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171116sh_0015-ATFwaveform.md

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171116sh_0015-ATFwaveform.abf

ABF Class Methods

  • abf.getInfoPage()
  • abf.saveABF1()
  • abf.setSweep()
  • abf.sweepArea()
  • abf.sweepAvg()
  • abf.sweepBaseline()
  • abf.sweepD()
  • abf.sweepMax()
  • abf.sweepMin()
  • abf.sweepStdev()

ABF Class Variables

  • abfDateTime = 2017-11-16 14:06:28.730000
  • abfDateTimeString = 2017-11-16T14:06:28.730
  • abfFileComment = SWHLab5[0102]
  • abfFilePath = C:/some/path/to/171116sh_0015-ATFwaveform.abf
  • abfID = 171116sh_0015-ATFwaveform
  • abfVersion = {'major': 2, 'minor': 6, 'bugfix': 0, 'build': 0}
  • abfVersionString = 2.6.0.0
  • adcNames = ['IN 0']
  • adcUnits = ['pA']
  • channelCount = 1
  • channelList = [0]
  • creatorVersion = {'major': 10, 'minor': 7, 'bugfix': 0, 'build': 3}
  • creatorVersionString = 10.7.0.3
  • dacNames = ['Cmd 0']
  • dacUnits = ['mV']
  • data = array (2d) with values like: -119.38476, -118.16405, -117.06542, ..., -101.80663, -104.85839, -103.27148
  • dataByteStart = 6656
  • dataPointByteSize = 2
  • dataPointCount = 300000
  • dataPointsPerMs = 10
  • dataRate = 10000
  • dataSecPerPoint = 0.0001
  • epochPoints = [0, 1562, 2562, 7562, 100000]
  • epochValues = [-70.0, -70.0, 0.0, -10.0, -70.0]
  • fileGUID = {6820CD72-752A-410F-8E09-121CF9BAFAFA}
  • holdingCommand = [-70.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • protocol = 0221 VC sine sweep 70 +- 5 mV
  • protocolPath = L:\Protocols\permanent\0221 VC sine sweep 70 +- 5 mV.pro
  • stimulusByChannel = [ChannelEpochs(ABF, 0)]
  • sweepC = array (1d) with values like: 0.00000, 0.00000, 0.00001, ..., 15.83390, 16.07410, 16.31030
  • sweepChannel = 0
  • sweepCount = 3
  • sweepLabelC = Membrane Potential (mV)
  • sweepLabelX = time (seconds)
  • sweepLabelY = Clamp Current (pA)
  • sweepLengthSec = 10.0
  • sweepList = [0, 1, 2]
  • sweepNumber = 0
  • sweepPointCount = 100000
  • sweepUnitsC = mV
  • sweepUnitsX = sec
  • sweepUnitsY = pA
  • sweepX = array (1d) with values like: 0.00000, 0.00010, 0.00020, ..., 9.99970, 9.99980, 9.99990
  • sweepY = array (1d) with values like: -119.38476, -118.16405, -117.06542, ..., -104.85839, -107.78808, -107.78808
  • tagComments = []
  • tagSweeps = []
  • tagTimesMin = []
  • tagTimesSec = []

Epochs for Channel 0

DAC waveform is controlled by custom file:
L:\Protocols\permanent\waveform stimulus\sine sweep magnitude 20.atf

ABF2 Header

The first several bytes of an ABF2 file contain variables located at specific byte positions from the start of the file.

  • abfDateTime = 2017-11-16 14:06:28.730000
  • abfDateTimeString = 2017-11-16T14:06:28.730
  • abfVersionDict = {'major': 2, 'minor': 6, 'bugfix': 0, 'build': 0}
  • abfVersionFloat = 2.6
  • abfVersionString = 2.6.0.0
  • creatorVersionDict = {'major': 10, 'minor': 7, 'bugfix': 0, 'build': 3}
  • creatorVersionFloat = 10.703
  • creatorVersionString = 10.7.0.3
  • fFileSignature = ABF2
  • fFileVersionNumber = [0, 0, 6, 2]
  • lActualEpisodes = 3
  • nCRCEnable = 0
  • nDataFormat = 0
  • nFileType = 1
  • nSimultaneousScan = 1
  • sFileGUID = {6820CD72-752A-410F-8E09-121CF9BAFAFA}
  • uCreatorNameIndex = 1
  • uCreatorVersion = [3, 0, 7, 10]
  • uFileCRC = 0
  • uFileGUID = [114, 205, 32, 104, 42, 117, 15, 65, 142, 9, 18, 28, 249, 186, 24, 250]
  • uFileInfoSize = 512
  • uFileStartDate = 20171116
  • uFileStartTimeMS = 50788730
  • uModifierNameIndex = 0
  • uModifierVersion = 0
  • uProtocolPathIndex = 2
  • uStopwatchTime = 2696

