sigTOOL Demo

Demo version of the sigTOOL analysis package for neuroscience.

Description

N.B. This is a 10Mb file

THIS IS A DEMO VERSION OF THE SIGTOOL SOFTWARE PACKAGE.
It does not have the complete range of file import functions or speed of the full version of sigTOOL.

The full version is freely downloadable from:
http://sigtool.sourceforge.net/

A paper summarizing the main features of sigTOOL is available:
M. Lidierth (2009). sigTOOL: a MATLAB-based environment for sharing laboratory-developed software to analyze biological signals. Journal of Neuroscience Methods (in press).
http://dx.doi.org/10.1016/j.jneumeth.2008.11.004

SUMMARY
sigTOOL provides a programming and analysis environment for processing neuroscience data. A graphical-user interface to this environment provides the end-user with a self-contained application for waveform and spike-train analysis. User-written extensions to this application can be added to the interface on-the-fly without the need to modify any of the existing code.

DATA IMPORT
The full version of sigTOOL provides the tools to import data into MATLAB from many commonly used proprietory data files. These tools are not included in this demo version. Supported file types include:
ABF Molecular Devices Inc
CFS Cambridge Electronic Design
MAP Alpha Omega
NEV Cyberkinetics Inc
NEX Nex Technologies
PLX Plexon Instruments
SMR/SON Cambridge Electronic Design

Most of these file formats are supported via a manufacturer-supplied Windows application extension (dll), either directly (ABF, CFS) or via the Neuroshare/MATLAB API(MAP/NEX/PLX). The data import stage for these formats is therefore presently supported only on Windows platforms. Support for the SMR/SON format is platform-independent.
sigTOOL also includes support for multi-media file formats (wav, api, mp3 etc).

DATA ANALYSIS
Many standard analysis methods have been built into sigTOOL. These provide facilities for analyzing waveform and spike-train data and presently include:
WAVEFORM: Averaging (mean and median), amplitude distribution, auto- and cross-correlation, power spectral analysis, independent component analysis, coherence estimation, digital filtering (IIR and FIR) and resampling.
SPIKE TRAINS: Interspike interval distributions, Poincaré plots, stimulus driven peri-event time and phase histograms and rasters, frequencygrams, event auto- and cross- correlations and spike-triggered averaging. Automatic spike recognition is supported through an interface to the Wave_clus spike sorting package.
In addition, spike trains can be transformed to rate histograms allowing any of the waveform analysis routines above to be applied to them.

Note: HTML help files below should load correctly in sigTOOL but might not do so from this web site

• MATLAB release: MATLAB 7.6 (R2008a)
• Other requirements: Some components require the Signal Processing Toolbox. For spike sorting, the Wavelet Toolbox is also required.

