Directives for Batch Processing and Template Files

Arguments to Copytomocoms
Other Setup Parameters
Coarse Alignment
Tracking Choices
Auto Seed Finding
RAPTOR Parameters
Patch Tracking
Tomogram Positioning
Aligned Stack Choices
Aligned Stack Parameters
SIRT Parameters
Tomogram Combination
External Commands

Arguments to Copytomocoms      
setupset.copyarg.nameRoot name of data setStringY   
setupset.copyarg.dualDual-axis data setBoolYYSO 
setupset.copyarg.montageData are montagedBoolYYSD 
setupset.copyarg.pixelPixel size of images in nanometersFloatYY Overrides value from scanHeader
setupset.copyarg.goldSize of gold beads in nanometersFloatYYSD 
setupset.copyarg.rotationAngle from the vertical to the tilt axis in raw imagesFloatYY Overrides value from scanHeader
setupset.copyarg.brotationAngle from the vertical to the tilt axis for B axisFloatYY Overrides value from scanHeader
setupset.copyarg.firstincFirst tilt angle and tilt angle increment2 FloatY   
setupset.copyarg.bfirstincFirst tilt angle and tilt angle increment for B axis2 FloatY   
setupset.copyarg.userawtltTake tilt angle from a .rawtlt file for A or only axisBoolYYSO 
setupset.copyarg.buserawtltTake tilt angle from a .rawtlt file for B axisBoolYYSO 
setupset.copyarg.extractExtract tilt angles from data file for A or only axisBoolYYSO 
setupset.copyarg.bextractExtract tilt angles from data file for B axisBoolYYSO 
setupset.copyarg.twodirStarting angle of bi-directional series for A or only axisFloatYYSO 
setupset.copyarg.btwodirStarting angle of bi-directional series for B axisFloatYYSO 
setupset.copyarg.skipList of views to exclude from processing for A or only axisListY   
setupset.copyarg.bskipList of views to exclude from processing for B axisListY   
setupset.copyarg.distortCorrect image distortion with the given .idf fileFileYYSO 
setupset.copyarg.binningBinning of raw imagesFloatYY  
setupset.copyarg.gradientCorrect for magnification gradients using the given .mgt fileFileYYSO 
setupset.copyarg.focusFocus was adjusted between frames when acquiring montageBoolYYSO 
setupset.copyarg.bfocusFocus was adjusted between montage frames for the B axisBoolYYSO 
setupset.copyarg.defocusDefocus in nanometers (underfocus positive)FloatYYSO 
setupset.copyarg.voltageMicroscope voltage in kVIntYYSO 
setupset.copyarg.CsSpherical aberration in mmFloatYYSO 
setupset.copyarg.ctfnoiseConfiguration file listing noise files for ctfplotterFileYYSD 
Other Setup Parameters      
setupset.scopeTemplateName of scope template file to useStringY  See notes at end
setupset.systemTemplateName of system template fileStringY  See notes at end
setupset.userTemplateName of user template fileStringY  See notes at end
setupset.scanHeaderWhether to scan image file headerBoolYY Etomo batch default is 1
setupset.datasetDirectoryFull path to directoryStringY   
runtime.Preprocessing.any.removeExcludedViewsRun excludeviews to remove and archive views to excludeBoolYYSDNot available until IMOD 4.8.47
runtime.Excludeviews.any.deleteOldFilesRemove the original stack when excluding viewsBoolYYSD 
runtime.Preprocessing.any.removeXraysRun ccderaser to remove X rays and other artifactsBoolYYNE 
runtime.Preprocessing.any.archiveOriginalRun archiveorig and delete original stackBoolYYNEEtomo batch default is 1
comparam.eraser.ccderaser.PeakCriterionPeak criterion # of SDsFloatYYSD 
comparam.eraser.ccderaser.DiffCriterionDifference criterion # of SDsFloatYYSD 
comparam.eraser.ccderaser.MaximumRadiusMaximum radius of peak areaFloatYYSD 
comparam.eraser.ccderaser.ModelFileManual replacement modelFileYYSO 
comparam.eraser.ccderaser.LineObjectsObjects with lines to removeListYYSOEtomo batch default is 2
comparam.eraser.ccderaser.BoundaryObjectsObjects with contours around areas to eraseListYYSOEtomo batch default is 3