SectionMap

Reading three numbers (int, int, long) at specific byte locations yields the block position, byte size, and item count of specific data stored in sections. Note that a block is 512 bytes. Some of these sections are not read by this class because they are either not useful for my applications, typically unused, or have an unknown memory structure.

  • ADCPerDACSection = [0, 0, 0]
  • ADCSection = [2, 128, 1]
  • AnnotationSection = [0, 0, 0]
  • DACSection = [3, 256, 8]
  • DataSection = [13, 2, 300000]
  • DeltaSection = [0, 0, 0]
  • EpochPerDACSection = [7, 48, 2]
  • EpochSection = [8, 32, 2]
  • MathSection = [0, 0, 0]
  • ProtocolSection = [1, 512, 1]
  • ScopeSection = [11, 769, 1]
  • StatsRegionSection = [9, 128, 1]
  • StatsSection = [0, 0, 0]
  • StringsSection = [10, 272, 22]
  • SynchArraySection = [1185, 8, 3]
  • TagSection = [0, 0, 0]
  • UserListSection = [0, 0, 0]
  • VoiceTagSection = [0, 0, 0]

ProtocolSection

This section contains information about the recording settings. This is useful for determining things like sample rate and channel scaling factors.

  • bEnableFileCompression = 0
  • fADCRange = 10.0
  • fADCSequenceInterval = 100.0
  • fAverageWeighting = 0.10000000149011612
  • fCellID = [0.0, 0.0, 0.0]
  • fDACRange = 10.0
  • fEpisodeStartToStart = 0.0
  • fFirstRunDelayS = 0.0
  • fRunStartToStart = 0.0
  • fScopeOutputInterval = 0.0
  • fSecondsPerRun = 7200.0
  • fStatisticsPeriod = 1.0
  • fSynchTimeUnit = 20.0
  • fTrialStartToStart = 0.0
  • fTriggerThreshold = 0.0
  • lADCResolution = 32768
  • lAverageCount = 1
  • lDACResolution = 32768
  • lEpisodesPerRun = 3
  • lFileCommentIndex = 3
  • lFinishDisplayNum = 100000
  • lNumSamplesPerEpisode = 100000
  • lNumberOfTrials = 1
  • lPreTriggerSamples = 10
  • lRunsPerTrial = 1
  • lSamplesPerTrace = 40000
  • lStartDisplayNum = 0
  • lStatisticsMeasurements = 5
  • lTimeHysteresis = 1
  • nActiveDACChannel = 0
  • nAllowExternalTags = 0
  • nAlternateDACOutputState = 0
  • nAlternateDigitalOutputState = 0
  • nAutoAnalyseEnable = 1
  • nAutoTriggerStrategy = 1
  • nAverageAlgorithm = 0
  • nAveragingMode = 0
  • nChannelStatsStrategy = 0
  • nCommentsEnable = 1
  • nDigitalDACChannel = 0
  • nDigitalEnable = 0
  • nDigitalHolding = 0
  • nDigitalInterEpisode = 0
  • nDigitalTrainActiveLogic = 1
  • nDigitizerADCs = 16
  • nDigitizerDACs = 4
  • nDigitizerSynchDigitalOuts = 8
  • nDigitizerTotalDigitalOuts = 16
  • nDigitizerType = 6
  • nExperimentType = 2
  • nExternalTagType = 2
  • nFirstEpisodeInRun = 0
  • nLTPType = 0
  • nLevelHysteresis = 64
  • nManualInfoStrategy = 1
  • nOperationMode = 5
  • nScopeTriggerOut = 0
  • nShowPNRawData = 0
  • nSignalType = 0
  • nStatisticsClearStrategy = 1
  • nStatisticsDisplayStrategy = 0
  • nStatisticsSaveStrategy = 1
  • nStatsEnable = 0
  • nTrialTriggerSource = -1
  • nTriggerAction = 0
  • nTriggerPolarity = 0
  • nTriggerSource = -3
  • nUndoPromptStrategy = 0
  • nUndoRunCount = 0
  • sDigitizerType = Digidata 1440
  • sUnused = ['\x00', '\x00', '\x00']
  • uFileCompressionRatio = 1

ADCSection

Information about the ADC (what gets recorded). There is 1 item per ADC.

  • bEnabledDuringPN = [0]
  • fADCDisplayAmplification = [39.999385833740234]
  • fADCDisplayOffset = [-140.0]
  • fADCProgrammableGain = [1.0]
  • fInstrumentOffset = [0.0]
  • fInstrumentScaleFactor = [0.0005000000237487257]
  • fPostProcessLowpassFilter = [100000.0]
  • fSignalGain = [1.0]
  • fSignalHighpassFilter = [1.0]
  • fSignalLowpassFilter = [5000.0]
  • fSignalOffset = [0.0]
  • fTelegraphAccessResistance = [0.0]
  • fTelegraphAdditGain = [5.0]
  • fTelegraphFilter = [2000.0]
  • fTelegraphMembraneCap = [0.0]
  • lADCChannelNameIndex = [4]
  • lADCUnitsIndex = [5]
  • nADCNum = [0]
  • nADCPtoLChannelMap = [0]
  • nADCSamplingSeq = [0]
  • nHighpassFilterType = [0]
  • nLowpassFilterType = [0]
  • nPostProcessLowpassFilterType = ['\x00']
  • nStatsChannelPolarity = [0]
  • nTelegraphEnable = [1]
  • nTelegraphInstrument = [24]
  • nTelegraphMode = [0]
  • sTelegraphInstrument = ['MultiClamp 700']

DACSection

Information about the DAC (what gets clamped). There is 1 item per DAC.

  • fBaselineDuration = [1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0]
  • fBaselineLevel = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fDACCalibrationFactor = [1.001173496246338, 1.0012290477752686, 1.001173496246338, 1.001173496246338, 1.0, 1.0, 1.0, 1.0]
  • fDACCalibrationOffset = [-4.0, -4.0, -7.0, -6.0, 0.0, 0.0, 0.0, 0.0]
  • fDACFileOffset = [-70.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fDACFileScale = [0.25, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
  • fDACHoldingLevel = [-70.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fDACScaleFactor = [20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0]
  • fInstrumentHoldingLevel = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fMembTestPostSettlingTimeMS = [100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0]
  • fMembTestPreSettlingTimeMS = [100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0]
  • fPNHoldingLevel = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fPNInterpulse = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fPNSettlingTime = [100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0, 100.0]
  • fPostTrainLevel = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • fPostTrainPeriod = [10.0, 10.0, 10.0, 10.0, 10.0, 10.0, 10.0, 10.0]
  • fStepDuration = [1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0]
  • fStepLevel = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
  • lConditNumPulses = [1, 0, 0, 0, 0, 0, 0, 0]
  • lDACChannelNameIndex = [6, 9, 11, 13, 15, 17, 19, 21]
  • lDACChannelUnitsIndex = [7, 10, 12, 14, 16, 18, 20, 22]
  • lDACFileEpisodeNum = [0, 0, 0, 0, 0, 0, 0, 0]
  • lDACFileNumEpisodes = [1, 0, 0, 0, 0, 0, 0, 0]
  • lDACFilePathIndex = [8, 0, 0, 0, 0, 0, 0, 0]
  • lDACFilePtr = [1186, 0, 0, 0, 0, 0, 0, 0]
  • nConditEnable = [0, 0, 0, 0, 0, 0, 0, 0]
  • nDACFileADCNum = [0, 0, 0, 0, 0, 0, 0, 0]
  • nDACNum = [0, 1, 2, 3, 4, 5, 6, 7]
  • nInterEpisodeLevel = [0, 0, 0, 0, 0, 0, 0, 0]
  • nLTPPresynapticPulses = [0, 0, 0, 0, 0, 0, 0, 0]
  • nLTPUsageOfDAC = [0, 0, 0, 0, 0, 0, 0, 0]
  • nLeakSubtractADCIndex = [0, 0, 0, 0, 0, 0, 0, 0]
  • nLeakSubtractType = [0, 0, 0, 0, 0, 0, 0, 0]
  • nMembTestEnable = [0, 0, 0, 0, 0, 0, 0, 0]
  • nPNNumADCChannels = [0, 0, 0, 0, 0, 0, 0, 0]
  • nPNNumPulses = [4, 4, 4, 4, 4, 4, 4, 4]
  • nPNPolarity = [1, 1, 1, 1, 1, 1, 1, 1]
  • nPNPosition = [0, 0, 0, 0, 0, 0, 0, 0]
  • nTelegraphDACScaleFactorEnable = [1, 0, 0, 0, 0, 0, 0, 0]
  • nWaveformEnable = [1, 0, 0, 0, 0, 0, 0, 0]
  • nWaveformSource = [2, 1, 1, 1, 0, 0, 0, 0]

EpochPerDACSection

This section contains waveform protocol information. These are most of the values set when using the epoch the waveform editor. Note that digital output signals are not stored here, but are in EpochSection.

  • fEpochInitLevel = [0.0, -10.0]
  • fEpochLevelInc = [0.0, 0.0]
  • lEpochDurationInc = [0, 0]
  • lEpochInitDuration = [1000, 5000]
  • lEpochPulsePeriod = [0, 0]
  • lEpochPulseWidth = [0, 0]
  • nDACNum = [0, 0]
  • nEpochNum = [0, 1]
  • nEpochType = [1, 1]

EpochSection

This section contains the digital output signals for each epoch. This section has been overlooked by some previous open-source ABF-reading projects. Note that the digital output is a single byte, but represents 8 bits corresponding to 8 outputs (7->0). When working with these bits, I convert it to a string like "10011101" for easy eyeballing.

  • nEpochDigitalOutput = [0, 0]
  • nEpochNum = [0, 1]

TagSection

Tags are comments placed in ABF files during the recording. Physically they are located at the end of the file (after the data). Later we will populate the times and sweeps (human-understandable units) by multiplying the lTagTime by fSynchTimeUnit from the protocol section.

  • lTagTime = []
  • nTagType = []
  • nVoiceTagNumberorAnnotationIndex = []
  • sComment = []
  • sweeps = []
  • timesMin = []
  • timesSec = []

StringsSection

Part of the ABF file contains long strings. Some of these can be broken apart into indexed strings. The first string is the only one which seems to contain useful information. This contains information like channel names, channel units, and abf protocol path and comments. The other strings are very large and I do not know what they do. Strings which contain indexed substrings are separated by \x00 characters.

  • strings = not shown due to non-ASCII characters

StringsIndexed

This object provides easy access to strings which are scattered around the header files. The StringsSection contains strings, but various headers contain values which point to a certain string index. This class connects the two, and provides direct access to those strings by their indexed name.

  • lADCChannelName = ['IN 0']
  • lADCUnits = ['pA']
  • lDACChannelName = ['Cmd 0', 'Cmd 1', 'Cmd 2', 'Cmd 3', 'AO #4', 'AO #5', 'AO #6', 'AO #7']
  • lDACChannelUnits = ['mV', 'mV', 'mV', 'mV', 'mV', 'mV', 'mV', 'mV']
  • lDACFilePath = ['L:\\Protocols\\permanent\\waveform stimulus\\sine sweep magnitude 20.atf', '', '', '', '', '', '', '']
  • lFileComment = SWHLab5[0102]
  • nLeakSubtractADC = ['', '', '', '', '', '', '', '']
  • uCreatorName = Clampex
  • uModifierName = ``
  • uProtocolPath = L:\Protocols\permanent\0221 VC sine sweep 70 +- 5 mV.pro