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mPhys

by Phil Larimer

 

27 Oct 2008 (Updated 03 Dec 2008)

Code covered by the BSD License  

Software for acquisition and manipulation of electrophysiological data from neurons.

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File Information
Description

This is a collection of GUIs and functions for use with an Instrutech ITC18 for acquisition of electrophysiological data. It has functionality for injecting waveforms into various amplifiers and recording the results. It also has a data file browser and a data manipulation GUI for detecting various events and filtering output signals. In addition it has functionality for image manipulation. All functions can also be used on Izhikevich or Hodgkin-Huxley style simulated neurons as a basic teaching tool for what electrophysiological recordings of neurons are like.
MATLAB release MATLAB 7.5 (R2007b)
Other requirements 32-bit windows ITC-18 data acquisition hardware Amplifiers
Zip File Content  
Other Files
mPhys/acquire/,
mPhys/acquire/experiment/,
mPhys/acquire/experiment/axoPatchAlpha.m,
mPhys/acquire/experiment/bridgeBalance.m,
mPhys/acquire/experiment/changeRunningChannel.m,
mPhys/acquire/experiment/Contents.m,
mPhys/acquire/experiment/doRepeat.m,
mPhys/acquire/experiment/doSingle.asv,
mPhys/acquire/experiment/doSingle.m,
mPhys/acquire/experiment/doStream.m,
mPhys/acquire/experiment/experiment.asv,
mPhys/acquire/experiment/experiment.fig,
mPhys/acquire/experiment/experiment.m,
mPhys/acquire/experiment/experimentTimer.asv,
mPhys/acquire/experiment/experimentTimer.m,
mPhys/acquire/experiment/generateStim.m,
mPhys/acquire/experiment/itc18.m,
mPhys/acquire/experiment/newSequence.m,
mPhys/acquire/experiment/reducedNeurons.m,
mPhys/acquire/experiment/saveExperiment.m,
mPhys/acquire/experiment/sealTest.m,
mPhys/acquire/experiment/setDataFolder.m,
mPhys/acquire/experiment/startRunningScope.asv,
mPhys/acquire/experiment/startRunningScope.m,
mPhys/acquire/experiment/updateExperiment.m,
mPhys/acquire/protocolViewer/,
mPhys/acquire/protocolViewer/addAmp.m,
mPhys/acquire/protocolViewer/changeAcquisitionRate.m,
mPhys/acquire/protocolViewer/changeAdBoard.m,
mPhys/acquire/protocolViewer/changeAmp.m,
mPhys/acquire/protocolViewer/changeCell.m,
mPhys/acquire/protocolViewer/changeCurrent.m,
mPhys/acquire/protocolViewer/changeTelegraph.m,
mPhys/acquire/protocolViewer/changeTtlType.m,
mPhys/acquire/protocolViewer/changeVoltage.m,
mPhys/acquire/protocolViewer/checkAcquisitionRate.m,
mPhys/acquire/protocolViewer/Contents.m,
mPhys/acquire/protocolViewer/createTTL.m,
mPhys/acquire/protocolViewer/currentAmps.m,
mPhys/acquire/protocolViewer/defaultProtocol.mat,
mPhys/acquire/protocolViewer/defaultProtocol16.mat,
mPhys/acquire/protocolViewer/defaultProtocol4.mat,
mPhys/acquire/protocolViewer/defaultProtocol8.mat,