comparam.eraser.ccderaser.AllSectionObjectsObjects to erase on all sectionsListYYSOEtomo batch default is 1-3
runtime.Preprocessing.any.endExcludeCriterionExclude views from end of tilt series with SD below nearby SD times criterionFloatYYNE 
runtime.Preprocessing.any.darkExcludeRatioExclude high tilt views with region darker by this ratio than lighter regionsFloatYYNEBRT default is 0.17 relative to light regions
runtime.Preprocessing.any.darkExcludeFractionExclude high tilt views with dark region occupying this fraction of areaFloatYYNEBRT default is 0.33
Coarse Alignment      
comparam.xcorr.tiltxcorr.FilterRadius2High frequency filter cutoffFloatYYSD 
comparam.xcorr.tiltxcorr.FilterSigma2High frequency filter falloffFloatYYSD 
comparam.xcorr.tiltxcorr.SearchMagChangesSearch for size changes at a list of viewsBoolYYSDUseful only for bidirectional series
comparam.xcorr.tiltxcorr.ExcludeCentralPeakExclude peak at 0 shift due to fixed pattern noiseBoolYYSD 
runtime.Fiducials.any.fiduciallessChoice to use fiducialless alignmentBoolYYSO 
comparam.prenewst.newstack.BinByFactorCoarse aligned stack binningIntYYSD 
comparam.prenewst.newstack.AntialiasFilterFilter to use for antialiased size reduction (-1 for default)IntYYSD 
comparam.prenewst.newstack.ModeToOutput0 to convert to bytes; empty not toIntYYSO 
comparam.preblend.blendmont.BinByFactorCoarse aligned stack binningIntYYSD 
Tracking Choices      
runtime.Fiducials.any.trackingMethodChoice of seed and track (0); patch track (1); or RAPTOR (2)IntYYSD 
runtime.Fiducials.any.seedingMethodChoice of manual (0); autofidseed (1); transferfid (2); both (3)IntYYSDNeed .b.seedingMethod = 2 to do just transferfid on second axis
comparam.track.beadtrack.LightBeadsWhether beads are lightBoolYYSO 
comparam.track.beadtrack.LocalAreaTrackingWhether to do localBoolYYSD 
comparam.track.beadtrack.LocalAreaTargetSizeSize of local areas2 IntYYSD 
comparam.track.beadtrack.SobelFilterCenteringWhether to use Sobel filterBoolYYSD 
comparam.track.beadtrack.KernelSigmaForSobelSigma for Sobel filterFloatYYSDNeeds to be 1.5 for cryo data
comparam.track.beadtrack.RoundsOfTrackingNumber of rounds of tracking in runIntYYSDEtomo batch default is 4
runtime.BeadTracking.any.numberOfRunsNumber of times to run beadtrack (fiducial as seed)IntYYNEEtomo batch default is 2
Auto Seed Finding      
comparam.autofidseed.autofidseed.TwoSurfacesWhether beads on 2 surfacesBoolYYSDNeeded only if different from tiltalign
comparam.autofidseed.autofidseed.TargetNumberOfBeads# of beads to findIntYYSO 
comparam.autofidseed.autofidseed.TargetDensityOfBeadsDensity of beads to find per megapixelFloatYYSD 
runtime.SeedFinding.any.rawBoundaryModelModel drawn on raw stack with areas to in/excludeFileY NE 
comparam.autofidseed.autofidseed.ExcludeInsideAreasWhether to exclude areasBoolYYSD 
comparam.autofidseed.autofidseed.MinGuessNumBeadsMinimum beads present per sectionIntY SO 
comparam.autofidseed.autofidseed.AdjustSizesAdjust parameters based on average bead sizeBoolYYSO 
RAPTOR Parameters      
runtime.RAPTOR.any.useAlignedStackWhether to use aligned stack in RAPTORBoolYYSD 
runtime.RAPTOR.any.numberOfMarkersNumber of markers to trackIntYYSO 
Patch Tracking      
comparam.xcorr_pt.tiltxcorr.SizeOfPatchesXandYSize in X and Y of patches to track2 IntYYSD 
comparam.xcorr_pt.tiltxcorr.IterateCorrelationsNumber of iterationsIntYYSD 
comparam.xcorr_pt.tiltxcorr.FilterRadius2Right cutoff radius for filterFloatYYSD 
comparam.xcorr_pt.tiltxcorr.FilterSigma2Sigma for Gaussian rolloff above radius2FloatYYSD 
runtime.PatchTracking.any.rawBoundaryModelModel file drawn on raw stack with boundary contoursFileY NE 
