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WaveSurfer ========== WaveSurfer is an application for acquiring electrophysiology data. It runs within Matlab R2015b and later (64-bit only). At present, you must have a Matlab license to use it. System Requirements ------------------- 64-bit Windows 7, 8, or 10 National Instruments X Series card (i.e. 63xx) National Instruments DAQmx driver, version 9.8.x or later. Matlab R2015b or later (64-bit) Installation ------------ 1. If you have a previous version of WaveSurfer installed, delete the entries for it from your Matlab path. 2. Download the .zip file for the latest release from here: http://wavesurfer.janelia.org/releases/index.html 3. Extract the .zip file contents to a convenient location. 4. In Matlab, cd to this just-created directory. 5. 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 "installWavesurferForNow" instead of the above. This modifies the path only for the current Matlab session.) 6. At the Matlab command line, execute "wavesurfer". You should now be presented with the WaveSurfer user interface. 7. Go to Protocol > Device & Channels... to specify what DAQ board you want to use, what channels you want to use, and to set channel units and scales, if desired. 8. Go to Protocol > General... to launch the general settings window. In it, click the Stimulation > Enabled checkbox to turn on stimulation. 9. In the main window, click the play button (the one with the black righward-pointing arrow) to acquire data without saving to disk. Click the record button (the one with the red circle) to acquire data and save it to disk. 10 To save your device settings, channel settings, and window positions, go to File > Save Protocol. These can then be loaded in a new WaveSurfer sessions by going to File > Open Protocol... 11. If you have questions, please contact the WaveSurfer developers. Copyright --------- Except where noted, all code, documentation, images, and anything else in WaveSurfer is copyright 2013-2022 by the Howard Hughes Medical Institute. License ------- Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 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. * 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. Authors ------- WaveSurfer was developed at the HHMI Janelia Research Campus. It started out as version 3 of Ephus, another electrophysiology package largely authored by Vijay Iyer, with contributions by Tim O'Connor and others. The original developer of WaveSurfer was Patrick Edson. WaveSurfer is currently developed by Adam L. Taylor, Ben J. Arthur, and David Ackerman. Contributions ------------- WaveSurfer includes code from the JSONlab project, by Qianqian Fang (https://github.com/fangq/jsonlab). This code is covered by its own copyright and licensing. We thank Dr. Fang for making it publicly available. Support ------- WaveSurfer is developed at the HHMI Janelia Research Campus. It is supported by the Svoboda Lab, who initiated the project, and by the Magee, Spruston, Jayaraman, Lee, Hantman, and Koyama Labs. The project is coordinated by Janelia's Scientific Computing Software group. Maintainers ----------- Adam L. Taylor Scientific Computing HHMI Janelia Research Campus Version History --------------- 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 Dec 01, 2015 Rechristened 0.9-beta-14 as 0.9. 0.901 Jan 07, 2016 Added support for DAQmx 15.1.x. Fixed bug in error dialog message if the installed version of DAQmx is not supported by WaveSurfer. 0.902 Jan 29, 2016 Fixed triggering issues that could cause acq tasks but not stim tasks to trigger for a finite-duration sweep, despite nominally using the same trigger. 0.91 Feb 12, 2016 All things that used to be set in the MDF file are now settable in the GUI, and stored in the protocol file. 0.912 Mar 01, 2016 Fixed bug in README. 0.913 Mar 02, 2016 Fixed bug which resulted in actual sampling rate being slightly different from nominal sampling rate for sampling rates (in Hz) that do not evenly divide 100 MHz. 0.914 Mar 11, 2016 Fixed bug where data was saved without scaling coefficients. Added code to ws.loadDataFile() convert nominal sampling rate for pre-0.913 data files to correct sampling rate. Added code to ws.loadDataFile() to error if asked to return floating-point (scaled) data when the data file lacks scaling coefficients, as a safeguard. 0.915 Mar 22, 2016 Added tool, ws.addScalingToHDF5FilesRecursively(), to automatically append device scaling information to .h5 data files that currently lack it. 0.916 Apr 14, 2016 All AI channels now explicitly set to differential terminal configuration. Stability and UI improvements. 0.917 Apr 15, 2016 Fixed bug in UI display of AO channel scale units. Verified bug went no deeper. 0.918 May 8, 2016 Fixed many small bugs, changed TemplateUserClass to ExampleUserClass, cleaned up ws.examples package. 