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Other Files

sigTOOL/About sigTOOL.pdf,
sigTOOL/CORE/,
sigTOOL/CORE/Edit/,
sigTOOL/CORE/Edit/menu_CopyFigure.m,
sigTOOL/CORE/Edit/menu_Preferences/,
sigTOOL/CORE/File/,
sigTOOL/CORE/File/group_jjjHistory/,
sigTOOL/CORE/File/group_jjjHistory/menu_ClearHistory.m,
sigTOOL/CORE/File/group_jjjHistory/menu_PauseRecording.m,
sigTOOL/CORE/File/group_jjjHistory/menu_StartRecording.m,
sigTOOL/CORE/File/group_jjjHistory/menu_zSaveHistory.m,
sigTOOL/CORE/File/group_jjjHistory/private/,
sigTOOL/CORE/File/group_jjjHistory/private/StandardHeader.m,
sigTOOL/CORE/File/group_zzzPrint/,
sigTOOL/CORE/File/group_zzzPrint/menu_Print.m,
sigTOOL/CORE/File/group_zzzPrint/menu_PrintPreview.m,
sigTOOL/CORE/File/menu_aaaOpen.m,
sigTOOL/CORE/File/menu_aabNew.m,
sigTOOL/CORE/File/menu_aSaveAs.m,
sigTOOL/CORE/File/menu_BatchProcess.m,
sigTOOL/CORE/File/menu_Export/,
sigTOOL/CORE/File/menu_Export/group_Bitmaps/,
sigTOOL/CORE/File/menu_Export/group_Bitmaps/menu_ExportToBMP.m,
sigTOOL/CORE/File/menu_Export/group_Bitmaps/menu_ExportToTIF.m,
sigTOOL/CORE/File/menu_Export/group_VectorFormats/,
sigTOOL/CORE/File/menu_Export/group_VectorFormats/menu_ExportToAdobeIllustrator.m,
sigTOOL/CORE/File/menu_Export/group_VectorFormats/menu_ExportToAdobePDF.m,
sigTOOL/CORE/File/menu_Export/group_VectorFormats/menu_ExportToEPS.m,
sigTOOL/CORE/File/menu_Export/menu_aaaExportToMATLAB.m,
sigTOOL/CORE/File/menu_Import/,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/ImportMultiMedia.m,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/ImportWAV.m,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/menu_ImportMultiMedia.m,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/menu_ImportWAV.m,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/Micah Richert's mmread/,
sigTOOL/CORE/File/menu_Import/group_MultiMedia Formats/Micah Richert's mmread/Readme.txt,
sigTOOL/CORE/File/menu_Import/menu_BatchImport.m,
sigTOOL/CORE/File/menu_Information.m,
sigTOOL/CORE/File/menu_Information/,
sigTOOL/CORE/File/menu_Preferences.m,
sigTOOL/CORE/icons/,
sigTOOL/CORE/icons/arrow.png,
sigTOOL/CORE/icons/ChannelTreeWaveformClosed.gif,
sigTOOL/CORE/icons/ChannelTreeWaveformOpen.gif,
sigTOOL/CORE/icons/CursorMovePointer.mat,
sigTOOL/CORE/icons/CursorMovePointer.png,
sigTOOL/CORE/icons/DecreaseXRange.gif,
sigTOOL/CORE/icons/DecreaseXRange.png,
sigTOOL/CORE/icons/FileImport.png,
sigTOOL/CORE/icons/FileOpen.png,
sigTOOL/CORE/icons/IncreaseXRange.gif,
sigTOOL/CORE/icons/IncreaseXRange.png,
sigTOOL/CORE/icons/Print.png,
sigTOOL/CORE/icons/QuestionMark.gif,
sigTOOL/CORE/icons/RubberBox.png,
sigTOOL/CORE/icons/ScrollDown.png,
sigTOOL/CORE/icons/ScrollUp.png,
sigTOOL/CORE/icons/sigTOOL Welcome.gif,
sigTOOL/CORE/icons/StandardButton.png,
sigTOOL/CORE/icons/VerticalCursor.png,
sigTOOL/CORE/sigTOOL Cursor Functions/,
sigTOOL/CORE/sigTOOL Cursor Functions/menu_aaaNewVerticalCursor.m,
sigTOOL/CORE/sigTOOL Cursor Functions/menu_Delete.m,
sigTOOL/CORE/sigTOOL Cursor Functions/menu_LoadCursors.m,
sigTOOL/CORE/sigTOOL Cursor Functions/menu_SaveCursors.m,
sigTOOL/CORE/utils/,
sigTOOL/CORE/utils/@adcarray/,
sigTOOL/CORE/utils/@adcarray/adcarray.m,
sigTOOL/CORE/utils/@adcarray/display.m,
sigTOOL/CORE/utils/@adcarray/double.m,
sigTOOL/CORE/utils/@adcarray/end.m,
sigTOOL/CORE/utils/@adcarray/get.m,
sigTOOL/CORE/utils/@adcarray/horzcat.m,
sigTOOL/CORE/utils/@adcarray/isreal.m,
sigTOOL/CORE/utils/@adcarray/issparse_.m,
sigTOOL/CORE/utils/@adcarray/length.m,
sigTOOL/CORE/utils/@adcarray/set.m,
sigTOOL/CORE/utils/@adcarray/size.m,
sigTOOL/CORE/utils/@adcarray/subsasgn.m,
sigTOOL/CORE/utils/@adcarray/subsref.m,
sigTOOL/CORE/utils/@adcarray/vertcat.m,
sigTOOL/CORE/utils/@jcontrol/,
sigTOOL/CORE/utils/@jcontrol/ancestor.m,
sigTOOL/CORE/utils/@jcontrol/close.m,
sigTOOL/CORE/utils/@jcontrol/Contents.m,
sigTOOL/CORE/utils/@jcontrol/delete.m,