comparam.xcorr_pt.imodchopconts.LengthOfPiecesContour length for breaking into pieces (-1 for default)IntYYSDMay not be entered with contourPieces
comparam.xcorr_pt.imodchopconts.MinimumOverlapOverlap if breaking contoursIntYYSD 
runtime.PatchTracking.any.contourPiecesNumber of pieces to break contours intoIntY NEMay not be entered with LengthOfPieces
runtime.PatchTracking.any.adjustTiltAnglesRun again with tilt angle offset from TiltalignBoolYYNE 
comparam.align.tiltalign.SurfacesToAnalyzeAnalyze angles for 1 or 2 surfacesIntYYSODefault in original com file is 2
comparam.align.tiltalign.LocalAlignmentsWhether to do local alignmentsBoolYYSD 
comparam.align.tiltalign.TargetPatchSizeXandYTarget minimum size for local patches2 IntYYSO 
comparam.align.tiltalign.MinFidsTotalAndEachSurfaceMinimum fiducials in local area2 IntYYSO 
comparam.align.tiltalign.MagOptionType of magnification solution (1 solve all; 3 group; 0 fix)IntYYSO 
comparam.align.tiltalign.TiltOptionType of tilt angle solution (1 solve all; 5 group; 0 fix)IntYYSO 
comparam.align.tiltalign.RotOptionType of rotation solution (1 solve all; 3 group; -1 solve one; 0 fix)IntYYSO 
comparam.align.tiltalign.BeamTiltOptionType of beam tilt solution (2 to search)IntYYSD 
comparam.align.tiltalign.FixedOrInitialBeamTiltFixed beam tilt value or initial value for searchFloatYYSD 
comparam.align.tiltalign.ProjectionStretchWhether to solve for single stretch in all projectionsBoolYYSD 
comparam.align.tiltalign.XtiltOptionEnter 4 to solve for X-axis tilt between separate groupsIntYYSD 
comparam.align.tiltalign.RobustFittingWhether to use robust fitting to downweight some pointsBoolYYSDEtomo batch default is 1
comparam.align.tiltalign.KFactorScalingFactor that determines how many points are downweightedFloatYYSD 
comparam.align.tiltalign.WeightWholeTracksApply weighting to entire contours from patch trackingBoolYYSO 
runtime.TiltAlignment.any.enableStretchingAllow stretching solution if bead number and distribution permitBoolYYNE 
comparam.align.tiltalign.ResidualReportCriterionCriterion # of SDs above mean residual error to reportFloat YSO 
runtime.RestrictAlign.any.targetMeasurementRatioTarget measurement/unknown ratio when there are few fiducialsFloatYYSD 
runtime.RestrictAlign.any.minMeasurementRatioMinimum measurement/unknown ratio when there are few fiducialsFloatYYSD 
runtime.RestrictAlign.any.orderOfRestrictionsOrdered list of parameter restrictions when there are few fiducialsStringYYSO 
runtime.RestrictAlign.any.skipBeamTiltWithOneRotWhether to skip beam tilt solution when switching to one rotationBoolYYSO 
Tomogram Positioning      
runtime.Positioning.any.sampleTypeDo positioning for given sample type (0 none; 1 plastic section; 2 cryo)IntYYNE 
runtime.Positioning.any.wholeTomogramWhether to make a whole tomogram for positioningBoolYYSDHas no effect in BRT currently
runtime.Positioning.any.binByFactorBinning for whole tomogramIntYYSDBRT has size-based default up to 4 for plastic; No effect for cryo
runtime.Positioning.any.thicknessUnbinned thickness (pixels) for samples or whole tomogramIntYYSDRequired for cryo; BRT has size-based defaults for plastic
runtime.Positioning.any.hasGoldBeadsCryopositioning needs to take gold beads into accountBoolYYNERelevant only for cryo after patch tracking or fiducialless
comparam.tomopitch.tomopitch.ExtraThicknessUnbinned pixels to add on each surface in positioningIntYYSDBRT default is 25 for cryo
comparam.cryoposition.cryoposition.BinningToApplyBinning to use in cryopositioningIntYYNE 
runtime.Positioning.any.centerOnGoldShift to center on gold if it is on two surfaces and not positioningBoolYYNERequires at least 4 fiducials on each surface
Aligned Stack Choices      
runtime.AlignedStack.any.correctCTFWhether to correct CTFBoolYYNE 