mPhys/acquire/protocolViewer/isProtocol.m,
mPhys/acquire/protocolViewer/loadProtocol.m,
mPhys/acquire/protocolViewer/makeProtocol.m,
mPhys/acquire/protocolViewer/protocolViewer.m,
mPhys/acquire/protocolViewer/removeAmp.m,
mPhys/acquire/protocolViewer/saveProtocol.m,
mPhys/acquire/protocolViewer/tabChange.m,
mPhys/acquire/protocolViewer/template/,
mPhys/acquire/protocolViewer/template/ampContainer.fig,
mPhys/acquire/protocolViewer/template/ampPanel.fig,
mPhys/acquire/protocolViewer/template/channelPanel.fig,
mPhys/acquire/protocolViewer/template/imagingPanel.fig,
mPhys/acquire/protocolViewer/template/main.fig,
mPhys/acquire/protocolViewer/template/ttlContainer.fig,
mPhys/acquire/protocolViewer/template/ttlPanel.fig,
mPhys/buildSource.m,
mPhys/Coupling/,
mPhys/Coupling/alpha.m,
mPhys/Coupling/averageCoupling.m,
mPhys/Coupling/averageOnly.m,
mPhys/Coupling/batchAverage.m,
mPhys/Coupling/batchClassification.m,
mPhys/Coupling/batchCoupling.m,
mPhys/Coupling/batchDelta.m,
mPhys/Coupling/batchSTA.m,
mPhys/Coupling/characterizePSPs.m,
mPhys/Coupling/checkCoupling.m,
mPhys/Coupling/checkSTA.m,
mPhys/Coupling/cleanUpCoupling.m,
mPhys/Coupling/Contents.m,
mPhys/Coupling/CV2.m,
mPhys/Coupling/detectPSPs.m,
mPhys/Coupling/excelCoupling.m,
mPhys/Coupling/featureVsPotential.m,
mPhys/Coupling/generateEpisodes.m,
mPhys/Coupling/generateStats.m,
mPhys/Coupling/generateTraces.m,
mPhys/Coupling/overlayPSPs.m,
mPhys/Coupling/pspGUI.fig,
mPhys/Coupling/pspGui.m,
mPhys/Coupling/setupCoupling.m,
mPhys/Coupling/setupSTA.m,
mPhys/Coupling/showFit.m,
mPhys/Coupling/stimStats.m,
mPhys/Coupling/zoomCoupling.m,
mPhys/Coupling/zoomSTA.m,
mPhys/experimentCommands.txt,
mPhys/FileBrowser/,
mPhys/FileBrowser/Columns/,
mPhys/FileBrowser/Columns/stimTypeColumn.m,
mPhys/FileBrowser/defaultColumns.txt,
mPhys/FileBrowser/defaultColumnsImage.txt,
mPhys/FileBrowser/Directory Characterization/,
mPhys/FileBrowser/Directory Characterization/categorizeHilarNeuron.m,
mPhys/FileBrowser/Directory Characterization/checkEpisodesCoupling.m,
mPhys/FileBrowser/Directory Characterization/checkEpisodesSTA.m,
mPhys/FileBrowser/Directory Characterization/checkWithinEpisodesSTA.m,
mPhys/FileBrowser/Directory Characterization/checkWithinEpisodesSTO.m,
mPhys/FileBrowser/Directory Characterization/compressZStack.m,
mPhys/FileBrowser/Directory Characterization/Read Me.txt,
mPhys/FileBrowser/Directory Characterization/reconstructCell.m,
mPhys/FileBrowser/Episode Characterization/,
mPhys/FileBrowser/Episode Characterization/checkSingleEpisodeCoupling.m,
mPhys/FileBrowser/Episode Characterization/checkSingleEpisodeSTA.m,
mPhys/FileBrowser/Episode Characterization/checkWithinSingleEpisodeSTA.m,
mPhys/FileBrowser/Episode Characterization/checkWithinSingleEpisodeSTO.m,
mPhys/FileBrowser/Episode Characterization/Read Me.txt,