sigTOOL/CORE/utils/@jcontrol/get.m,
sigTOOL/CORE/utils/@jcontrol/getappdata.m,
sigTOOL/CORE/utils/@jcontrol/isappdata.m,
sigTOOL/CORE/utils/@jcontrol/jcontrol.m,
sigTOOL/CORE/utils/@jcontrol/private/,
sigTOOL/CORE/utils/@jcontrol/private/VisibleProperty.m,
sigTOOL/CORE/utils/@jcontrol/README.TXT,
sigTOOL/CORE/utils/@jcontrol/rmappdata.m,
sigTOOL/CORE/utils/@jcontrol/set.m,
sigTOOL/CORE/utils/@jcontrol/setappdata.m,
sigTOOL/CORE/utils/@jcontrol/subsasgn.m,
sigTOOL/CORE/utils/@jcontrol/subsref.m,
sigTOOL/CORE/utils/@scchannel/,
sigTOOL/CORE/utils/@scchannel/convIndex2Time.m,
sigTOOL/CORE/utils/@scchannel/convTime2PhysicalEpochs.m,
sigTOOL/CORE/utils/@scchannel/convTime2PhysicalIndex.m,
sigTOOL/CORE/utils/@scchannel/convTime2ValidEpochs.m,
sigTOOL/CORE/utils/@scchannel/convTime2ValidIndex.m,
sigTOOL/CORE/utils/@scchannel/display.m,
sigTOOL/CORE/utils/@scchannel/extractPhase.m,
sigTOOL/CORE/utils/@scchannel/extractPhysicalEpochData.m,
sigTOOL/CORE/utils/@scchannel/extractPhysicalEpochTimes.m,
sigTOOL/CORE/utils/@scchannel/extractPhysicalFrames.m,
sigTOOL/CORE/utils/@scchannel/extractValidEpochData.m,
sigTOOL/CORE/utils/@scchannel/extractValidEpochTimes.m,
sigTOOL/CORE/utils/@scchannel/extractValidFrames.m,
sigTOOL/CORE/utils/@scchannel/findMaxPostTime.m,
sigTOOL/CORE/utils/@scchannel/findMaxPreTime.m,
sigTOOL/CORE/utils/@scchannel/findPhysicalEpochs.m,
sigTOOL/CORE/utils/@scchannel/findPhysicalFrameIndices.m,
sigTOOL/CORE/utils/@scchannel/findValidEpochs.m,
sigTOOL/CORE/utils/@scchannel/findValidFrameIndices.m,
sigTOOL/CORE/utils/@scchannel/findVectorIndices.m,
sigTOOL/CORE/utils/@scchannel/get.m,
sigTOOL/CORE/utils/@scchannel/getData.m,
sigTOOL/CORE/utils/@scchannel/getPhase.m,
sigTOOL/CORE/utils/@scchannel/getPhysicalTriggers.m,
sigTOOL/CORE/utils/@scchannel/getSampleInterval.m,
sigTOOL/CORE/utils/@scchannel/getSampleRate.m,
sigTOOL/CORE/utils/@scchannel/getTimeUnits.m,
sigTOOL/CORE/utils/@scchannel/getTimeVector.m,
sigTOOL/CORE/utils/@scchannel/getValidEpochNumbers.m,
sigTOOL/CORE/utils/@scchannel/getValidTriggers.m,
sigTOOL/CORE/utils/@scchannel/inspect.m,
sigTOOL/CORE/utils/@scchannel/isInSynch.m,
sigTOOL/CORE/utils/@scchannel/isMultiplexed.m,
sigTOOL/CORE/utils/@scchannel/isSwapNeeded.m,
sigTOOL/CORE/utils/@scchannel/plot.m,
sigTOOL/CORE/utils/@scchannel/private/,
sigTOOL/CORE/utils/@scchannel/private/ConvertTimeToIndex.m,
sigTOOL/CORE/utils/@scchannel/scchannel.m,
sigTOOL/CORE/utils/@scchannel/set.m,
sigTOOL/CORE/utils/@scchannel/size.m,
sigTOOL/CORE/utils/@scchannel/subsasgn.m,
sigTOOL/CORE/utils/@scchannel/subsref.m,
sigTOOL/CORE/utils/@sigTOOLDataView/,
sigTOOL/CORE/utils/@sigTOOLDataView/filesaveas.m,
sigTOOL/CORE/utils/@sigTOOLDataView/get.m,
sigTOOL/CORE/utils/@sigTOOLDataView/postprinttidy.m,
sigTOOL/CORE/utils/@sigTOOLDataView/print.m,
sigTOOL/CORE/utils/@sigTOOLDataView/printprepare.m,
sigTOOL/CORE/utils/@sigTOOLDataView/printpreview.m,
sigTOOL/CORE/utils/@sigTOOLDataView/sigTOOLDataView.m,
sigTOOL/CORE/utils/@sigTOOLResultData/,
sigTOOL/CORE/utils/@sigTOOLResultData/display.m,
sigTOOL/CORE/utils/@sigTOOLResultData/get.m,
sigTOOL/CORE/utils/@sigTOOLResultData/plot.m,
sigTOOL/CORE/utils/@sigTOOLResultData/set.m,
sigTOOL/CORE/utils/@sigTOOLResultData/sigTOOLResultData.m,
sigTOOL/CORE/utils/@sigTOOLResultData/subsasgn.m,
sigTOOL/CORE/utils/@sigTOOLResultData/subsref.m,
sigTOOL/CORE/utils/@sigTOOLResultView/,
sigTOOL/CORE/utils/@sigTOOLResultView/filesaveas.m,
sigTOOL/CORE/utils/@sigTOOLResultView/get.m,
sigTOOL/CORE/utils/@sigTOOLResultView/postprinttidy.m,
sigTOOL/CORE/utils/@sigTOOLResultView/print.m,
sigTOOL/CORE/utils/@sigTOOLResultView/printprepare.m,
sigTOOL/CORE/utils/@sigTOOLResultView/printpreview.m,
sigTOOL/CORE/utils/@sigTOOLResultView/sigTOOLResultView.m,
sigTOOL/CORE/utils/@tstamp/,
sigTOOL/CORE/utils/@tstamp/display.m,
sigTOOL/CORE/utils/@tstamp/end.m,
sigTOOL/CORE/utils/@tstamp/get.m,
