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mPhys

[Answer choices]=inputdlg(Pro... INPUTDLG Input dialog box.
audioScope creates an audioScope figure
captureGUI
changeAdBoard(figHandle) called after the hardware source of the protocolViewer changes
doRepeat performs a repeated episode at the interval assigned
experiment(inData) loads the experiment figure and sets it up
exportSettings
generateEpisodes generates a list of file names ranked by amplitude
imageBrowser(startingDir) can pass a starting directory, a file to open, or a zImage structure
loadProtocol(inData) loads a protocol into the viewer
newScope(varargin) display data channels in a scrollable window
pspGui(lastVals) GUI for detecting PSPs
pspGui(lastVals) GUI for detecting PSPs
rasterScan(fileName) paradigm for drawing a rotated raster
saveExperiment saves the current experiment
saveProtocol(inData, fileName... save the current protocol to a file or to appdata
setupCoupling(protocol, windo... create display window
setupSTA(protocol, windowSize... create display window
startRunningScope
timeControl(right, bottom)
updateExperiment add appropriate check boxes on the experimental pane
CV2(spikeTimes, order) function CV2_value = CV2(spikeTimes, order)
HH(I, dt, Vo) numerical solution of the space-clamped Hodgkin-Huxley equations
MTEO(inData, kData, threshold... after Choi and Kim, Electronics Letters, 38(12) 2002, 541-3 and
TTestParam(m,s,n,tail,alpha) TTestParam: Two-sample t-test, given only the parameters (means, standard deviations,
[methodinfo,structs,enuminfo]... ITC18 Create structures to define interfaces found in 'ITC18VB'.
addAmp(figHandle) adds an amp to the currently visible protocol
alpha(Params, x)
analysisAxis(plotName, axisHa... linkaxes([handles.analysisAxis{whichAxis}.(tempFields{end - 1}) handles.analysisAxis{whichAxis}.(plotName)], 'y');
apHeight(inData, timePerPoint... spikeHeights = APHeight(dataTrace, timerPerPoint, startTime, outputAxisHandle);
apRiseFallRatio(traceData, ti... apWidths = apRiseFallRatio(dataTrace, timerPerPoint, startTime, outputAxisHandle);
apThreshold(inData, timePerPo... thresholds = APthreshold(dataTrace, timerPerPoint, startTime, outputAxisHandle);
apWidth(traceData, timePerPoi... apWidths = APWidth(dataTrace, timerPerPoint, startTime, outputAxisHandle);
apWidthHM(inData, timePerPoin... apWidthsAtHalfMax = APWidthHM(dataTrace, timerPerPoint, startTime, outputAxisHandle);
asiGui
autoCorrelate(varargin) show an autocorrelogram
autoNotch(inData, timePerPoin... generate a notch filter for a data set
averageCoupling
averageOnly(PSPtype)
axoPatchAlpha(magFactor, alph...
bandStop(inData, lowStopBand,... band stop filter data
batchAverage(directory) search through specified directory and generate raster plots of spiking
batchClassification(directory... looks through coupling traces for the following characteristics:
batchCoupling(directory) search through specified directory and generate raster plots of spiking
batchDelta(directory) search through specified directory and generate raster plots of spiking
batchParseAll(directory, func... generates a preParse file to speed fileBrowser loads
batchSTA(directory) search through specified directory and generate raster plots of spiking
bestShift(imageData)
binopdf(x,n,p) BINOPDF Binomial probability density function.
blue(m) BLUE Shades of blue color map.
bnw(m) BNW Shades of Black aNd White color map.
bridgeBalance(ampNumber) don't allow a current and voltage step at the same time
buildSource this just compiles the source using mcc
burstingProbability(inData, t... pValue = burstingProbability(traceData, threshTime);
calcBurstProb(varargin)
calcMean(inData) find the greatest value of the all points histogram
calcROI(ROI) calculates the array roiData that contains the sum of each roi in each
calcSTA(varargin)
calcSTO(varargin)
categorizeHilarNeuron(src, ev... calculates the distance metric of Larimer and Strowbridge 2008
cell2mat(c) CELL2MAT Convert the contents of a cell array into a single matrix.
cell2mat(c) CELL2MAT Convert the contents of a cell array into a single matrix.
changeAcquisitionRate called after the acquisition rate (in kHz) is changed
changeAmp(ampNum, figHandle) loads the types of current channels into the appropriate channel
changeAudioChannel(varargin)
changeCell(ampNum, newValue, ...
changeCurrent(ampNum, figHand... loads the types of current channels into the appropriate channel
changeRunningChannel(varargin...