mPhys/FileBrowser/fileBrowser.asv,
mPhys/FileBrowser/fileBrowser.jar,
mPhys/FileBrowser/fileBrowser.m,
mPhys/FileBrowser/Icons/,
mPhys/FileBrowser/Icons/drive.gif,
mPhys/FileBrowser/Icons/empty.gif,
mPhys/FileBrowser/Icons/folderClosed.gif,
mPhys/FileBrowser/Icons/folderOpen.gif,
mPhys/FileBrowser/Icons/folderZip.gif,
mPhys/FileBrowser/Icons/imageCellPart.gif,
mPhys/FileBrowser/Icons/imageCellRecon.gif,
mPhys/FileBrowser/Icons/imageLowRes.gif,
mPhys/FileBrowser/Icons/imageWholeCell.gif,
mPhys/FileBrowser/Icons/imgPics.gif,
mPhys/FileBrowser/Icons/imgs.gif,
mPhys/FileBrowser/Icons/imgsTraces.gif,
mPhys/FileBrowser/Icons/imgsTracesPics.gif,
mPhys/FileBrowser/Icons/myComputer.gif,
mPhys/FileBrowser/Icons/pics.gif,
mPhys/FileBrowser/Icons/sequence.gif,
mPhys/FileBrowser/Icons/Thumbs.db,
mPhys/FileBrowser/Icons/traces.gif,
mPhys/FileBrowser/Icons/tracesPics.gif,
mPhys/FileBrowser/Single Compartment/,
mPhys/FileBrowser/Single Compartment/Contents.m,
mPhys/FileBrowser/Single Compartment/gA.m,
mPhys/FileBrowser/Single Compartment/gK.m,
mPhys/FileBrowser/Single Compartment/gNa.m,
mPhys/FileBrowser/Single Compartment/HH.m,
mPhys/FileBrowser/User-Added Dependecies/,
mPhys/FileBrowser/User-Added Dependecies/fastAHPSlope2.m,
mPhys/FileBrowser/User-Added Dependecies/numSpikes.asv,
mPhys/FileBrowser/User-Added Dependecies/numSpikes.m,
mPhys/Hardware/,
mPhys/Hardware/asiGUI.fig,
mPhys/Hardware/asiGui.m,
mPhys/Hardware/audioScope.fig,
mPhys/Hardware/audioScope.m,
mPhys/Hardware/captureGUI.fig,
mPhys/Hardware/captureGUI.m,
mPhys/Hardware/changeAudioChannel.m,
mPhys/Hardware/Contents.m,
mPhys/Hardware/ezVidC60.ocx,
mPhys/Hardware/focusMode.m,
mPhys/Hardware/mitutoyoGui.asv,
mPhys/Hardware/mitutoyoGUI.fig,
mPhys/Hardware/mitutoyoGui.m,
mPhys/Hardware/readASI.m,
mPhys/Hardware/readMitutoyo.m,
mPhys/Hardware/setupASI.m,
mPhys/Hardware/setupMitutoyo.m,
mPhys/Hardware/takeTwoPhotonImage.m,
mPhys/Hardware/twoPhotonGUI.m,
mPhys/imageBrowser/,
mPhys/imageBrowser/bestShift.m,
mPhys/imageBrowser/blue.m,
mPhys/imageBrowser/bnw.m,
mPhys/imageBrowser/calcROI.m,
mPhys/imageBrowser/clearROI.m,
mPhys/imageBrowser/clusterHist.m,
mPhys/imageBrowser/combineImageStacks.m,
mPhys/imageBrowser/compressImageStack.m,
mPhys/imageBrowser/Contents.m,
mPhys/imageBrowser/convertPock.m,
mPhys/imageBrowser/correctX.m,
mPhys/imageBrowser/correctY.m,
mPhys/imageBrowser/cyan.m,
mPhys/imageBrowser/cyan2red.m,
mPhys/imageBrowser/determineScannerSpeed.m,
mPhys/imageBrowser/displayImage.m,
mPhys/imageBrowser/drawROI.m,
mPhys/imageBrowser/ellipseScan.m,
mPhys/imageBrowser/exportFrame.m,
mPhys/imageBrowser/green.m,
mPhys/imageBrowser/highlightROI.m,
mPhys/imageBrowser/imageBrowser.fig,
mPhys/imageBrowser/imageBrowser.m,
mPhys/imageBrowser/lineScan.m,
mPhys/imageBrowser/lissajousScan.m,
mPhys/imageBrowser/loadROI.m,