sigTOOL/CORE/utils/@tstamp/horzcat.m,
sigTOOL/CORE/utils/@tstamp/length.m,
sigTOOL/CORE/utils/@tstamp/set.m,
sigTOOL/CORE/utils/@tstamp/size.m,
sigTOOL/CORE/utils/@tstamp/subsasgn.m,
sigTOOL/CORE/utils/@tstamp/subsref.m,
sigTOOL/CORE/utils/@tstamp/tstamp.m,
sigTOOL/CORE/utils/@tstamp/vertcat.m,
sigTOOL/CORE/utils/callbackgetparam.m,
sigTOOL/CORE/utils/CopyObjects.m,
sigTOOL/CORE/utils/Cursors/,
sigTOOL/CORE/utils/Cursors/CreateCursor.m,
sigTOOL/CORE/utils/Cursors/CursorDemo.m,
sigTOOL/CORE/utils/Cursors/CursorWindowButtonMotionFcn.m,
sigTOOL/CORE/utils/Cursors/DeleteCursor.m,
sigTOOL/CORE/utils/Cursors/GetCursorLocation.m,
sigTOOL/CORE/utils/Cursors/KEEP/,
sigTOOL/CORE/utils/Cursors/KEEP/CreateCursor.m,
sigTOOL/CORE/utils/Cursors/KEEP/CursorWindowButtonMotionFcn.m,
sigTOOL/CORE/utils/Cursors/SetCursorLocation.m,
sigTOOL/CORE/utils/CurveFitting.m,
sigTOOL/CORE/utils/DataView/,
sigTOOL/CORE/utils/DataView/ChannelManager/,
sigTOOL/CORE/utils/DataView/ChannelManager/scChannelManager.m,
sigTOOL/CORE/utils/DataView/ChannelManager/scChannelTreeRowToChannelList.m,
sigTOOL/CORE/utils/DataView/ChannelManager/scGetChannelTree.m,
sigTOOL/CORE/utils/DataView/ExpandX.bmp,
sigTOOL/CORE/utils/DataView/scCleanUpAxes.m,
sigTOOL/CORE/utils/DataView/scCreateDataView.m,
sigTOOL/CORE/utils/DataView/scCreateFigControls.m,
sigTOOL/CORE/utils/DataView/scDataViewDrawChannelList.m,
sigTOOL/CORE/utils/DataView/scDataViewDrawData.m,
sigTOOL/CORE/utils/DataView/scGetFigureType.m,
sigTOOL/CORE/utils/DataView/scIncreaseXRange.m,
sigTOOL/CORE/utils/DataView/scInsertLogo.m,
sigTOOL/CORE/utils/DataView/scMarkerButtonDownFcn.m,
sigTOOL/CORE/utils/DataView/scReduceXRange.m,
sigTOOL/CORE/utils/DataView/scResizeFigControls.m,
sigTOOL/CORE/utils/DataView/scSliderAct.m,
sigTOOL/CORE/utils/DataView/scUpdateAxisControls.m,
sigTOOL/CORE/utils/DataView/scViewImageData.m,
sigTOOL/CORE/utils/DataView/scXAxisControls.m,
sigTOOL/CORE/utils/DataView/ShrinkX.bmp,
sigTOOL/CORE/utils/DataView/Untitled-3.bmp,
sigTOOL/CORE/utils/debounce.m,
sigTOOL/CORE/utils/Export/,
sigTOOL/CORE/utils/Export/scSendToExternalInterface.m,
sigTOOL/CORE/utils/Export/scSendToSigBrowse.m,
sigTOOL/CORE/utils/Export/Send To/,
sigTOOL/CORE/utils/Export/Send To/scSendToExcel.m,
sigTOOL/CORE/utils/Export/Send To/scSendToOrigin.m,
sigTOOL/CORE/utils/Export/Send To/scSendToSigmaPlot.m,
sigTOOL/CORE/utils/filtfilthd.m,
sigTOOL/CORE/utils/FirstRunMessage.m,
sigTOOL/CORE/utils/GetFit.m,
sigTOOL/CORE/utils/help2doc.m,
sigTOOL/CORE/utils/isOOM.m,
sigTOOL/CORE/utils/jcontrolDemo.m,
sigTOOL/CORE/utils/lpredict.m,
sigTOOL/CORE/utils/MAT/,
sigTOOL/CORE/utils/MAT/AddDimension.m,
sigTOOL/CORE/utils/MAT/AppendColumns.m,
sigTOOL/CORE/utils/MAT/AppendMatrix.m,
sigTOOL/CORE/utils/MAT/AppendVector.m,
sigTOOL/CORE/utils/MAT/CheckIsLastEntry.m,
sigTOOL/CORE/utils/MAT/Contents.m,
sigTOOL/CORE/utils/MAT/CreateMatrix.m,
sigTOOL/CORE/utils/MAT/endian.m,
sigTOOL/CORE/utils/MAT/GetLastEntry.m,
sigTOOL/CORE/utils/MAT/MATOpen.m,
sigTOOL/CORE/utils/MAT/private/,
sigTOOL/CORE/utils/MAT/private/AppendData.m,
sigTOOL/CORE/utils/MAT/private/argcheck.m,
sigTOOL/CORE/utils/MAT/private/ByteAlign.m,
sigTOOL/CORE/utils/MAT/private/ChangeDimensions.m,
sigTOOL/CORE/utils/MAT/private/Contents.m,
sigTOOL/CORE/utils/MAT/private/GetSmallDataElement.m,
sigTOOL/CORE/utils/MAT/private/PadToEightByteBoundary.m,
sigTOOL/CORE/utils/MAT/private/sizeof.m,
sigTOOL/CORE/utils/MAT/private/StandardMiCodes.m,
sigTOOL/CORE/utils/MAT/private/StandardMxCodes.m,
sigTOOL/CORE/utils/MAT/README.doc,
sigTOOL/CORE/utils/MAT/README.pdf,
sigTOOL/CORE/utils/MAT/README.txt,
sigTOOL/CORE/utils/MAT/RestoreDiscClass.m,
sigTOOL/CORE/utils/MAT/VarRename.m,
sigTOOL/CORE/utils/MAT/where.m,
sigTOOL/CORE/utils/PasteObjects.m,
sigTOOL/CORE/utils/RecordHistory.m,
sigTOOL/CORE/utils/ResultView/,
sigTOOL/CORE/utils/ResultView/KEEP/,