changeTelegraph(ampNum, figHa... loads the types of current channels into the appropriate channel
changeTtlType(ttlNum, newValu...
changeVoltage(ampNum, figHand... loads the types of current channels into the appropriate channel
characterizePSPs(PSPs, totalT...
characterizePSPs(PSPs, totalT...
checkAcquisitionRate verify that the rate chosen is possible
checkCoupling(zData, windowSi... looks for synaptic coupling between cells (output is graphical)
checkEpisodesCoupling(match)
checkEpisodesSTA(match)
checkSTA(zData, windowSize, w... used to find possible coupling via a spike-triggered average across cells.
checkSingleEpisodeCoupling(fi...
checkSingleEpisodeSTA(fileNam...
checkWithinEpisodesSTA(match)
checkWithinEpisodesSTO(match)
checkWithinSingleEpisodeSTA(f...
checkWithinSingleEpisodeSTO(f...
chiTest(cT) computes a chi-squared from a 2x2 contingency table cT
cleanUpCoupling
clearROI(varargin) clears current set of ROI
clusterHist(spikes, clusters) plot a profile of spike heights
colorSpread(m) COLORCUBE Enhanced color-cube color map.
combFilter(inData, selectedFr... remove sinusoidal noise at selectedFrequencies by finding the phase and
combineImageStacks(matchText) reads a .img stack and compresses it
commonEvents(varargin) outData = allCoincidents;
compressImageStack(matchText) takes a pattern or a cell array of full paths and generates a single
compressZStack(match)
convertPock(inData) converts percentages from 0-100 to pockel cell voltage commands from 0-1V
correctX(inX, sinFreq) correct x sin amplitude for sin frequency using the boltzman distribution
correctY(inY, sinFreq) correct y sin amplitude for sin frequency using the boltzman distribution
covPlot(inData, dataNames) plot normalized covariances and R^2 values
createTTL(figHandle, numTTL)
crossCorr(data, corrVals, coi... determine if we're doing an autocorrelogram
crosscorrelateSetup(varargin) smoothData = hist(spikeTimes, diff(correlationBounds) + 1);
currentAmps end any current channel name with I, voltage with V for the browser to
cyan(m) CYAN Shades of green to blue.
cyan2red(m) CYAN2RED Shades of cyan to red.
deltaF(inData, baselineDataEn... returns delta data assuming that the first half of the data is
deltaFoverF(inData, filterLen... pass baselineDataEnd as nan to avoid bleach subtraction
detectCellAttached(inData, ti...
detectExtracellular(inData, t...
detectPSP(inData, timePerPoin...
detectPSPs(data, varargin) use this function to detect the PSPs in your data using a PSP finding algorithm
detectPSPs(data, varargin) use this function to detect the PSPs in your data using a PSP finding algorithm
detectSpikes(inData, spikeHei... spikes = detectSpikes(inData, spikeHeight, whereCall)
detectWCAPs(inData, timePerPo...
displayImage(varargin)
distchck(nparms,varargin) DISTCHCK Checks the argument list for the probability functions.
doSingle called by the experiment Single button to record a single episode
doStream called by pressing the doStream button on the GUI
drawROI(whichROI) put ROI on their plot form
ellipseScan(ROI, tValues) create an ellipse scan pattern for the given ROI
eventTriggeredAverage(events,... calculate the event-triggered average in postTrace using preTrace's spikes
excelCoupling(PSPdata, FileNa... writes couplings to an excel file in the phil format
experimentTimer(varargin) handles all calls to the itc18
exportFigure(src, eventInfo, ... function for converting a figHandle to paper, clipboard memory, or file
exportFrame(figHandle, axisHa... get the axis
exportWithAxes(figure) function for converting a newScope to an enhanced meta-file on the clipboard
exportWithScaleBars(figure) function for converting a newScope to an enhanced meta-file on the clipboard
fastAHP(inData, timePerPoint,... ahpDepths = fastAHP(dataTrace, timerPerPoint, startTime, outputAxisHandle);
fastAHPSlope(inData, timePerP... ahpDepths = fastAHP(dataTrace, timerPerPoint, startTime, outputAxisHandle);
fastAHPSlope2(inData, timePer... ahpDepths = fastAHP(dataTrace, timerPerPoint, startTime, outputAxisHandle);
fcnMin(inData, number, type) finds the minima of the given input data
featureVsPotential(cell, stim... open all of the files and calculate the all-points histogram mean in the
fieldFilter(inData, protocol) remove the slow drift
fileBrowser(startingDir) browse data files or a given data file
findSteps(protocol, ampNum) function stepData = findSteps(protocol, ampNum)
findStims(protocol, isIndex) ... stimTimes is a cell array of n x 2 matrices where column one is the
fit1Exp(yData, timePerPoint, ... fits single exponent to data
fit2Exp(yData, timePerPoint, ... fits two exponents to data
fit3Exp(yData, timePerPoint, ... fits three exponents to data
fitAlpha(yData, timePerPoint,... fits single alpha function to data
fitDecayDouble(yData, PSPtype... fits taus to ydata that is slowing in x (only determined by the initial offset)
fitDecaySingle(yData, PSPtype... fits tau to ydata that is slowing in x (only determined by the initial offset)
fitDecayTriple(yData, PSPtype... fits taus to ydata that is slowing in x (only determined by the initial offset)
fitLine(yData, timePerPoint, ... fits line to data
fitSine(yData, timePerPoint, ... fits single sine wave to data
focusMode(obj, eventStruct, z...