mPhys/imageBrowser/locateCells.m,
mPhys/imageBrowser/makeRaster.m,
mPhys/imageBrowser/micronsPerPixel.m,
mPhys/imageBrowser/pixelsPerMicron calibration.opj,
mPhys/imageBrowser/printFrame.m,
mPhys/imageBrowser/processImage.m,
mPhys/imageBrowser/purple.m,
mPhys/imageBrowser/purple2green.m,
mPhys/imageBrowser/rasterScan.fig,
mPhys/imageBrowser/rasterScan.m,
mPhys/imageBrowser/readRaster.m,
mPhys/imageBrowser/red.m,
mPhys/imageBrowser/redSat.m,
mPhys/imageBrowser/resizeImage.m,
mPhys/imageBrowser/saveImageAs.m,
mPhys/imageBrowser/saveMovie.m,
mPhys/imageBrowser/saveROI.m,
mPhys/imageBrowser/scaleBar.m,
mPhys/imageBrowser/sequenceScan.m,
mPhys/imageBrowser/setCrossHairs.m,
mPhys/imageBrowser/setCursor.m,
mPhys/imageBrowser/setReference.m,
mPhys/imageBrowser/setSliders.m,
mPhys/imageBrowser/shapeRaster.m,
mPhys/imageBrowser/shapeRasterBackup.m,
mPhys/imageBrowser/showHighPower.m,
mPhys/imageBrowser/showScaleBar.m,
mPhys/imageBrowser/spiralScan.m,
mPhys/imageBrowser/traceCell.m,
mPhys/imageBrowser/transferCellOutline.m,
mPhys/imageBrowser/transferPoints.m,
mPhys/imageBrowser/transferROI.m,
mPhys/imageBrowser/updateAverage.m,
mPhys/imageBrowser/yellow.m,
mPhys/imageBrowser/yellow2blue.m,
mPhys/imageBrowser/zStack.fig,
mPhys/imageBrowser/zStackGui.m,
mPhys/imageBrowserCommands.txt,
mPhys/ITC18VB.dll,
mPhys/newScopeCommands.txt,
mPhys/Scope/,
mPhys/Scope/Corel Importer.txt,
mPhys/Scope/Event Characterization/,
mPhys/Scope/Event Characterization/autoCorrelate.m,
mPhys/Scope/Event Characterization/calcBurstProb.m,
mPhys/Scope/Event Characterization/calcSTA.m,
mPhys/Scope/Event Characterization/calcSTO.m,
mPhys/Scope/Event Characterization/commonEvents.m,
mPhys/Scope/Event Characterization/crosscorrelateSetup.m,
mPhys/Scope/Event Characterization/intervalHist.m,
mPhys/Scope/Event Characterization/isiCvEvents.m,
mPhys/Scope/Event Characterization/jointDist.m,
mPhys/Scope/Event Characterization/metaCorrEvents.m,
mPhys/Scope/Event Characterization/plotAverageFreq.m,
mPhys/Scope/Event Characterization/plotFreq.m,
mPhys/Scope/Event Characterization/plotPercentCorrelation.m,
mPhys/Scope/Event Characterization/Read Me.txt,
mPhys/Scope/Event Detection/,
mPhys/Scope/Event Detection/detectCellAttached.m,
mPhys/Scope/Event Detection/detectExtracellular.m,
mPhys/Scope/Event Detection/detectPSP.m,
mPhys/Scope/Event Detection/detectWCAPs.m,
mPhys/Scope/Event Detection/Read Me.txt,
mPhys/Scope/Experiment Characterization/,
mPhys/Scope/Experiment Characterization/freqVsTimePlot.m,
mPhys/Scope/Experiment Characterization/generateIV.m,
mPhys/Scope/Experiment Characterization/Read Me.txt,
mPhys/Scope/Experiment Characterization/rIn.asv,
mPhys/Scope/Experiment Characterization/rIn.m,
mPhys/Scope/Experiment Characterization/sag.m,
mPhys/Scope/Experiment Characterization/slowAHP.m,
mPhys/Scope/Fitting/,
mPhys/Scope/Fitting/fit1Exp.m,
