A Matlab application for browsing and analysis of electrophysiology data.
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+groundswell Improved error messages when Groundswell has difficulty loading a file. Jan 22, 2016
+roving Added option to export ROI mask from Roving. Jan 26, 2018
spike_scripts Add latest version of the Spike script for importing .tcs files. Sep 25, 2013
tmt_116 Improved error messages when Groundswell has difficulty loading a file. Jan 22, 2016
utility master: Fixed bugs in Roving under >= R2014b. Added "parula" colormap… Dec 8, 2015
NO_FRAME_TRANSFER_20exposures_rois.tcs Changed example data file name. May 22, 2012
README.md Updated.README. Jan 26, 2018
bayley_LHS_OK371_04.txt Added ability to load Bayley-style text files. Works. Jan 26, 2012
build.m Modified changes.txt in prep for release 1.18. Works. Sep 25, 2012
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groundswell.m Fixed enablement of Import ROI Data menu. Also added ability to give … Apr 14, 2012
hhmi_janelia_160px.png Added support for R2014b, added license, consolidated various notices… Jun 29, 2015
modpath.m Updated in-repo modpath.m script. Jan 26, 2018
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README.md

Groundswell

Groundswell is a Matlab application for browsing and analysis of electrophysiology data, optionally in concert with video data. It was developed by Adam L. Taylor, under the direction of Stefan R. Pulver, while Dr. Pulver was a fellow at HHMI Janelia.

System Requirements

Matlab R2013b or later (64-bit)

Installation

  1. Unzip the .zip file to a place of your choosing.

  2. In Matlab, go to File > Set Path...

  3. Remove any paths for older versions of Groundswell.

  4. Still in File > Set Path, click on "Add with Subfolders..." and select the Groundswell-release_(whatever) folder that was created when you unzipped the .zip file.

  5. Restart Matlab.

  6. Type "groundswell" or "roving" at the Matlab prompt to run the desired application.

Copyright

Except where noted, all code, documentation, images, and anything else in Groundswell is copyright 2009-2017 by Adam L. Taylor.

Contributions

Groundswell includes code from the TIFFStack project (https://github.com/DylanMuir/TIFFStack). This code carries a different copyright and license (see the project README for details).

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

Adam L. Taylor, taylora@hhmi.org
Scientific Computing
Janelia Research Campus
Howard Hughes Medical Institute

Picture

Version History

1.00 Original version. Includes Taylor Matlab Toolbox v1.06.


1.00->1.01 (August 31, 2011) Updated to use TMT v1.10.


1.01->1.02 (September 7, 2011)

Made each trace have its own timeline. This will be useful for, for example, looking at optical and electrical signals at the same time, since those often have very different sampling rates. Also added the ability to load data from a .tcs file.


1.02->1.03 (never completed)

Plan is to add ability to calculate coherency, cohereograms, and TFs. This will require some way to select two traces that is asymmetric, in that one signal will be the test, and one the reference, signal. Think I will add a visual indication of the last signal selected. Aborted this one. Doing coherences, etc. with different sampling rates is a royal pain, and I think not worth the effort.


1.01->1.04 (September 9, 2011)

Reverting to 1.01, starting from there. Dealing with calculating cross-power spectra from signals on different time bases is a pain in the ass at best. Also, it's arguably a bad idea, because then the user has to wonder about how the resampling is done.

Changed selections so that selected axes are indicated by a boldface axis label. I hope this makes it more apparent that the axes are the things selected, not a particular stretch of the data.

Changed selections so that the most-recently-selected axes (which I call the "pivot") is indicated visually, but italicizing the axis label. This also creates an asymmetry in the selection when two axes are selected, which enables the input and output signals to be specified when calculating coherency and TFs.

Fixed a bug with selections. Have to keep track of complete sequence of selection, so that the pivot one can change back to the previous one when you ctrl-select the pivot.

Added ability to calculate coherency, cohereograms, and TFs.

Added ability to set arbitrary y ranges on axes, and optimize the y ranges just on the selected axes.


1.04->1.05 (September 13, 2011)

Added the ability to read .tcs files. This involves upsampling of signals to a common time base in some cases, which is warned about.

Also changed the code that does resampling to the pixel grid, to eliminate use of blkproc(), which is deprecated. Re-coded in JIT-able Matlab. Is now ~2x faster.


1.05->1.06 (September 20, 2011)

Refactored the code so that there is a Groundswell_main class which implements the main Groundswell window. This let me move the groundswell progam state into this object, and out of the figure, axes, etc. userdata fields. This was always one the biggest weirdnesses with GUI programming in Matlab.

Fixed bug where debugging messages about the resampling method went to the command window.

Fixed bug where Groundswell_main.get_spectrogram_params() and Groundswell_main.get_spectrogram_params() didn't return enough args if user hit 'Cancel' or there was a problem with the params.

Changed what Groundswell_main methods I could to static class methods.

Fixed bug where errordlg() would sometimes cause the main figure contents to shrink.

Made it so y axis labels all line up w/ each other.