freqVsTimePlot(traceData, pro... plot short time fft vs time in colors as a surface
gA(v, dt) An IA current
gK(v, dt) Hodgkin and Huxley K+ channel
gNa(v, dt) Hodgkin and Huxley Na+ channel
generateIV(traceData, protoco... generate an IV curve given the input data and calculate a input
generateStats looks for significant differences in PSPdata
generateStim(protocolData, ex... generates a stimulus vector that is numPoints by numChannels and starts
generateTraces(resultData, fi... [dataVals indices] = generateTraces(resultData, fileNames, matchName, cell, stim, pspType, timeWindow, rezero)
green(m) GREEN Shades of green.
highPass(inData, passBand, sa... high pass filter data
highlightROI(ROInum) highlight a ROI by number
histfit(data,varargin) HISTFIT Histogram with superimposed fitted normal density.
histfit(data,varargin) HISTFIT Histogram with superimposed fitted normal density.
imline(h_parent,x_init,y_init... IMLINE Create draggable, resizable line.
interprocessInstalled look to see if MB interprocess is installed and return its progID if so
intervalHist(varargin) show an interval histogram
isProtocol(inStructure) verifies that a variable is an appropriate protocol structure
isiCv(inData) calculates the coefficient of variation for the inter-spike interval
isiCvEvents(varargin)
jointDist(varargin) show a joint distribution
lineScan(ROI) create a line scan pattern for the given ROI
lissajousScan(ROI, tValues) create a Lissajous scan pattern for the given ROI
loadROI loads a ROI set from a file
locateCells find cells
lowPass(inData, passBand, sam... low pass filter data
makeProtocol(inStructure) removes any inappropriate fields from a structure so that it can be a
makeRaster generate a raster plot given ROI and a stack of images
meanVariance(inData, windowLe... outValue = meanVariance(inData, windowLength, overlapRatio, outputAxis);
metaBar(titles, xData, yData) generate mega plot
metaCorrEvents(varargin)
micronsPerPixel(objective, xV... calculate the number of microns per pixel
mitutoyoGui
movingAverage(inData, windowS... use a boxcar filter of length windowSize points on inData
movingBlock(inData, windowSiz... use a boxcar filter of length windowSize points on inData
msec2point(inString, pointsPe...
nanmean(x,dim) NANMEAN Mean value, ignoring NaNs.
nanstd(varargin) NANSTD Standard deviation, ignoring NaNs.
newScale(objectHandle, eventI...
newSequence increments the sequence by 1
nlinfit(X,y,model,beta,option... Check sizes of the model function's outputs while initializing the fitted
normalizeMatrix(inMatrix, dim... normalize a matrix along a given dimension
normcdf(x,mu,sigma,pcov,alpha) NORMCDF Normal cumulative distribution function (cdf).
norminv(p,mu,sigma,pcov,alpha... More checking if we need to compute confidence bounds.
normpdf(x,mu,sigma) NORMPDF Normal probability density function (pdf).
notchFilter(inData, samplingF... notch filters data
numSpikes(fileName) find the number of action potentials on the first amp
onScreen(figHandle)
oneSidedDeviation(inData) use an outlier-insensitive deviation measure that assumes a mean of zero
overlayPSPs(inData, timeWindo... display the PSPs for a given trace overlayed
overlayPSPs(inData, timeWindo... display the PSPs for a given trace overlayed
plotAverageFreq(varargin)
plotFreq(varargin)
plotPercentCorrelation(vararg...