sigTOOL/CORE/utils/ResultView/KEEP/Edit/,
sigTOOL/CORE/utils/ResultView/KEEP/Edit/menu_CopyFigure.m,
sigTOOL/CORE/utils/ResultView/menu/,
sigTOOL/CORE/utils/ResultView/ResultManager/,
sigTOOL/CORE/utils/ResultView/ResultManager/private/,
sigTOOL/CORE/utils/ResultView/ResultManager/private/addLabel.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/CameraTool.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/DisplayMode.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/getPosition.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/LineColorCallback.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/LineOptions.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/LineWidthCallback.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/Options3D.m,
sigTOOL/CORE/utils/ResultView/ResultManager/private/ResetView.m,
sigTOOL/CORE/utils/ResultView/ResultManager/scResultManager.m,
sigTOOL/CORE/utils/ResultView/scDisplayResult.m,
sigTOOL/CORE/utils/ResultView/scPrepareResult.m,
sigTOOL/CORE/utils/scAddDistributionTool.m,
sigTOOL/CORE/utils/scAddPlot.m,
sigTOOL/CORE/utils/scBar.m,
sigTOOL/CORE/utils/scChannelInfo.m,
sigTOOL/CORE/utils/scCommit.m,
sigTOOL/CORE/utils/scContour.m,
sigTOOL/CORE/utils/scCreateKCLFile.m,
sigTOOL/CORE/utils/scCreateNewKCLFile.m,
sigTOOL/CORE/utils/scDecimate.m,
sigTOOL/CORE/utils/scDeleteFigure.m,
sigTOOL/CORE/utils/scDistributionTool.m,
sigTOOL/CORE/utils/scDrawSelectedChannels.m,
sigTOOL/CORE/utils/scEpochToVector.m,
sigTOOL/CORE/utils/scExecute.m,
sigTOOL/CORE/utils/scExportFigure.m,
sigTOOL/CORE/utils/scFilter.m,
sigTOOL/CORE/utils/scFindMatchingFs.m,
sigTOOL/CORE/utils/scFindSynchronized.m,
sigTOOL/CORE/utils/scFrames.m,
sigTOOL/CORE/utils/scGetBaseFolder.m,
sigTOOL/CORE/utils/scGetChannelsByType.m,
sigTOOL/CORE/utils/scGetChannelValues.m,
sigTOOL/CORE/utils/scGetCursorValues.m,
sigTOOL/CORE/utils/scGetFirstSampleTime.m,
sigTOOL/CORE/utils/scGetIcon.m,
sigTOOL/CORE/utils/scGetSubchannelList.m,
sigTOOL/CORE/utils/scGetTimePeriod.m,
sigTOOL/CORE/utils/scImagesc.m,
sigTOOL/CORE/utils/scImport.m,
sigTOOL/CORE/utils/scImportTrigger.m,
sigTOOL/CORE/utils/scLineSmoothing.m,
sigTOOL/CORE/utils/scMakeTempChannel.m,
sigTOOL/CORE/utils/scMaxSeconds.m,
sigTOOL/CORE/utils/scMaxTime.m,
sigTOOL/CORE/utils/scMinTime.m,
sigTOOL/CORE/utils/scOpen.m,
sigTOOL/CORE/utils/scParam.m,
sigTOOL/CORE/utils/scPlaySound.m,
sigTOOL/CORE/utils/scProcessDataView.m,
sigTOOL/CORE/utils/scProgressBar.m,
sigTOOL/CORE/utils/scRemap.m,
sigTOOL/CORE/utils/scResultViewButtonMotion.m,
sigTOOL/CORE/utils/scSaveAs.m,
sigTOOL/CORE/utils/scSaveImportedChannel.m,
sigTOOL/CORE/utils/scSavePreferences.m,
sigTOOL/CORE/utils/scScatter.m,
sigTOOL/CORE/utils/scSec.m,
sigTOOL/CORE/utils/scSetSubchannelList.m,
sigTOOL/CORE/utils/scSurf.m,
sigTOOL/CORE/utils/scVersion.m,
sigTOOL/CORE/utils/scWaterfall.m,
sigTOOL/CORE/utils/scWindowButtonDownFcn.m,
sigTOOL/CORE/utils/scWindowKeyPressFcn.m,
sigTOOL/CORE/utils/SincResample.m,
sigTOOL/CORE/utils/SmoothingContextMenu.m,
sigTOOL/CORE/utils/uifunctions/,
sigTOOL/CORE/utils/uifunctions/jvAddAverage.m,
sigTOOL/CORE/utils/uifunctions/jvAddCoherence.m,
sigTOOL/CORE/utils/uifunctions/jvAddCorrelation.m,
sigTOOL/CORE/utils/uifunctions/jvAddCurrentSourceDensity.m,
sigTOOL/CORE/utils/uifunctions/jvAddFastICA.m,
sigTOOL/CORE/utils/uifunctions/jvAddFFT.m,
sigTOOL/CORE/utils/uifunctions/jvAddFrequencygram.m,
sigTOOL/CORE/utils/uifunctions/jvAddIcasso.m,
sigTOOL/CORE/utils/uifunctions/jvAddPanel.m,
sigTOOL/CORE/utils/uifunctions/jvAddPETH.m,
sigTOOL/CORE/utils/uifunctions/jvAddPhaseHistogram.m,
sigTOOL/CORE/utils/uifunctions/jvAddPhaseRaster.m,
sigTOOL/CORE/utils/uifunctions/jvAddRaster.m,
sigTOOL/CORE/utils/uifunctions/jvAddRateChannel.m,
sigTOOL/CORE/utils/uifunctions/jvCreateUI.m,
sigTOOL/CORE/utils/uifunctions/jvDefaultPanel.m,
sigTOOL/CORE/utils/uifunctions/jvDisplay.m,
sigTOOL/CORE/utils/uifunctions/jvElement.m,