runtime.AlignedStack.any.eraseGoldWhether to erase gold (1 for fid-based; 2 for 3d)IntYYNE 
runtime.AlignedStack.any.filterStackWhether to do 2D filteringBoolYYNE 
Aligned Stack Parameters      
runtime.AlignedStack.any.linearInterpolationUse linear interpolationBoolYYNES 
runtime.AlignedStack.any.binByFactorBinning to applyIntYYSD 
comparam.newst.newstack.AntialiasFilterFilter to use for antialiased size reductionIntYYSD 
runtime.AlignedStack.any.sizeInXandYUnbinned size of output in X and Y2 IntYYSD 
runtime.CTFplotting.any.autoFitRangeAndStepRange and step for autofitting2 FloatYYSOMust be present for fitting to occur
comparam.ctfplotter.ctfplotter.InvertTiltAnglesInvert the sign of the tilt anglesBoolYYSD 
comparam.ctfplotter.ctfplotter.FrequencyRangeToFitStarting and ending frequencies of range to fit2 FloatYYSO 
comparam.ctfplotter.ctfplotter.ExtraZerosToFitExtent to fit past 2nd zero as multiple of interzero distance2 FloatYYSO 
comparam.ctfplotter.ctfplotter.VaryExponentInFitVary exponent of CTF function when fittingBoolYYSO 
comparam.ctfplotter.ctfplotter.BaselineFittingOrderOrder for polynomial fit to flatten baselineIntYYSO 
comparam.ctfcorrection.ctfphaseflip.InvertTiltAnglesInvert the sign of the tilt anglesBoolYYSD 
comparam.mtffilter.mtffilter.LowPassRadiusSigmaRadius and sigma for 2D filtering2 FloatYYSO 
runtime.GoldErasing.any.binningBinning to use in finding goldIntYYSOBRT default: bead size / 5 rounded to integer
runtime.GoldErasing.any.extraDiameterExtra (binned) pixels of diameter to eraseFloatYYNE 
runtime.GoldErasing.any.thicknessUnbinned reconstruction thicknessIntYYSORequired if there are not fiducials on two surfaces
comparam.golderaser.ccderaser.ExpandCircleIterationsIterations for expanding patches around circlesIntYYSDBRT default 2
comparam.tilt.tilt.THICKNESSThickness for reconstructionIntYYSO 
runtime.Reconstruction.any.binnedThicknessThickness in binned pixelsIntYYNEMay not be entered with THICKNESS
runtime.Reconstruction.any.fallbackThicknessUnbinned thickness if computed distance non-existent or too smallIntYYNEMay not be entered with THICKNESS or binnedThickness
runtime.Reconstruction.any.extraThicknessAdded thickness if derived from align.log or positioningIntYYNE 
comparam.tilt.tilt.RADIALRadius and sigma for 1D filter2 FloatYYSO 
comparam.tilt.tilt.LOGDifferent log base or empty for no logFloatYYSD 
comparam.tilt.tilt.SCALEScaling values to add and multiply by2 FloatYYSO 
comparam.tilt.tilt.FakeSIRTiterationsUse SIRT-like radial filter equivalent to given # of SIRT iterationsIntYYSOMay not be entered with useSIRT
runtime.Reconstruction.any.useSirtWhether to do SIRTBoolYYSO 
runtime.Reconstruction.any.doBackprojAlsoWhether to do BP in addition to SIRTBoolYYNE 
SIRT Parameters      
comparam.sirtsetup.sirtsetup.LeaveIterationsIterations to leaveListYYSD 
comparam.sirtsetup.sirtsetup.ScaleToIntegerScaling to integer min/max2 IntYYSDUse -20000 20000
comparam.sirtsetup.sirtsetup.RadiusAndSigmaRadius and sigma for radial filter2 FloatYYSD 
Tomogram Combination      
runtime.Combine.any.matchAtoBThickRatioCriterion ratio of B to A thickness for matching A to BFloatYYNEDefault 0.9; use < 0.2 to match B to A or > 5 for A to B
runtime.Combine.any.findSecBoxSizeBox size for running Findsection on tomogramsIntYYNEBRT default 32
runtime.Combine.any.findSecNumScalesNumber of scales to analyze when running FindsectionIntYYNEBRT default 4
runtime.Combine.any.patchSizeStarting patch size for patch correlationsStringYY Use single letter (S M L E); avoid size (default M)
runtime.Combine.any.finalPatchSizeFinal size for patch correlationsStringYY Use single letter (S M L E) or size in X-Y-Z (default E)
runtime.Combine.any.extraTargetsExtra residual targets for final trialStringYY BRT default 0.4 0.45 (with a comma!)