Deleted leading spaces from names & units on data load.


1.06 -> 1.07 (September 21, 2011)

Refactored code into some approximation of the MVC style. I think this will make it easier to think about and maintain going forward.

Put the test code into the groundswell directory, so that I can distribute the test code with the code proper.

First code checked into Janelia internal Subversion repository.

As with all versions since 1.01, groundswell 1.07 relies upon the Taylor Matlab Toolbox, version 1.10.


1.07 -> 1.08 (December 16, 2011)

Made the pivot signal the reference/input signal. This is better for making polar plots of the coherency of many channels with respect to a common reference (see below).

Added polar plots of coherency at a specified frequency, for multiple test signals. Raw data is also written to the clipboard in CSV format.

Changed the way selected channels are shown, to make more salient.

Fixed bugs in display of spectrograms, coherograms when the time origin for the current viewport is not zero.

Added display of f_res_diam, N_fft for all spectral plots.

This version relies upon Taylor Matlab Toolbox version 1.11.


1.08 -> 1.09 (April 24, 2012)

Many many changes and improvements, including the integration of Roving, a GUI for browsing and analyzing optical data.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.09 -> 1.10 (May 22, 2012)

Improved synching of ROI data, especially when there are many more exposure pulses than there are frames.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.10 -> 1.11 (July 17, 2012)

Roving now reads movies from disk, only loading a frame at a time into main memory. Also fixed a bug in which the "Coherency at probe frequency" report that is written to the clipboard was in the order that signals were selected, not the order they appear on screen. They now appear in the same order as onscreen.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.11 -> 1.12 (July 18, 2012)

In the "Coherency at probe frequency" report that is written to the clipboard, when the coherency magnitude is not significant, the coherency phase (and associated CI bounds) are reported as NaN.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.12 -> 1.13 (July 18, 2012)

Fixed a bug in which exporting ROI signals to a .tcs file didn't work.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.13 -> 1.14 (August 13, 2012)

Minor changes.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.14 -> 1.15 (August 14, 2012)

Fixed bug on Windows. Re-enabled "Play as audio" function, because it's very useful when it works.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.15 -> 1.16 (August 14, 2012)

Made shift-drag for square/circle ROI in Roving less fragile. Tested Roving on Windows XP. Groundswell no longer chokes on reading an all-nan signal from a .tcs file. Other minor changes.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.16 -> 1.17 (August 21, 2012)

The various menu items for automatically setting the colorbar bounds now look only at the current frame, not the whole movie.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.17 -> 1.18 (September 24, 2012)

Made the functions for adding ROI data more robust and more general, and renamed them to reflect this.

This version relies upon Taylor Matlab Toolbox version 1.13.


1.18 -> 1.19 (November 16, 2012)

Added scrollbar for time axis in Groundswell. Added options for modifying various aspects of the view in spectrogram, coherency plots. Added ability to resize Roving window. Implemented a minimum window size in Groundswell, Roving. Improved handling of videos with no frame rate information. Now use shaded backdrop for displaying power spectrum confidence interval. Added "Revert" function to Groundswell. Added ability to draw arbitrary polygonal ROIs in Roving.

This version relies upon Taylor Matlab Toolbox version 1.14.


1.19 -> 1.20 (December 11, 2012)

Fixed bug in Scrollbar that occurred when t0!=0.

This version relies upon Taylor Matlab Toolbox version 1.14.


1.20 -> 1.21 (April 26, 2013)

Refactored parts of Roving to improve scriptability.

This version relies upon Taylor Matlab Toolbox version 1.14.


1.21 -> 1.22 (January 2, 2013)

Included a Spike2 script for importing .tcs files into Spike2.

This version relies upon Taylor Matlab Toolbox version 1.14.


1.22 -> 1.23 (January 3, 2013)

Changed git repository to automatically include TMT 1.14 as a submodule.

Updated installation insttructions to match the .zip file names that GitHub assigns automatically.


1.23 -> 1.24 (January 23, 2015)

Added ability to import text files with column labels and time stamps.


1.24 -> 1.25 (May 3, 2015)

Changed to TMT 1.16, to get bugfixes relating to underspecification of character sets in load_abf() and .tcs functions.


1.25 -> 1.26 (June 29, 2015)

Consolided README.txt, copyright.txt into README.md. Added BSD 3-clause license. Added support for R2014b and later. Had to remove a couple of UI hacks, including support for Mac command key instead of Alt/Option key.


1.27 (June 29, 2015)

Included TMT 1.16 "by-hand", not as a submodule. GitHub doesn't include submodules in their automatic .zip files, which is how we currently distribute Groundswell. Fixed bug in README install instructions.


1.28 (December 8, 2015)

Fixed bugs in Roving under >= R2014b. Added "parula" colormap to Roving if using >= R2014b. Improved initial positioning of Groundswell, Roving windows.


1.29 (January 25, 2017)

Added support for ImageJ "jumbo" TIFF files.


1.30 (January 26, 2017)

Added ability to export ROI mask image.