Lab Software

Oscilloscope

    Oscilloscope is a Macintosh program for visualization and analysis of waveforms generated by neurons or by computer simulations of neurons.  The current version (version 4.5) is a carbon universal application that works in OS X.   Oscilloscope can analyze waveforms generated in a variety of ways and by a host of other programs, because it can read and write data stored in two simple and widely-used file formats.  One of these is the tab-delimited text file format used by spreadsheets and many graphics programs.  The other is a binary format, the HDF scientific data format described and supported by the National Center for Supercomputing Applications (NCSA) and used by a large number of commercial and freeware programs. Oscilloscope can also read Axon Binary Files (version 1.6) created by the popular PClamp data acquisition software. The waveforms are seen as if on the screen of a digital oscilloscope.  As many as 10 files may be open at any time, and the traces from each are shown in a window representing the file.  Each file can contain up to 100 different waveforms (called traces) that can be seen simultaneously. Traces can be selectively hidden or shown by choosing them from a menu that lists them by name. The vertical gain of each trace can be adjusted individually, as can its vertical position on the screen.  Likewise, the sweep speed and horizontal position of each trace can be adjusted.  There is (practically) no limit to the number of points in a trace, but all traces in a file must have the same number of points and the same time increment between points. The typical appearance of traces on the screen is illustrated below. 


    Traces are individual time series of voltage or current.  Traces can be cut and pasted between files, and can be aligned and superimposed.  Existing traces can be integrated, differentiated, DC balanced, or smoothed.  It is also possible to create new traces using a waveform generator window, or to generate them by arithmetic alterations of existing traces.         

Traces can be printed or they can be saved as a vector Adobe Illustrator file, or as a bitmap at a specified resolution in a TIFF file.  Traces can also be  transferred as an image in the clipboard for direct use in another program.  Printed traces and traces saved to Adobe Illustrator (eps) files maintain their full original resolution, up to the maximal resolution of most printers (600 dpi).

    Oscilloscope can also perform some kinds of measurements on traces.  A cursor similar to that used in many digital oscilloscopes is available for measurement of the value of the waveform at any time point (see above screen shot).  A separate window is used to fit an exponential or a sum of two exponentials to a trace or a part of a trace using the graphical method called “Peeling Exponentials”.  Another window allows fitting of any user specified function to a specified region of a trace or a portion of a trace. Results of various measurements can be logged to a text file.


    Oscilloscope is scriptable using AppleScript, and users may make their own scripts available in the menu simply by inserting them in a folder.  The scripts should be created using Apple’s Script Editor or a similar product, and compiled.  They can be executed from the script editor or directly by Oscilloscope from the Script menu.

 

The sources include a complete XCode 2.4 project for compiling Oscilloscope on the Macintosh, including universal binaries of the NCSA HDF version 4 file format library.


Oscilloscope Sources (10.1 Mbytes)

 

The binary version contains a mac os x (universal) application, and some sample scripts.


Oscilloscope Binary (1.4 Mbyte)

 

Download

Oscilloscope QuickLook Plugin

    This is a quicklook generator for oscilloscope hdf files (not text or pClamp abf).  Put it in the /Library/Quicklook directory or in ~/Library/Quicklook, and it should start to work right away.  It is a universal binary so should be fine in either intel or ppc.  But Quicklook is a Leopard and later feature.

oscopeqlgen.qlgenerator (1.2 MBytes)Software_files/oscopeqlgen.qlgenerator.zip