest)

 Chi Squared test: asses how well a fitted curve describes the data
 T test: compare the means of two data sets
 KS test: compare two distributions (also known as KolmogorovSmirnov test)
 F test: compare the quality of two different fits to the same data set
 Amplitude histogram

 zerocentered or zeroaligned bins
 results displayed as a traditional binned histogram or a probability density function
 Power spectrum displayed with loglog 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, deltay, 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 plugin programs
 supports C, Basic, Pascal or Fortran
 add new menu items and menus, pose dialogs
 precompiled plugins can be created for numbercrunching
Additional features included with Electrophysiology Tools
 ChemicalKinetic model of voltage and ligandgated 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 timecourse, or voltage timecourse
 calculates the evolution of state occupancy and predicts the timecourse of the channel current
 Event detection package

 used by neuroscientists for analyzing spiketrains or miniature postsynaptic currents (mPSCs)
 stateoftheart sliding template event detection
 alternatively detect events using an amplitude or first derivative threshold
 automatically measure and graph event amplitudes, shape parameters, frequency, etc.
 postdetection filters eliminate falsepositives based on event risetime, width, etc.
 Population spike analysis

 used by neuroscientists for analyzing extracellular field recordings
 commonly used in longterm potentiation (LTP) studies
 maximum slope measures EPSP amplitude
 population spike area measures evoked action potentials
 CurrentVoltage (IV) 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



