WaveSurfer is an application for acquiring electrophysiology data. It runs within Matlab R2013b and later (64-bit only). At present, you must have a Matlab license to use it.
PLEASE NOTE THAT WAVESURFER IS CURRENTLY PRE-RELEASE SOFTWARE. THERE WILL ALMOST CERTAINLY BE BREAKING CHANGES TO FILE FORMATS, ETC. BEFORE VERSION 1.0 IS RELEASED, AND WE CAN MAKE NO PROMISES ABOUT BACKWARD COMPATIBILITY.
64-bit Windows 7 computer
National Instruments X Series card (i.e. 63xx)
National Instruments DAQmx driver, version 9.8.x or 14.5.x
Matlab R2013b or later (64-bit)
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Download the .zip file from GitHub.
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Extract the .zip file contents to a convenient location.
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In Matlab, cd to this just-created directory.
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At the Matlab command line, execute "installWavesurfer". This will permanently modify your Matlab path so that all components needed by WaveSurfer are on it. (If you don't want to permanently modify the path, execute "installWavesruferForNow" instead of the above. This modifies the path only for the current Matlab session.)
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To use WaveSurfer, you must create a "machine data file". This file specifies which National Instruments board you want to use with WaveSurfer, and which channels, and a few other things. An example machine data file is located at:
+ws/+test/+hw/Machine_Data_File_WS_Test.mwithin the WaveSurfer directory. You should copy this file to a convenient location, and customize it as needed.
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At the Matlab command line, execute "wavesurfer". You should now be presented with the WaveSurfer UI, but almost all the controls will be grayed.
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Go to File > Load Machine Data File... and select the file you created in step 5 above.
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Most of the WaveSurfer controls will ungray, and at this point everything should be more-or-less self-explanatory.
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If you have questions, please contact the WaveSurfer developer(s).
Except where noted, all code, documentation, images, and anything else in WaveSurfer is copyright 2013-2015 by the Howard Hughes Medical Institute.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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Neither the name of HHMI nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
WaveSurfer started out as version 3 of Ephus, another electrophysiology package largely authored by Vijay Iyer, with contributions by Tim O'Connor and others. Vijay is also the primary author of the DABS library, from which the code in +ws/+dabs/+ni was taken, and of the MOST library, in +ws/+most.
The original developer of WaveSurfer was Patrick Edson.
WaveSurfer is currently developed by Adam L. Taylor and Ben J. Arthur.
Adam L. Taylor, taylora@hhmi.org
Scientific Computing
Janelia Research Campus
Howard Hughes Medical Institute
0.74: (February 26, 2015) Added Axon Multiclamp support. Now store stimulus metadata in the data file header. Now save data as int16 instead of double-precision floating point. Improved ScanImage integration.
0.75: (March 9, 2015) Fixed bug with scope x-span.
0.76: (March 11, 2015) Fixed bug with README(!).
0.77: (March 17, 2015) Now supports timed digital outputs.
0.771: (March 18, 2015) Updated README to reflect true NI DAQmx driver requirements.
0.772: (March 18, 2015) Can now change scope y limits during ongoing acquisition.
0.773: (March 23, 2015) Fixed bug with trial duration setting not getting propagated to DAQ board on .cfg file load.
0.774: (March 25, 2015) Fixed a few more bugs.
0.775: (March 25, 2015) Fixed bug that prevented acquisition if some AI channels specified in MDF were marked as inactive.
0.776: (April 2, 2015) Added ability to playback arbitrary stimuli from .wav file. Fixed bugs with multiple DO lines and long-duration stimuli, and with stimuli not being generated properly after 1st stimulus episode when externally triggered.
0.777: (April 3, 2015) Fixed issue that prevented acquisition if Matlab was installed on a drive other than the C drive.
0.778: (April 14, 2015) Now have toggle-able autoscaling of y-axis limits for both scope windows and the test pulse window. Added per-trialset and per-trial (approximate) timestamps to data file. No longer rely upon DABS callbacks during data acquisition, but poll instead. All internally-generated triggers are now themselves triggered off a common "master" trigger on PFI8.