sigTOOL/CORE/utils/uifunctions/jvGetControlValue.m,
sigTOOL/CORE/utils/uifunctions/jvLinkChannelSelectors.m,
sigTOOL/CORE/utils/uifunctions/jvMakeFieldName.m,
sigTOOL/CORE/utils/uifunctions/jvPanel.m,
sigTOOL/CORE/utils/uifunctions/jvSetHelp.m,
sigTOOL/CORE/View/,
sigTOOL/CORE/View/menu_DataViewHiRes.m,
sigTOOL/CORE/View/menu_ToggleSmoothing.m,
sigTOOL/CORE/View/menu_ToggleText.m,
sigTOOL/demos/,
sigTOOL/demos/demo.kcl,
sigTOOL/documentation/,
sigTOOL/documentation/sigTOOL GUI User Guide.pdf,
sigTOOL/Installing sigTOOL.pdf,
sigTOOL/program/,
sigTOOL/program/AltLogo.bmp,
sigTOOL/program/AltLogo.gif,
sigTOOL/program/dir2menu.m,
sigTOOL/program/external_Cursors.m,
sigTOOL/program/external_SpikeTrainToolkit.m,
sigTOOL/program/File/,
sigTOOL/program/File/external_File.m,
sigTOOL/program/File/external_NeuroscienceFileImport.m,
sigTOOL/program/GetEmailAddress.m,
sigTOOL/program/Logo.bmp,
sigTOOL/program/Logo.gif,
sigTOOL/program/menu_Channels/,
sigTOOL/program/menu_Channels/_menu_ImportTrigger.m,
sigTOOL/program/menu_Channels/filters/,
sigTOOL/program/menu_Channels/filters/CursorEventFilter.m,
sigTOOL/program/menu_Channels/filters/cursorpositions.m,
sigTOOL/program/menu_Channels/filters/evenepochs.m,
sigTOOL/program/menu_Channels/filters/everynthepoch.m,
sigTOOL/program/menu_Channels/filters/matchall.m,
sigTOOL/program/menu_Channels/filters/matchany.m,
sigTOOL/program/menu_Channels/filters/oddepochs.m,
sigTOOL/program/menu_Channels/filters/private/,
sigTOOL/program/menu_Channels/filters/private/GetMatch.m,
sigTOOL/program/menu_Channels/group_zChannel Operations/,
sigTOOL/program/menu_Channels/group_zChannel Operations/private/,
sigTOOL/program/menu_Channels/group_zChannel Operations/private/help/,
sigTOOL/program/menu_Channels/group_zChannel Operations/private/help/_notes/,
sigTOOL/program/menu_Channels/menu_EventFilter.m,
sigTOOL/program/menu_Channels/menu_SelectSubchannel.m,
sigTOOL/program/menu_Channels/private/,
sigTOOL/program/menu_Channels/private/help/,
sigTOOL/program/menu_Channels/private/help/_notes/,
sigTOOL/program/menu_Channels/private/help/Marker Filters.jpg,
sigTOOL/program/menu_Channels/scApplyEventFilter.m,
sigTOOL/program/menu_Channels/scEventFilter.m,
sigTOOL/program/menu_Channels/scSelectSubchannel.m,
sigTOOL/program/menu_Waveform/,
sigTOOL/program/menu_Waveform/group_aaaWaveform/,
sigTOOL/program/menu_Waveform/group_aaaWaveform/menu_AmplitudeHistogram.m,
sigTOOL/program/menu_Waveform/group_aaaWaveform/menu_Average.m,
sigTOOL/program/menu_Waveform/group_aaaWaveform/menu_CurrentSourceDensity.m,
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sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/menu_JointIntervalDistribution.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/menu_PETH.m,
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sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/menu_Spike Sorting/,
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sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/eventcorr.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/private/,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/private/Cusum.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/rasterprep.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spCreateRateChannel.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spEventCorrelation.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spInterspikeInterval.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spJointIntervalDistribution.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spPeriEventFrequency.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spPhaseCorrelation.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spPhaseRaster.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spPoincare.m,
sigTOOL/sigTOOL Neuroscience Toolkit/Spike Train Toolkit/utils/spRaster.m