mPhys/Scope/Fitting/fit2Exp.m,
mPhys/Scope/Fitting/fit3Exp.m,
mPhys/Scope/Fitting/fitAlpha.m,
mPhys/Scope/Fitting/fitLine.m,
mPhys/Scope/Fitting/fitSine.m,
mPhys/Scope/Fitting/Read Me.txt,
mPhys/Scope/Helper Functions/,
mPhys/Scope/Helper Functions/analysisAxis.m,
mPhys/Scope/Helper Functions/colorSpread.m,
mPhys/Scope/Helper Functions/Contents.m,
mPhys/Scope/Helper Functions/exportSettings.m,
mPhys/Scope/Helper Functions/exportWithAxes.m,
mPhys/Scope/Helper Functions/exportWithScaleBars.m,
mPhys/Scope/Helper Functions/msec2point.asv,
mPhys/Scope/Helper Functions/msec2point.m,
mPhys/Scope/Helper Functions/newScale.m,
mPhys/Scope/Helper Functions/prepForPrint.m,
mPhys/Scope/Helper Functions/printWithAxes.asv,
mPhys/Scope/Helper Functions/printWithAxes.m,
mPhys/Scope/Helper Functions/printWithScaleBars.m,
mPhys/Scope/Helper Functions/setAxisLabels.m,
mPhys/Scope/Helper Functions/showEvents.m,
mPhys/Scope/Helper Functions/showFrameMarker.m,
mPhys/Scope/Helper Functions/showStims.m,
mPhys/Scope/Helper Functions/timeControl.m,
mPhys/Scope/newScope.asv,
mPhys/Scope/newScope.m,
mPhys/Scope/Trace Characterization/,
mPhys/Scope/Trace Characterization/apHeight.m,
mPhys/Scope/Trace Characterization/apRiseFallRatio.m,
mPhys/Scope/Trace Characterization/apThreshold.m,
mPhys/Scope/Trace Characterization/apWidth.m,
mPhys/Scope/Trace Characterization/apWidthHM.m,
mPhys/Scope/Trace Characterization/autoNotch.m,
mPhys/Scope/Trace Characterization/fastAHP.m,
mPhys/Scope/Trace Characterization/fastAHPSlope.m,
mPhys/Scope/Trace Characterization/Read Me.txt,
mPhys/Scope/User Manual.rtf,
mPhys/Scope/User-Added Dependencies/,
mPhys/Scope/User-Added Dependencies/bandStop.m,
mPhys/Scope/User-Added Dependencies/burstingProbability.m,
mPhys/Scope/User-Added Dependencies/calcMean.m,
mPhys/Scope/User-Added Dependencies/cell2mat.m,
mPhys/Scope/User-Added Dependencies/characterizePSPs.m,
mPhys/Scope/User-Added Dependencies/crossCorr.m,
mPhys/Scope/User-Added Dependencies/detectPSPs.m,
mPhys/Scope/User-Added Dependencies/detectSpikes.m,
mPhys/Scope/User-Added Dependencies/eventTriggeredAverage.asv,
mPhys/Scope/User-Added Dependencies/eventTriggeredAverage.m,
mPhys/Scope/User-Added Dependencies/fcnMin.m,
mPhys/Scope/User-Added Dependencies/findSteps.m,
mPhys/Scope/User-Added Dependencies/findStims.m,
mPhys/Scope/User-Added Dependencies/fitDecayDouble.m,
mPhys/Scope/User-Added Dependencies/fitDecaySingle.m,
mPhys/Scope/User-Added Dependencies/fitDecayTriple.m,
mPhys/Scope/User-Added Dependencies/highPass.m,
mPhys/Scope/User-Added Dependencies/isiCv.m,
mPhys/Scope/User-Added Dependencies/lowPass.m,
mPhys/Scope/User-Added Dependencies/metaBar.m,
mPhys/Scope/User-Added Dependencies/movingAverage.m,
mPhys/Scope/User-Added Dependencies/movingBlock.m,
mPhys/Scope/User-Added Dependencies/MTEO.m,
