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mPhys

by Phil Larimer

 

27 Oct 2008 (Updated 03 Dec 2008)

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

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