[hello hi]

 

[lee ..]

wow, this is AWESOME. I just started coding some of my own matlab analysis programs for plexon data, this program saves A LOT of time. Seems very well made, easy to install, and very intuitive interface. Does everything and more than NEX and does it in matlab so adds a lot of versatility. You can interface with it with your own code. It even has a a trigger filter which is just what I needed for some data (cuts all odd or even or nth triggers from data if you want it to).

[Evan Thomas]

Seems good but but the 'Pirate copy' popup that keeps appearing renders it unusable.

[Malcolm Lidierth]

Evan,
The 'Pirate Copy' message should only appear if you are a commercial user and have not followed the message contents:
"sigTOOL is free to academic and not-for-profit organizations only.
This PC appears to be on a commercial network.
Please contact [e-mail]".

[Yunguo]

Excellent MATLAB-based package I've ever seen for neural signal processing.

But I did encounter a problem with spiking sorting (using wave_clus under the menu "Spike Train". Can anyone tell me what the problem is? Thanks a lot in advance. The errors are:

Warning: File 'data_wc.dg_01.lab' not found.
> In run_cluster at 7
  In menu_InterfaceTo_wave_clus>Run at 235
Warning: File 'data_wc.dg_01' not found.
> In run_cluster at 8
  In menu_InterfaceTo_wave_clus>Run at 235
'.' is not recognized as an internal or external command,
operable program or batch file.
??? Error using ==> load
Unable to read file data_wc.dg_01.lab: No such file or directory.

Error in ==> run_cluster at 57
clu=load([fname '.dg_01.lab']);

Error in ==> menu_InterfaceTo_wave_clus>Run at 235
    [clu,tree]=run_cluster(handles);

??? Error while evaluating uicontrol Callback

[Malcolm Lidierth]

Yunguo

I am glad you like it.

menu_InterfaceTo_Wave_clus changes the present working directory to the system temprary folder so that temporary files created by wave_clus are written to that. It looks as though the directory is changing before the wave_clus run_cluster function is called- hence the file not found warnings and eventual error.

Put a breakpoint at line 8 of run_cluster and run clustering from the wave_clus GUI. When the debugger halts exection, try pwd and tempdir at the command line:
K>> pwd
ans =
C:\DOCUME~1\ML\LOCALS~1\Temp
K>> tempdir
ans =
C:\DOCUME~1\ML\LOCALS~1\Temp\

If these are not the same that explains the errors. Next you need to find why they are not the same because the command
cd(tempdir());
is issued in menu_InterfaceTo_Wave_clus. Are there any other routines running that might be changing the working directory?

The "'.' is not recognized as an internal or external command,
operable program or batch file. " may be related as the cluster executable is also copied to tempdir.
What OS are you using?

As a temporary fix, you may find the typing
K>>cd(tempdir());
when you hit the break point solves your problem.

[Malcolm Lidierth]

Yunguo
That breakpoint should be line 7 not 8.
ML

[Yunguo]

Dear Malcolm,

Thanks a lot.

I did what you said here. But the same error messages appeared

BY the way, I use Windows XP 64-bit,

Thanks again.

[Malcolm Lidierth]

OK.
The problem is 64 bit Windows. Wave_clus relies on a 32-bit Windows exe file.
Can that be run in a DOS window on 64-bit Windows?
Is it safe to try?
I do not know, so I will leave those questions to you.

If it is OK to run the cluster.exe file, then:
Put a break point at line 34 in run_cluster and check the value of handles.par.system which (I think) will be 'PCWIN64'. If it is, change line 35 of run_cluster to

case {'PCWIN', 'PCWIN64'}
(at present, the switch is defaulting to Linux).

Save the change and exit the debugger, then try again.

Good luck
Malcolm

[Yunguo]

Dear Malcolm,

Thank you so much. The cluster.exe can run in console of Windows XP 64 bit.

I change the PCWIN32 to PCWIN64, then wave_clus is working fine now.

Thanks again!!!

Yunguo

[Yunguo]

 

[Yunguo]

Dear Malcolm,

It is very nice that sigTOOL integrates the wave_clus to do spike-sorting. But I just wonder how can I do batch spike-sorting of multiple-channel recordings by using sigTOOL. Specifically, I would like to do is:
1. let sigTOOL to open mutiple files ( that I think it is possible to use menu batch process).
2. use Wave_clus to sort these files (each file contains multiple spiking channels).
3. save sorted spikes to a new channels and save file, then do next file and so on.

I have tried to use batch process in the menu, but not much success. It would be very kind of you if you can comment on this point. I think a lot of people out there would like to have the capability of doing batch spiking.

Thanks in advance.