0.779: (April 14, 2015) Fixed bug where couldn't test pulse after acquiring data.
0.78: (April 15, 2015) Data files for continuous recordings now use the same file naming scheme as trial-based recordings. Fixed bug with fast protocols not getting cleared when you click that button. Added a very simple example user function .m file.
0.781: (April 20, 2015) Added more options for data file naming.
Fixed several small bugs.
0.782: (April 22, 2015) Added a two-pulse stimulus.
0.783: (April 22, 2015) Added a generic Matlab expression stimulus.
0.784: (April 29, 2015) Test pulser now uses sampling rate of acquisition system.
0.785: (May 11, 2015) Inactived AI channels are now really and truly inactivated.
0.786: (May 12, 2015) Fixed bug with TestPulser model not getting persisted to disk properly.
0.787: (May 12, 2015) Commented out debugging fprintf. Doh!
0.8: (May 19, 2015) Added support for digital inputs, untimed digital outputs. Changed user hook function infrastructure to more powerful object-based scheme. Added example user hook classes that implement treadmill- and VR-triggered spike rasters. Many other small tweaks and improvements. Note that version 0.8 will not generally read protocol files from earlier versions.
0.801: (June 4, 2015) Made electrodes window narrower, so that it fits on a 1280x1024 screen. Added zoom in/out, scroll up/down buttons to scope windows, got rid of green-on-black color scheme. Test pulser now shows resistance in units tailored to the scale of the resistance value. Protocol and user settings file formats were not changed from release 0.8.
0.802: (June 12, 2015) Fixed error on MDF load under R2013b. Added ability to turn on/off scope grids. Protocol and user settings files from release 0.8+ will still work with this release.
0.803: (June 29, 2015) Fixed bug in ws.loadDataFile() that made it error if any channels were not active. Protocol and user settings files from release 0.8+ will still work with this release.
0.804: (July 3, 2015) Fixed bug that caused warnings on .cfg load if the acquisition sample rate had been changed. Restored green-on-black theme for scope windows as an option. Scope window buttons are now hidden if the window is not tall enough. Added option to always hide scope window buttons. Protocol and user settings files from release 0.8+ will still work with this release.
0.805: (July 23, 2015) Fixed bug that made it impossible to record if a user class was in use.
0.9-beta-1: (October 12, 2015) Major redesign of WaveSurfer to support low-latency (< 5 ms) real-time feedback loops. WaveSurfer now spawns two additional Matlab processes when you lauch it: one to aquire data and run real-time feedback loop code, and another to ensure that the sweep-based output buffer is refilled properly. Also some streamlining of the triggering settings, and changes in terminology (e.g. "trials" are now sweeps, an "experiment" is now a run). Note that this is a beta release, so is likely somewhat buggier than a regular release.
0.9-beta-2: (October 15, 2015) Fixed several bugs.
0.9-beta-3: (October 15, 2015) Fixed capitalization issues in the README.
0.9-beta-4: (October 17, 2015) Fixed another silly cosmetic bug.
0.9-beta-5: (October 29, 2015) Added missing DLL.
0.9-beta-6: (October 30, 2015) Fixed bug where satellite processes didn't have proper search path.
0.9-beta-7: (November 3, 2015) Fixed bug where zero digital inputs caused eventual error during acquisition.
0.9-beta-8: (November 9, 2015) Fixed several bugs.
0.9-beta-9: (November 9, 2015) Cosmetic fix.
0.9-beta-10: (November 11, 2015) Test Pulser now reports resistance in VC mode, instead of conductance. Minor improvements to ws.example.RasterTreadMill.
0.9-beta-11: (November 13, 2015) Fixes to WS-SI coordination code.
0.9-beta-12: (November 18, 2015) Fixed bug with triggering schemes, fixed bug with loading older WS data files.
0.9-beta-13: (November 18, 2015) Fixed bug with mimic()'ing cell arrays.
0.9-beta-14: (November 20, 2015) Fixed bug where didn't work if no input channels were defined.
0.9: (December 1, 2015) Rechristened 0.9-beta-14 as 0.9.