mPhys/Scope/User-Added Dependencies/normalizeMatrix.m,
mPhys/Scope/User-Added Dependencies/notchFilter.asv,
mPhys/Scope/User-Added Dependencies/notchFilter.m,
mPhys/Scope/User-Added Dependencies/oneSidedDeviation.m,
mPhys/Scope/User-Added Dependencies/overlayPSPs.m,
mPhys/Scope/User-Added Dependencies/pspGui.m,
mPhys/Scope/User-Added Dependencies/whichChannel.m,
mPhys/setupFiles.m,
mPhys/Stats/,
mPhys/Stats/binopdf.m,
mPhys/Stats/distchck.m,
mPhys/Stats/histfit.m,
mPhys/Stats/nanmean.m,
mPhys/Stats/nanstd.m,
mPhys/Stats/nlinfit/,
mPhys/Stats/nlinfit/nlinfit.m,
mPhys/Stats/nlinfit/statrobustsigma.m,
mPhys/Stats/nlinfit/statrobustwfun.m,
mPhys/Stats/nlinfit/statset.m,
mPhys/Stats/normcdf.m,
mPhys/Stats/normpdf.m,
mPhys/User Manual.rtf,
mPhys/Utility/,
mPhys/Utility/batchParseAll.m,
mPhys/Utility/cell2mat.m,
mPhys/Utility/chiTest.m,
mPhys/Utility/combFilter.m,
mPhys/Utility/covPlot.m,
mPhys/Utility/deltaF.m,
mPhys/Utility/deltaFoverF.m,
mPhys/Utility/exportFigure.m,
mPhys/Utility/fieldFilter.m,
mPhys/Utility/histfit.m,
mPhys/Utility/imlineCopy.m,
mPhys/Utility/inputdlg.m,
mPhys/Utility/interprocessInstalled.m,
mPhys/Utility/meanVariance.m,
mPhys/Utility/norminv.m,
mPhys/Utility/onScreen.m,
mPhys/Utility/prefutilsReplacer.m,
mPhys/Utility/range.m,
mPhys/Utility/read2PRaster.m,
mPhys/Utility/readBen.m,
mPhys/Utility/readBenOld.m,
mPhys/Utility/readBiorad.m,
mPhys/Utility/readImage.m,
mPhys/Utility/readTrace.m,
mPhys/Utility/searchExperiments.m,
mPhys/Utility/sec2time.m,
mPhys/Utility/showFFT.m,
mPhys/Utility/stimulus.m,
mPhys/Utility/subplot.m,
mPhys/Utility/time2sec.m,
mPhys/Utility/TTestParam.m,
mPhys/Utility/updatePreParse.bat,
mPhys/Utility/variance.m,
mPhys/Utility/write2PRaster.m,
mPhys/Utility/writeBiorad.m
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Comments and Ratings (1)
05 May 2009 Chad Bircher

When I attempt to use these programs I get the following error
Undefined function or method 'nlinfit' for input arguments of type
'function_handle'.
 Do you know why MatLab would respond to the programs this way?
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Updates
21 Nov 2008

Corrected errors caused by the ITC18 having a delay in updating its instruction sequence. Added a script for compiling.
03 Dec 2008

Fixed data acquisition to run in emulation mode without ITC18 present. Fixed scope cursors to reflect data traces that have been altered. Fixed problem with fileBrowser during new data acquisition that caused experiments to show up twice.
Tag Activity for this File
Tag Applied By Date/Time
electrophysiology Phil Larimer 27 Oct 2008 11:11:47
instrutech Phil Larimer 27 Oct 2008 11:11:47
patchclamp Phil Larimer 27 Oct 2008 11:11:47
acquisition Phil Larimer 27 Oct 2008 11:11:47
neurons Phil Larimer 27 Oct 2008 11:11:47
 

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