0.919 Jun 1, 2016 Can now set test pulse y limits manually. Satellite Matlab windows are now hidden. Fixed issue with sweep timestamps being somewhat off. Improved speed of loading protocol files. Improved handling of old protocol files. Added ability to duplicate stimulus maps. Fixed issue with adding scaling coefficients to data files from WS v0.8. 0.9191 Jun 3, 2016 Fixed bug with listing device AI terminals when device has more than 16 (single-ended) AI terminals. 0.9192 Jun 3, 2016 Fixed bug with adding calibration coefficients to old files taken with devices with more than 16 (single-ended) AI terminals. 0.92 Jun 27, 2016 Added support for more recent versions of DAQmx. Can now duplicate stimuli, maps, sequences. Better support for old protocol files. Fixed bug causing errors on stimulus deletion in some cases. Can now write calibration data to disk, use that file to add calibration to data files. Fixed bug with electrode AO scaling. Added debugging mode which shows satellite windows running in full-JVM Matlab sessions. Added checkbox to optionally turn off electrode gain reading before a run or a test pulse. Added tooltips to fast protocol buttons. Improved speed of protocol file loading. Improvements to display and data scaling speed, especially for long sweeps. Fixed bug where stopping a run at an unlucky moment would put WS into a weird, unusable state. 0.921 Jul 26, 2016 Fixed another bug with manual stopping. 0.93 Aug 12, 2016 New chart-recorder-like display of traces. Improvements to user class handling. Includes two more custom user classes. 0.931 Aug 23, 2016 Fixed bug with loading protocol file with fewer input channels after taking data. 0.932 Sep 6, 2016 Fixed bug where outputs didn't get zeroed after a user-initiated stop. 0.933 Sep 6, 2016 README bug fix. 0.94 Oct 6, 2016 Changes to triggering to make it more flexible. Also made satellite processes leaner, and made changes to the stimulus library go through the main WavesurferModel. 0.941 Oct 14, 2016 Run will now continue past end of acquisition if stimulation is ongoing. Also fixed hangs in some situations. 0.942 Jan 11, 2017 User classes now print debug info to terminal. Updated and streamlined Bias user code. Also fixed bug with map durations loaded from protocol files. 0.943 Feb 22, 2017 Fixes to BIAS-WS interface, incorporating our own version of JSONLab. 0.945 Mar 10, 2017 Bug fix for MultiClamp 700A support. 0.946 Apr 3, 2017 Added support for MultiClamp 700B Commander 2.2. Fixed bug with y auto-scaling. Enhanced ws.examples.TriggerOnThresholdCrossingClass. 0.947 Apr 6, 2017 Added support for very-low sampling rates, down to ~1/(40 s). 0.95 Aug 9, 2017 Improved SI-WS integration, now using SI-WS communication protocol version 2.0.0. Input signals now displayed in main window, acquisition/stimulation settings moved to "General" window. Eliminated direct external access to WavesurferModel subsystems in user code. Eliminated Parent properties in all ws.Model objects. 0.951 Aug 24, 2017 Fixed bug where WS used built-in contains() function, only introduced in R2016b. 0.952 Aug 25, 2017 Fixed bug where Channels window didn't properly update after changes in the Electrodes window. 0.96 Sep 5, 2017 Added support for multiple DAQ boards. 0.961 Oct 14, 2017 Bug fixes. 0.962 Oct 18, 2017 Added new stimulus type. Streamlined handling of stimulus parameters. 0.963 Oct 18, 2017 Fixed bug. 0.964 Oct 19, 2017 Fixed bug with two square pulse stimulus. 0.965 Dec 13, 2017 Added Micro-Manager user class. Fixed bugs. 0.966 Jan 29, 2018 Fixed bug with untimed DO during TP not working. 0.967 Feb 1, 2018 Fixed bug with stim library figure not getting updated after protcol file load. 0.968 Feb 5, 2018 Fixed bugs with user code management. 0.97 Feb 7, 2018 Added wake() method to user classes. 0.98 Sep 13, 2018 Improvements to ws.loadDataFile(). 0.981 Oct 1, 2018 Bug fixes. 0.982 Apr 6, 2019 Fixed bug with finding NI DAQmx .h file. Fixed bug with HEKA integration in Matlab 2018a/b. Added example user class for controlling Hantman Lab pez dispenser. Added new user class method, willSaveToProtocolFile(). File stimulus can now load a .mat file. Fixed a few other bugs. 1.0 Apr 14, 2019 User settings files have been replaced with user profiles that act as preferences, requiring less user fiddling. WaveSurfer now does a better job of warning the user when they try to close a protocol with unsaved changes. Stimulus preview is no longer a second-class window, and now automatically updates when the current stimulus/map/sequence is changed. Dropped support for soft-real-time controllers in user code. Dropped support for Matlab 2014b and 2015a. 1.0.1 May 11, 2019 Fixed bugs. Pez controller example code is now suitable for the v2 pez dispenser. Switched to semantic versioning (https://semver.org/). 1.0.2 Jun 05, 2019 Fixed bug with opening old protocol files. 1.0.5 Dec 01, 2020 Updates to pez controller example. Added method to query whether logging is enabled to ws.WavesurferModel. 1.0.6 Apr 25, 2022 Fixed bug with TP not updating in recent Matlab versions, and TP window not resizing properly.