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Data Analysis

The following screen-shots illustrate the main data analysis features found in AxoGraph X.
A comprehensive list of analysis features is provided elsewhere.

The main analysis features include..

Mouse Measure

Measuring basic graph features is as simple as point and click.

Mouse Measure

Multiple mouse clicks measure the amplitudes of several features



Mouse measure log

Results accumulate in the log window


Optionally measure the location of each single click, or the distance between pairs of clicks...

Mouse Measure Options



Group Traces

Flexible analysis of graphs with multiple traces, or groups of traces. Temporarily mask traces to exclude them from analysis. Conveniently reorganize traces into different groups for display or measurement.

I-V Plot

Simultaneous 'cursor measurement' of the amplitudes of all eleven traces
in both the 'Membrane Voltage' group and the 'Current' group


Cursor Measure

Place two vertical cursors on a graph and between then analyze the data points between the cursors...

Cursor Measure Optoins


Process Numeric Results

Analysis results accumulate as tab-delimited tables in the 'log' window. Combine and transpose tables, then create a graph from the results. Compute basic statistics for each column in a table.

I-V Results

A table of results from a single 'cursor measurement', as shown above


I-V Graph

A current-voltage plot generated directly from the above table of results




Peak Measure

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.

Peak measure

A more sophisticated 'Event Detection Package' is included with 'Electrophysiology Tools' (below). It uses a sensitive 'sliding template' algorithm to identify events with a selected time course.


Linear, Exponential and General Curve Fit

Standard linear regression, and fast multi-exponential fits. Type in any equation and fit it to a data trace using general curve fit. Optionally append the fitted curve to the graph. Fitted parameters accumulate in the log window.

Exp fit


Baseline Subtraction

Subtract the steady-state level from every trace in a group or window.

Baseline before Baseline after
Before baseline subtraction After baseline subtraction

Three different baseline subtraction algorithms are available...

Baseline options
  • 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.

X-axis zero

Time zero will be reset to the start of the event (10 ms)


Toolbars

Convenient toolbar access to the main analysis and display features...

Analysis
 Graph Appearance
 Navigation
analysis appearance navigation


... and for running frequently-used plug-in programs. New plug-in toolbars can be created, and existing toolbars can be customized.

Bottom Toolbar


Programmable and Extensible

If none of the built-in analysis features fit your requirements, or if you want to automate a sequence of analysis steps, then a scripting / programming environment is available.
  • automate analysis, or add new analysis features by writing plug-in programs
  • supports C, Basic, Pascal or Fortran
  • add new menus and toolbars
  • pose alerts and dialogs
  • read and write binary files
  • precompiled plug-ins can be created for fast number-crunching



File Import and Export

To import a foreign file, select File -> Open then in the standard dialog, change the "Enable" popup menu either to "All Files", or to the desired file format.

File import

To import tab-delimited text data to a graph window, the "Other Text Data" option must be selected. If "All Files" is selected, the file will be read into a text edit window, not a graph window.


To export a graph to a forein format, select File -> Export then in the standard dialog, change the "Format" popup menu to the desired file type.

File export


Notes on Import and Export

Igor Pro Packed Experiment and Binary Wave
Igor Pro packed experiment files (extension ".pxp") files typically contain multiple waves ('traces' in AxoGraph X terminology). All the waves in the experiment file are imported to a single graph window.

In contrast, binary wave files (extension ".ibw" or ".bwav") only contain a single wave. When AxoGraph X exports a graph to binary wave format, each trace in the graph window is saved to a separate file.

pCLAMP and AxoScope
AxoGraph can directly read and write ABF data files, the format used by pCLAMP and AxoScope (Axon Instrument's data acquisition applications for Windows) up to version 9.x. However, with the introduction of pCLAMP version 10.0, a new ABF-2 file format was introduced. Axon Instruments have not documented their new file structure, but they have supplied a Windows library to read these files. Thus AxoGraph X for Windows can read ABF-2 files, but they can't be read by AxoGraph X for OS X.

MacLab Chart
Data acquired using versions 1.x to 3.x of the MacLab Chart program from AD Instruments can be read directly by AxoGraph X. However, with the introduction of Chart version 4.0, AxoGraph can no longer directly read Chart binary data files. AD Instruments have not documented their new file structure. As an alternative, Chart version 4.x and later can export to ABF format, which AxoGraph X can then import.