Yunguo

[Malcolm Lidierth]

Yunguo
To the best of my knowledge, this is the the only place where batch processing is presently not supported. I should have stated that in the documentation.
sigTOOL does not support Wave_clus for batch processing because it works through the Wave_clus GUI: Wave_clus parameters etc are extracted from the GUI userdata areas and user interaction is assumed. Wave_clus was designed to run as a stand-alone GUI, not in sigTOOL so it would take some work to include batch processing.
However, Wave_clus does provide batch processing routines and, in principle, unsupervised batch processing could be added to sigTOOL if enough users requested it.
Regards
Malcolm
 

[Lingyun Zhao]

Good tool and easy to use, especially it include a lot of file format. This is unique among the neural softwares.

[ste costa]

Hi all,

I think sigTOOL can be a powerfull tool for analyzing neural data, but I could not explore its full potentiality because I'm not able to import my plexon dataset into it (until now I visualised data in wav format, but without events information):

I use Matlab R2008a and after launching sigTOOL gui, I run this:

>> ns_SetLibrary(which('nsPlxLibrary.dll'))

it return:

ans =

          0

After, I try to import *****.plx file but loading bar freezes at 13%; matlab command displays this errors:

??? In an assignment A(:) = B, the number of elements in A and B
must be the same.

Error in ==> ImportNS at 171
                imp.adc((k-1)*blocksize+1:(k-1)*blocksize+count)=data;

Error in ==> scImport at 50
targetfile=funchandle(fullfile(pathname, name), targetpath);

Error in ==> menu_ImportPLX at 38
    scImport(@ImportNS, '*.plx');

??? Error while evaluating uimenu Callback

can someone help me????

thank a lot!
Ste

[Malcolm Lidierth]

For ste costa

The file import functions are not included in this demo version because TMW no longer allows dlls to be included on MATLAB Cental submissions.

To get the full version of sigTOOL, complete with the import functions you require visit

http://sigtool.sourceforge.net/

[ste costa]

thanks, Malcom

I already have complete version of sigTOOL, but this was not the correct place where having a discussion about.

best,
Ste

[Yunguo]

the new version Wave_clus (2.0) does not work with the sigTOOL:

http://www.vis.caltech.edu/~rodri/Wave_clus/Wave_clus_home.htm

[Malcolm Lidierth]

Wave_clus 2.0 is supported in the latest version of sigTOOL at http://sigtool.sourceforge.net/

[Xiping Zhan]

It's nice software. But how to export the graph into a spreadsheet style data or send ActiveX.

[Malcolm Lidierth]

Xiping
Just right-click and choose Send To. That gives you a choice of Excel, SigmaPlot and Origin and will export the data to those (if installed).

[Xiping Zhan]

Thank you. Malcolm,
It seems to me that there is no choice of Excel, SigmaPlot or Origin when right-click the mouse. There is only Signal browser and sgTool open automatically.

Besides, it is not consistent to export figures as pdf,tif,or ai,etc.

[Malcolm Lidierth]

Xiping
I think I see what is happening. The option to export data in PDF, TIF etc, and also to Send data to Excel, Sigmaplot etc is available in a sigTOOL result view showing e.g. averages. The GUI manual gives details.
It is not supported in a data view which is the view you appear to be clicking on. It could be if there were enough demand.
Regards
Malcolm

[Flor]

 How do I import signals that are already in .mat format? Thanks

[Malcolm Lidierth]

Flor,
You would need to write an import function that would create a MAT file containing the variables required by sigTOOL. The Programmer Guide contains details
Regards
ML

[Ryan Maloney]

 

[Ryan Maloney]

Hi Malcolm,
Thanks for sharing this great new package, it's an excellent time-saver and very user-friendly: it's been a long time coming on the Matlab platform.
I agree with Yunguo that it would be good to batch process spike sorting via the interface with wave_clus.
One suggestion though, there are some parameters not on the Edit Parameters GUI (such as the max. no. of clusters allowed) that could be included. It wasn't clear to me at first that they'd need to be edited directly in the set_parameters_simulation.m file included with wave_clus.
Regards,
Ryan M

[Malcolm Lidierth]

Ryan
It is easy to add more parameters. Just edit the 'names' cell array in the EditStructureGUI function in menu_InterfaceTo_wave_clus.m. E.g.

names={'stdmin',...
    'stdmax',...
    ................
    ................
    'max_spk',...
    'max_clus'};

Remember though, that these values are reset via set_parameters_simulation.m when you load a new channel so editing set_parameters_simulation.m may be more convenient.

As for batch processing, that could probably be included if there were enough demand but there are a lot of other things on the TODO list.

[Spencer Chen]

I just started using this tool. Very impressive Malcolm. I like the look and feel of the GUI. Much better than the other toolbox I have also been playing around with (FIND).

Anyways, I implemented my custom importer for TDT data using the Neuroshare interface. The data loaded okay, but in the process of using features of this toolbox, I find myself having to debug through several show-stopping errors. A little anonying and frustrating, but I speak Matlab enough to be able to work through them.

[Malcolm Lidierth]

Spencer
Great. I have had a few enquiries about TDT. How about sharing your importer?
As far as those errors are concerned - if they are in sigTOOL, please supply details.
Regards
Malcolm