prefutils(varargin) PREFUTILS Utilities used by set/get/is/add/rmpref
prepForPrint(currentAxis, yVa... Hides axes and places a scale bar with y-units set by yVal (a character
printFrame(figHandle, axisHan... get the axis
printWithAxes(figure) function for printing a newScope
printWithScaleBars(figure) function for printing a newScope
processImage used to update the current image
protocolViewer(appdataName) opens a gui that allows viewing of a protocol structure
purple(m) PURPLE Shades of red to blue.
purple2green(m) PURPLE2GREEN Shades of green to blue.
rIn(traceData, protocol, ampN...
range(x,dim) RANGE Sample range.
read2PRaster(FileName, infoOn...
readASI
readBen(filename, infoOnly) reads in a Ben file given its name (and directory if necessary)
readBen(filename, infoOnly) reads in a Ben file given its name (and directory if necessary)
readImage(FileName, infoOnly) reads a quantix image file
readMitutoyo ask for the current position
readPic(filename) adapted from:
readRaster(FileName)
readTrace(filename, infoOnly) reads data traces generated by the data acquisition program
reconstructCell(match)
red(m)
redSat(m) REDSAT Shades of Black aNd White color map that saturates at red.
reducedNeurons(cellType, I, t... This MATLAB file generates cells as per Izhikevich E.M. (2004)
removeAmp(panelHandle, junk) deletes the currently selected amplifier
resizeImage resize the current image form
sag(traceData, protocol, ampN...
saveImageAs(imageHandle, file...
saveMovie saves a movie of the current cell
saveROI this file saves the current regions of interest as well as the fiducials
scaleBar(currentAxis, info)
sealTest(ampNumber) don't allow a current and voltage step at the same time
searchExperiments(database, h... search through a database and return all cells that match the searchStrings
sec2time(numSecs) convert seconds to hh:mm:ss.s format
sequenceScan(scanOrder) Generate a galvo trajectory that rings the perimeter of all ellipses
setAxisLabels(axisHandle)
setCrossHairs(xCoord, yCoord)
setCursor(varargin)
setDataFolder set the folder to which data files will be saved
setReference(fileName) sets the current image as a location reference for future images
setSliders set sliders to visible or not
setupASI
setupFiles
setupMitutoyo
shapeRaster(ROI) (x,y) coordinates of points in a ROI = shapeRaster(ROI_data)
shapeRaster(ROI) (x,y) coordinates of points in a ROI = shapeRaster(ROI_data)
showEvents(axisHandle)
showFFT(dataIn, samplingRate) displays power spectrum of data
showFit(cell, stim, pspNumber... pulls up data trace and fits the alpha function to the PSP
showFrameMarker(axisHandle) deal with frame marker if present
showHighPower show the current images location on the reference image
showScaleBar
showStims(figHandle, showLege... show TTL stimuli if they are blanked
slowAHP(traceData, protocol, ...
spiralScan(ROI, tValues) create a spiral scan pattern for the given ROI
statrobustsigma(wfun,r,p,s,t,... Include tuning constant in sigma value
statrobustwfun(wfun,tune) Convert name of weight function to a handle to a local function, and get
statset(varargin) Print out possible values of properties.
stimStats(j, i) looks for significant differences in PSPdata
stimTypeColumn(headerData) create a string that is the bias current/voltage for a given episode
stimulus(protocol, ampNum) generate the stimulus that a protocol would have used (assuming it is
subplot(nrows, ncols, thisPlo... SUBPLOT Create axes in tiled positions.
tabChange(varargin)
takeTwoPhotonImage(fileName, ... tells raster to take a 2p image
time2sec(time) convert hh:mm:ss.s format to a number of seconds
traceCell(inImage) find cells
transferCellOutline show the current cell's location on the reference image
transferPoints(inCoords, from... transfer points from one objective to another
transferROI places the ROI that we have onto the reference image
twoPhotonGUI
updateAverage updates what frames are available for a given set of averaging specs
variance(inData) actually calculates the variance-to-mean ratio
whichChannel(protocol, ampNum... determine which channel a given amp is using
write2PRaster(zImage, FileNam...
writeBiorad(fileName, imageLo... write a biorad format file
yellow(m) YELLOW Shades of red to green.
yellow2blue(m) YELLOW2BLUE Shades of green to blue.
zStackGui
zoomCoupling(varargin) this function blows up the plot over which the mouse is hovering when
zoomSTA
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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

Tags for This File
Everyone's Tags	acquisition, electrophysiology, instrutech, neurons, patchclamp
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Comments and Ratings (2)
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?
17 Aug 2010	Phil Larimer	I moved this file to filer.case.edu/~pel6 as it contains some java code and therefore I can't post updates to it here.

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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

Highlights from mPhys

mPhys

Highlights from
mPhys