runtime.Combine.any.wedgeReductionFraction to reduce amplitudes in missing wedge regionsFloatYY  
runtime.Combine.any.lowFromBothRadiusFourier radius below which to take components from both tomogramsFloatYY  
runtime.Combine.any.doSIRTifBoth1 to combine SIRT reconstructions if BP was done alsoIntYYNE 
comparam.solvematch.solvematch.MaximumResidualMaximum error when fitting to corresponding pointsFloatYY  
comparam.dualvolmatch.dualvolmatch.MaximumResidualError in fit to patch vectors that makes it fall back to preliminary transform FloatYY  
comparam.patchcorr.corrsearch3d.KernelSigmaSigma for kernel filter in patch correlationsFloatYY BRT default 1.45
comparam.matchorwarp.matchorwarp.RefineLimitMean residual limit for using linear fit and transformationFloatYY  
comparam.matchorwarp.matchorwarp.WarpLimitsSeries of mean residual limits for Findwarp try to reach with warpingStringYY  
runtime.Postprocess.any.doTrimvolRun Trimvol on the reconstructionBoolYYNEruntime.Trimvol directives are ignored if this is 0
runtime.Trimvol.any.findSecAddThicknessFraction or # of pixels to add to Findsection Z extentFloatYYNEFor plastic sections only
runtime.Trimvol.any.reorientReorientation in trimvol (0 none; 1 flip; 2 rotate)IntYYNEBRT default is 2
runtime.Trimvol.any.thicknessFraction or # of slices to trim thickness toFloatYYNEMay not be entered with findSecAddThickness
runtime.Trimvol.any.sizeInXFraction or # of pixels to trim to in XFloatYYNE 
runtime.Trimvol.any.sizeInYFraction or # of pixels to trim to in YFloatYYNE 
runtime.Trimvol.any.scaleFromXFraction or # of pixels in X to use to set scaling to bytesFloatYYNEBRT default is 0.8
runtime.Trimvol.any.scaleFromYFraction or # of pixels in Y to use to set scaling to bytesFloatYYNEBRT default is 0.8
runtime.Trimvol.any.scaleFromZFraction or # of slices in Z to use to set scaling to bytesFloatYYNEBRT default is 0.33
runtime.Trimvol.any.scaleToMeanSDMean and standard deviation to scale to for converting to bytes2 FloatYYNEScale to given mean/SD instead of using Findcontrast
runtime.Trimvol.any.doAorBofDualAxisTrim a/b.rec of dual axis setBoolYYNE 
runtime.Trimvol.any.doSIRTifBoth1 to trim SIRT or 2 to trim both if BP done alsoIntYYNE 
runtime.NAD.any.iterationsNumber of iterations for running NADIntYYNEBoth iterations and Kvalue must be entered
runtime.NAD.any.KvalueK value to use when running NADFloatYYNE 
runtime.NAD.any.chunkMemoryMBMemory available for each chunk in MBIntYYNEBRT default 512
External Commands      
runtime.ReplaceStep.any.9Command to run in place of CtfplotterStringYYNE 
runtime.RunAfterStep.any.9Command to run after CtfplotterStringYYNE 
runtime.ReplaceStep.any.13Command to run in place of MtffilterStringYYNE 
runtime.RunAfterStep.any.13Command to run after MtffilterStringYYNE 


  1. The type entries indicate the kind of data expected to be in the field: one or two integers (separated by a comma), one or two floating point numbers, a boolean value of 0 or 1, or a text string. Text string entries marked as "File" will be shown with a file chooser button in the template editor in Etomo.
  2. Template directives must either specify absolute paths or have just a filename with no path. In the latter case, the files are sought in their default locations:
  3. Template and batch directive filenames must end in the extension ".adoc".
  4. Rules for the treatment of directives and the format of values are described in the man page for Batchruntomo. Some essentials are:
  5. Directives marked with Y in the Batch column can be included in a batch directive file and will be acted on by Batchruntomo.
  6. Directives marked with Y in the Tmplt column can be included in a template file. The entry in the Batch column determines whether such directives have an effect when the relevant step is run by Batchruntomo. The entry in the Etomo column determines whether they have an effect when running the relevant step for the first time in Etomo as well as the behavior of the directive editor.
  7. The entry in the Etomo column has these meanings:
  8. "BRT default" refers to a default value applied by Batchruntomo. "Etomo batch default" refers to a default value that the Etomo batch interface obtains from IMOD/com/batchDefaults.adoc.
  9. Directives to run a command in place of or after a given step have these rules: