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
CTF Correction Parameters
SIRT Parameters
Tomogram Combination
Data Set Cleanup
External Commands

Arguments to Copytomocoms     
setupset.copyarg.nameRoot name of data setString   
setupset.copyarg.stackextExtension of input stack(s) omitting dotString  Must be final extension; required in the -directive entry to Etomo
setupset.copyarg.dualDual-axis data setBoolYSO 
setupset.copyarg.montageData are montagedBoolYSD 
setupset.copyarg.pixelPixel size of images in nanometersFloatY Overrides value from scanHeader
setupset.copyarg.goldSize of gold beads in nanometersFloatYSD 
setupset.copyarg.rotationAngle from the vertical to the tilt axis in raw imagesFloatY Overrides value from scanHeader; applies to B axis unless brotation used
setupset.copyarg.brotationAngle from the vertical to the tilt axis for B axisFloatY Overrides value from scanHeader
setupset.copyarg.firstincFirst tilt angle and tilt angle increment for A or only axis2 Float  May not be entered with userawtlt or extract
setupset.copyarg.bfirstincFirst tilt angle and tilt angle increment for B axis2 Float  May not be entered with buserawtlt or bextract
setupset.copyarg.userawtltTake tilt angle from a .rawtlt file for A or only axisBoolYSOMay not be entered with firstinc or extract
setupset.copyarg.buserawtltTake tilt angle from a .rawtlt file for B axisBoolYSOMay not be entered with fbirstinc or bextract
setupset.copyarg.extractExtract tilt angles from data file for A or only axisBoolYSOMay not be entered with firstinc or userawtlt
setupset.copyarg.bextractExtract tilt angles from data file for B axisBoolYSOMay not be entered with fbirstinc or buserawtlt
setupset.copyarg.twodirStarting angle of bi-directional series for A or only axisFloatYSO 
setupset.copyarg.btwodirStarting angle of bi-directional series for B axisFloatYSO 
setupset.copyarg.reversedFirst part of bidirectional tilt series is in second part of file for A or only axisBoolY  
setupset.copyarg.breversedFirst part of bidirectional tilt series is in second part of file for B axisBoolY  
setupset.copyarg.dosesymStarting angle of dose-symmetric series for A or only axisFloatYNESee notes at end
setupset.copyarg.bdosesymStarting angle of dose-symmetric series for B axisFloatYNE 
setupset.copyarg.skipList of views to exclude from processing for A or only axisList   
setupset.copyarg.bskipList of views to exclude from processing for B axisList   
setupset.copyarg.distortCorrect image distortion with the given .idf fileFileYSO 
setupset.copyarg.binningBinning of raw imagesFloatY  
setupset.copyarg.gradientCorrect for magnification gradients using the given .mgt fileFileYSO 
setupset.copyarg.focusFocus was adjusted between montage frames for A or only axisBoolYSO 
setupset.copyarg.bfocusFocus was adjusted between montage frames for the B axisBoolYSO 
setupset.copyarg.defocusDefocus in nanometers (underfocus positive)FloatYSO 
setupset.copyarg.voltageMicroscope voltage in kVIntYSO 
setupset.copyarg.CsSpherical aberration in mmFloatYSO 
setupset.copyarg.ctfnoiseConfiguration file listing noise files for ctfplotterFileYSD 
Other Setup Parameters     
setupset.scopeTemplateName of scope template file to useString  See notes at end
setupset.systemTemplateName of system template fileString  See notes at end
setupset.userTemplateName of user template fileString  See notes at end
setupset.scanHeaderWhether to scan image file headerBoolY Etomo batch default is 1
setupset.makeSymbolicLinksMake symbolic links instead of delivering stack and other files (ignored on Windows)BoolY Proprocessing (defect removal) will result in a separate new stack
setupset.datasetDirectoryFull path to directoryString   
setupset.currentStackExtExisting extension on only or A-axis input stack omitting dotString  For Etomo to use to keep track of file renames when it runs batch
setupset.currentBStackExtExisting extension on B-axis input stack omitting dotString  Ignored if setupset.currentStackExt entered
runtime.Preprocessing.any.removeExcludedViewsRun excludeviews to remove and archive views to excludeBoolYSDNot available until IMOD 4.8.47
runtime.Excludeviews.any.deleteOldFilesRemove the original stack when excluding viewsBoolYSD 
runtime.Preprocessing.any.removeXraysRun ccderaser to remove X rays and other artifactsBoolYNE 
runtime.Preprocessing.any.archiveOriginalRun archiveorig and delete original stackBoolYNEEtomo batch default is 1
comparam.eraser.ccderaser.PeakCriterionPeak criterion # of SDsFloatYSD 
comparam.eraser.ccderaser.DiffCriterionDifference criterion # of SDsFloatYSD 
comparam.eraser.ccderaser.MaximumRadiusMaximum radius of peak areaFloatYSD 
comparam.eraser.ccderaser.ModelFileManual replacement modelFileYSO 
comparam.eraser.ccderaser.LineObjectsObjects with lines to removeListYSOEtomo batch default is 2
comparam.eraser.ccderaser.BoundaryObjectsObjects with contours around areas to eraseListYSOEtomo batch default is 3
comparam.eraser.ccderaser.AllSectionObjectsObjects to erase on all sectionsListYSOEtomo batch default is 1-3
runtime.Preprocessing.any.endExcludeCriterionExclude views from end of tilt series with SD below nearby SD times criterionFloatYNE 
runtime.Preprocessing.any.darkExcludeRatioExclude high tilt views with region darker by this ratio than lighter regionsFloatYNEBRT default is 0.17 relative to light regions
runtime.Preprocessing.any.darkExcludeFractionExclude high tilt views with dark region occupying this fraction of areaFloatYNEBRT default is 0.33
Coarse Alignment     
comparam.xcorr.tiltxcorr.FilterRadius2High frequency filter cutoffFloatYSD 
comparam.xcorr.tiltxcorr.FilterSigma2High frequency filter falloffFloatYSD 
comparam.xcorr.tiltxcorr.SearchMagChangesSearch for size changes at a list of viewsBoolYSDUseful only for bidirectional series
comparam.xcorr.tiltxcorr.ExcludeCentralPeakExclude peak at 0 shift due to fixed pattern noiseBoolYSD 
comparam.xcorr.tiltxcorr.NoCosineStretchDo not use cosine stretching to correlate views (add if angles are very high)BoolYSO 
runtime.Fiducials.any.fiduciallessChoice to use coarse alignment onlyBoolYSO 
comparam.prenewst.newstack.BinByFactorCoarse aligned stack binningIntYSD 
comparam.prenewst.newstack.AntialiasFilterFilter to use for antialiased size reduction (-1 for default)IntYSD 
comparam.prenewst.newstack.ModeToOutput0 to convert to bytes; empty not toIntYSO 
comparam.preblend.blendmont.BinByFactorCoarse aligned stack binningIntYSD 
Tracking Choices     
runtime.Fiducials.any.trackingMethodChoice of seed and track (0); patch track (1); or RAPTOR (2)IntYSD 
runtime.Fiducials.any.seedingMethodChoice of manual (0); autofidseed (1); transferfid (2); both (3)IntYSDNeed .b.seedingMethod = 2 to do just transferfid on second axis
comparam.track.beadtrack.LightBeadsWhether beads are lightBoolYSO 
comparam.track.beadtrack.LocalAreaTrackingWhether to do localBoolYSD 
comparam.track.beadtrack.LocalAreaTargetSizeSize of local areas2 IntYSD 
comparam.track.beadtrack.SobelFilterCenteringWhether to use Sobel filterBoolYSD 
comparam.track.beadtrack.KernelSigmaForSobelSigma for Sobel filter in binned pixelsFloatYSDNeeds to be 1.5 for cryo data
comparam.track.beadtrack.ScalableSigmaForSobelSigma for Sobel filter as fraction of bead diameterFloat Y Cannot be used with KernelSigmaForSobel; 0.12 is good value
comparam.track.beadtrack.LowPassCutoffInverseNmStart of falloff for high-frequency filter (in reciprocal nanometers)FloatYSO 
comparam.track.beadtrack.RoundsOfTrackingNumber of rounds of tracking in runIntYSDEtomo batch default is 4
runtime.BeadTracking.any.numberOfRunsNumber of times to run beadtrack (fiducial as seed)IntYNEEtomo batch default is 2
Auto Seed Finding     
comparam.autofidseed.autofidseed.TwoSurfacesWhether beads on 2 surfacesBoolYSDNeeded only if different from tiltalign
comparam.autofidseed.autofidseed.TargetNumberOfBeads# of beads to findIntYSO 
comparam.autofidseed.autofidseed.TargetDensityOfBeadsDensity of beads to find per megapixelFloatYSD 
runtime.SeedFinding.any.rawBoundaryModelModel drawn on raw stack with areas to in/excludeFile NE 
runtime.SeedFinding.any.prealiBoundaryModelModel drawn on prealigned stack with areas to in/excludeFile NESupersedes raw model; both a and b models can be specified
comparam.autofidseed.autofidseed.ExcludeInsideAreasWhether to exclude areas inside or outside boundary contoursBoolYSD 
comparam.autofidseed.autofidseed.MinGuessNumBeadsMinimum beads present per sectionInt SO 
comparam.autofidseed.autofidseed.AdjustSizesAdjust parameters based on average bead sizeBoolYSO 
comparam.autofidseed.autofidseed.ElongatedPointsAllowedInclude beads that appear elongated in the given number of tracksIntYSOBRT default 3 when there are few beads
comparam.autofidseed.autofidseed.ClusteredPointsAllowedInclude beads that are very close to others and may overlap at higher tiltIntYSO 
comparam.autofidseed.autofidseed.LowerTargetForClusteredOnly include clustered or elongated beads when there are fewer than this #IntY BRT default 5
RAPTOR Parameters     
runtime.RAPTOR.any.useAlignedStackWhether to use aligned stack in RAPTORBoolYSD 
runtime.RAPTOR.any.numberOfMarkersNumber of markers to trackIntYSO 
Patch Tracking     
comparam.xcorr_pt.tiltxcorr.SizeOfPatchesXandYSize in X and Y of patches to track2 IntYSD 
comparam.xcorr_pt.tiltxcorr.NumberOfPatchesXandYNumber of patches to track in X and Y2 IntYSDMay not be entered with OverlapOfPatchesXandY
comparam.xcorr_pt.tiltxcorr.OverlapOfPatchesXandYOverlap of patches in X and Y (negative allowed; default is 0.33 0.33)2 FloatYSDMay not be entered with NumberOfPatchesXandY
comparam.xcorr_pt.tiltxcorr.IterateCorrelationsNumber of iterationsIntYSD 
comparam.xcorr_pt.tiltxcorr.FilterRadius2Right cutoff radius for filterFloatYSD 
comparam.xcorr_pt.tiltxcorr.FilterSigma2Sigma for Gaussian rolloff above radius2FloatYSD 
runtime.PatchTracking.any.rawBoundaryModelModel file drawn on raw stack with boundary contoursFile NE 
runtime.PatchTracking.any.prealiBoundaryModelModel file drawn on prealigned stack with boundary contoursFile NESupersedes raw model; both a and b models can be specified
comparam.xcorr_pt.imodchopconts.LengthOfPiecesContour length for breaking into pieces (-1 for default)IntYSDValue > 0 may not be entered with ContourPieces
comparam.xcorr_pt.imodchopconts.MinimumOverlapOverlap if breaking contoursIntYSD 
runtime.PatchTracking.any.contourPiecesNumber of pieces to break contours intoInt NEMay not be entered with LengthOfPieces > 0; overrides LengthOfPieces -1
runtime.PatchTracking.any.adjustTiltAnglesRun again with tilt angle offset from TiltalignBoolYNE 
runtime.PatchTracking.any.maxTiltAdjustmentMaximum adjustment to tilt angles allowed before rerunning (default 20)FloatYNE 
runtime.PatchTracking.any.maxAdjustedAngleMaximum adjusted tilt angle allowed before rerunning (default 78)FloatYNE 
comparam.align.tiltalign.SurfacesToAnalyzeAnalyze angles for 1 or 2 surfacesIntYSODefault in original com file is 2
comparam.align.tiltalign.LocalAlignmentsWhether to do local alignmentsBoolYSD 
comparam.align.tiltalign.TargetPatchSizeXandYTarget minimum size for local patches2 IntYSO 
comparam.align.tiltalign.MinFidsTotalAndEachSurfaceMinimum fiducials in local area2 IntYSO 
comparam.align.tiltalign.MagOptionType of magnification solution (1 solve all; 3 group; 0 fix)IntYSO 
comparam.align.tiltalign.TiltOptionType of tilt angle solution (2 solve all except minimum tilt; 5 group; 0 fix)IntYSO 
comparam.align.tiltalign.RotOptionType of rotation solution (1 solve all; 3 group; -1 solve one; 0 fix)IntYSO 
comparam.align.tiltalign.BeamTiltOptionType of beam tilt solution (2 to search)IntYSD 
comparam.align.tiltalign.FixedOrInitialBeamTiltFixed beam tilt value or initial value for searchFloatYSD 
comparam.align.tiltalign.ProjectionStretchWhether to solve for single stretch in all projectionsBoolYSD 
comparam.align.tiltalign.XTiltOptionEnter 4 to solve for X-axis tilt between separate groupsIntYSD 
comparam.align.tiltalign.RobustFittingWhether to use robust fitting to downweight some pointsBoolYSDEtomo batch default is 1
comparam.align.tiltalign.KFactorScalingFactor that determines how many points are downweightedFloatYSD 
comparam.align.tiltalign.WeightWholeTracksApply weighting to entire contours from patch trackingBoolYSOEtomo batch default is 1
runtime.TiltAlignment.any.enableStretchingAllow stretching solution if bead number and distribution permitBoolYNE 
comparam.align.tiltalign.ResidualReportCriterionCriterion # of SDs above mean residual error to reportFloatYSO 
runtime.RestrictAlign.any.targetMeasurementRatioTarget measurement/unknown ratio when there are few fiducialsFloatYSD 
runtime.RestrictAlign.any.minMeasurementRatioMinimum measurement/unknown ratio when there are few fiducialsFloatYSD 
runtime.RestrictAlign.any.orderOfRestrictionsOrdered list of parameter restrictions when there are few fiducialsStringYSOApplies only to restriction based on measurement/unknown ratio
runtime.RestrictAlign.any.skipBeamTiltWithOneRotWhether to skip beam tilt solution when switching to one rotationBoolYSO 
comparam.restrictalign.restrictalign.UseCrossValidationRun tiltalign and restrict parameters to optimize the leave-out errorIntY Etomo and batch use 1; use 0 to avoid cross-validation
comparam.restrictalign.restrictalign.CrossValTestOrderOrder in which different variables are tested with cross-validationStringY  
comparam.restrictalign.restrictalign.TestPermutationsList of variables for which to try all permutations in testing order (3 4 5 = rot mag tilt)StringY  
comparam.restrictalign.restrictalign.VerboseOutputGive output on effect of each test when doing cross-validationBoolY  
Tomogram Positioning     
runtime.Positioning.any.sampleTypeDo positioning for given sample type (0 none; 1 plastic section; 2 cryo)IntYNE 
runtime.Positioning.any.wholeTomogramWhether to make a whole tomogram for positioningBoolYSDHas no effect in BRT currently
runtime.Positioning.any.binByFactorBinning for whole tomogramIntYSDBRT has size-based default up to 4 for plastic; No effect for cryo
runtime.Positioning.any.thicknessUnbinned thickness (pixels) for samples or whole tomogramIntYSDRequired for cryo; BRT has size-based defaults for plastic
runtime.Positioning.any.hasGoldBeadsCryopositioning needs to take gold beads into accountBoolYNERelevant only for cryo after patch tracking or fiducialless
comparam.tomopitch.tomopitch.ExtraThicknessUnbinned pixels to add on each surface in positioningIntYSDBRT default is 25 for cryo
comparam.cryoposition.cryoposition.BinningToApplyBinning to use in cryopositioningIntYNE 
runtime.Positioning.any.centerOnGoldShift to center on gold if it is on two surfaces and not positioningBoolYNERequires at least 4 fiducials on each surface
Aligned Stack Choices     
runtime.AlignedStack.any.correctCTFWhether to correct CTFBoolYNE 
runtime.AlignedStack.any.eraseGoldWhether to erase gold (1 for fid-based; 2 for 3d)IntYNE 
runtime.AlignedStack.any.filterStackWhether to do 2D filteringBoolYNE 
Aligned Stack Parameters     
runtime.AlignedStack.any.linearInterpolationUse linear interpolationBoolYNES 
runtime.AlignedStack.any.binByFactorBinning to applyIntYSD 
comparam.newst.newstack.TaperAtFillExtent to taper (1 for default) and 0 or 1 to taper outside or inside2 IntY  
comparam.newst.newstack.FillValueValue with which to fill empty areas created by shifting imagesFloatY  
comparam.newst.newstack.AntialiasFilterFilter to use for antialiased size reductionIntYSD 
runtime.AlignedStack.any.sizeInXandYUnbinned size of output in X and Y2 IntYSD 
comparam.mtffilter.mtffilter.LowPassRadiusSigmaRadius and sigma for 2D filtering2 FloatYSO 
comparam.mtffilter.mtffilter.TypeOfDoseFileDose-weighting file type (1-3: dose data one line per tilt; 4: mdoc file)IntYSOCannot be used with FixedImageDose
comparam.mtffilter.mtffilter.FixedImageDoseApply dose weighting with this dose for every viewFloatYSO 
comparam.mtffilter.mtffilter.DoseWeightingFileName of file with dose information or possibly a generic entry to use .mdocFileYSODefault in original com file is correct except in one case; see notes at end
comparam.mtffilter.mtffilter.OptimalDoseScalingScaling applied to optimal dose value that determines weightingFloatYSOA value > 1 or < 1 for specimen more or less resistant to dose
comparam.mtffilter.mtffilter.InitialDoseDose applied before the tilt series startedFloatY  
comparam.mtffilter.mtffilter.DensityScaleFactorFactor to scale filtered values byFloatY  
comparam.mtffilter.mtffilter.ModeToOutputData mode to output (0: byte; 1: signed 16-bit; 6: unsigned 16-bit; 2: float; 12: 16-bit float)IntY  
runtime.GoldErasing.any.binningBinning to use in finding goldIntYSOBRT default: bead size / 5 rounded to integer
comparam.findbeads3d.findbeads3d.LightBeadsWhether beads are lightBoolY Not needed and ignored in BRT; entry governs this
runtime.GoldErasing.any.extraDiameterExtra (binned) pixels of diameter to eraseFloatYNE 
runtime.GoldErasing.any.thicknessUnbinned reconstruction thicknessIntYSORequired if there are not fiducials on two surfaces
comparam.golderaser.ccderaser.ExpandCircleIterationsIterations for expanding patches around circlesIntYSDBRT default 2; cryoTemplate overrides with 3
comparam.golderaser.ccderaser.PolynomialOrderMethod of fitting to background for filling pixels (-1 noise; 0 mean; 1 planar)IntYSOcryoTemplate default is -1
CTF Correction Parameters     
runtime.CTFplotting.any.autoFitRangeAndStepRange and step for autofitting2 FloatYSOMust be present for fitting to occur
comparam.ctfplotter.ctfplotter.ScanDefocusRangeDo initial scan for best defocus from low to high value2 FloatY  
comparam.ctfplotter.ctfplotter.TuneFittingAndSamplingAutotune fitting range and spectrum samplingBoolY  
comparam.ctfplotter.ctfplotter.AssessTiltAngleOffsetEstimate and set tilt angle offset from left-right differences on startupBoolY  
comparam.ctfplotter.ctfplotter.TiltAngleOffsetOffset to add to tilt angles when adjusting strip spectra for defocusFloatY  
comparam.ctfplotter.ctfplotter.InvertTiltAnglesInvert the sign of the tilt anglesBoolYSD 
comparam.ctfplotter.ctfplotter.FrequencyRangeToFitStarting and ending frequencies of range to fit2 FloatYSO 
comparam.ctfplotter.ctfplotter.ExtraZerosToFitExtent to fit past 2nd zero as multiple of interzero distanceFloatYSO 
comparam.ctfplotter.ctfplotter.VaryExponentInFitVary exponent of CTF function when fittingBoolYSO 
comparam.ctfplotter.ctfplotter.BaselineFittingOrderOrder for polynomial fit to flatten baselineIntYSO 
comparam.ctfplotter.ctfplotter.FitMoreViewsAboveAngleHigher number of views to autofit at high tilt and angle above which to do so2 IntY  
comparam.ctfplotter.ctfplotter.CropToPixelSizePixel size in nanometers to crop power spectrum toFloatYSO 
comparam.ctfplotter.ctfplotter.PhaseShiftInDegreesExpected value of phase shift from a phase plateFloatY  
comparam.ctfplotter.ctfplotter.SearchAstigmatismFind astigmatismBoolY  
comparam.ctfplotter.ctfplotter.SearchPhaseShiftFind phase shiftBoolY  
comparam.ctfplotter.ctfplotter.SearchCutonFrequencyFind cut-on frequency when finding phaseBoolY Cut-on entry is ignored when not finding phase shift
comparam.ctfplotter.ctfplotter.MinViewsAstigAndPhaseMinimum number of views to analyze when finding astigmatism and phase2 IntY Default is 3 and 1
comparam.ctfplotter.ctfplotter.ViewsToSkipList of views to exclude from all analysis or just from astigmatism/phaseList   
comparam.ctfplotter.ctfplotter.SkipOnlyForAstigPhaseExclude the skipped views only from analysis of astigmatism and phaseBoolY  
comparam.ctfplotter.ctfplotter.PSResolutionNumber of bins in the power spectrum and points available for fitting CTFIntY  
comparam.ctfplotter.ctfplotter.TileSizeTile size for computing spectra in pixelsIntY  
comparam.ctfplotter.ctfplotter.DefocusTolDefocus range in nanometers for tiles included in a stripIntY  
comparam.ctfcorrection.ctfphaseflip.PhaseShiftInDegreesConstant value of phase shift from a phase plateFloatY  
comparam.ctfcorrection.ctfphaseflip.InvertTiltAnglesInvert the sign of the tilt anglesBoolYSD 
comparam.ctfcorrection.ctfphaseflip.InterpolationWidthSpacing in pixels between adjacent corrected strips that are interpolatedIntYSD 
comparam.ctfcorrection.ctfphaseflip.ScaleByCtfPowerScale frequency components by calculated CTF to the given powerFloatYNES 
runtime.CTFcorrection.any.correctForXAxisTiltCorrect for X-axis tilt that will be used to make reconstructionBoolYNE 
comparam.tilt.tilt.THICKNESSThickness for reconstructionIntYSO 
runtime.Reconstruction.any.binnedThicknessThickness in binned pixelsIntYNEMay not be entered with THICKNESS
runtime.Reconstruction.any.fallbackThicknessUnbinned thickness if computed distance non-existent or too smallIntYNEMay not be entered with THICKNESS or binnedThickness
runtime.Reconstruction.any.extraThicknessAdded thickness if derived from align.log or positioningIntYNE 
comparam.tilt.tilt.RADIALRadius and sigma for 1D filter2 FloatYSO 
comparam.tilt.tilt.LOGDifferent log base or empty for no logFloatYSD 
comparam.tilt.tilt.SCALEScaling values to add and multiply by2 FloatYSO 
comparam.tilt.tilt.FakeSIRTiterationsUse SIRT-like radial filter equivalent to given # of SIRT iterationsIntYSOMay not be entered with useSIRT
comparam.tilt.tilt.SuperSampleFactorCompute slices in pixels smaller by this factor to reduce artifactsIntY  
comparam.tilt.tilt.ExpandInputLinesExpand projection lines by Fourier padding when supersamplingBoolY May not be entered with ctf3dsetup.UseUnalignedImages
runtime.Reconstruction.any.useSirtWhether to do SIRTBoolYSO 
runtime.Reconstruction.any.doBackprojAlsoWhether to do regular BP in addition to SIRT or SIRT-like filterBoolYNE 
runtime.Reconstruction.any.noXAxisTiltKeep X axis tilt at 0 in final reconstruction and positioning one (if any)BoolYNE 
comparam.ctf3dsetup.ctf3dsetup.SlabThicknessInNmMake 3D CTF-corrected reconstruction with this slab thickness in nmIntYNEMust be used instead of NumberOfSlabs to get 3-D CTF correction
comparam.ctf3dsetup.ctf3dsetup.RunSlabsInParallelMake each slab with one processor or GPU and run in parallelBoolYNEWill create as many aligned stacks as CPUs or GPUs used
comparam.ctf3dsetup.ctf3dsetup.UseUnalignedImagesGenerate 3D CTF corrected tomogram directly from raw stack imagesBoolYNEMay not be entered with tilt.ExpandInputLines
comparam.ctf3dsetup.ctf3dsetup.FourierReduceByFactorFactor by which to reduce raw stack with Fourier cropping for 3D CTFIntYNE 
SIRT Parameters     
comparam.sirtsetup.sirtsetup.LeaveIterationsIterations to leaveListYSD 
comparam.sirtsetup.sirtsetup.ScaleToIntegerScaling to integer min/max2 IntYSDUse -20000 20000
comparam.sirtsetup.sirtsetup.RadiusAndSigmaRadius and sigma for radial filter2 FloatYSD 
Tomogram Combination     
runtime.Combine.any.matchAtoBThickRatioCriterion ratio of B to A thickness for matching A to BFloatYNEDefault 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 tomogramsIntYNEBRT default 32
runtime.Combine.any.findSecNumScalesNumber of scales to analyze when running FindsectionIntYNEBRT default 4
runtime.Combine.any.patchSizeStarting patch size for patch correlationsStringY Use single letter (S M L E); avoid size (default M)
runtime.Combine.any.finalPatchSizeFinal size for patch correlationsStringY Use single letter (S M L E) or size in X-Y-Z (default E)
runtime.Combine.any.extraTargetsExtra residual targets for final trialStringY BRT default 0.4 0.45 (with a comma!)
runtime.Combine.any.wedgeReductionFraction to reduce amplitudes in missing wedge regionsFloatY  
runtime.Combine.any.lowFromBothRadiusFourier radius below which to take components from both tomogramsFloatY  
runtime.Combine.any.doSIRTifBoth1 to combine SIRT or SIRT-like reconstructions if BP was done alsoIntYNE 
comparam.solvematch.solvematch.MaximumResidualMaximum error when fitting to corresponding pointsFloatY  
comparam.dualvolmatch.dualvolmatch.MaximumResidualError in fit to patch vectors that makes it fall back to preliminary transform FloatY  
comparam.patchcorr.corrsearch3d.KernelSigmaSigma for kernel filter in patch correlationsFloatY BRT default 1.45
comparam.matchorwarp.matchorwarp.RefineLimitMean residual limit for using linear fit and transformationFloatY  
comparam.matchorwarp.matchorwarp.WarpLimitsSeries of mean residual limits for Findwarp try to reach with warpingStringY  
runtime.Postprocess.any.doTrimvolRun Trimvol on the reconstructionBoolYNEruntime.Trimvol directives are ignored if this is 0
runtime.Trimvol.any.findSecAddThicknessFraction or # of pixels to add to Findsection Z extentFloatYNEFor plastic sections only
runtime.Trimvol.any.reorientReorientation in trimvol (0 none; 1 flip; 2 rotate)IntYNEBRT default is 2
runtime.Trimvol.any.thicknessFraction or # of slices to trim thickness toFloatYNEMay not be entered with findSecAddThickness
runtime.Trimvol.any.sizeInXFraction or # of pixels to trim to in XFloatYNE 
runtime.Trimvol.any.sizeInYFraction or # of pixels to trim to in YFloatYNE 
runtime.Trimvol.any.scaleFromXFraction or # of pixels in X to use to set scaling to bytesFloatYNEBRT default is 0.8
runtime.Trimvol.any.scaleFromYFraction or # of pixels in Y to use to set scaling to bytesFloatYNEBRT default is 0.8
runtime.Trimvol.any.scaleFromZFraction or # of slices in Z to use to set scaling to bytesFloatYNEBRT default is 0.33
runtime.Trimvol.any.scaleToMeanSDMean and standard deviation to scale to for converting to bytes2 FloatYNEScale to given mean/SD instead of using Findcontrast
runtime.Trimvol.any.doAorBofDualAxisTrim a/b.rec of dual axis setBoolYNE 
runtime.Trimvol.any.doSIRTifBoth1 to trim SIRT/SIRT-like or 2 to trim both if BP done alsoIntYNE 
runtime.NAD.any.iterationsNumber of iterations for running NADIntYNEBoth iterations and Kvalue must be entered
runtime.NAD.any.KvalueK value to use when running NADFloatYNE 
runtime.NAD.any.chunkMemoryMBMemory available for each chunk in MBIntYNEBRT default 512
runtime.Postprocess.any.doReduceFiltRun Reducefiltvol to reduce and/or filter the final tomogramBoolYNEAn option specifying reduction or filtering must be entered
comparam.reducefiltvol.reducefiltvol.ReductionFactorReduction factor to apply to volume; can be non-integerFloatY  
comparam.reducefiltvol.reducefiltvol.LowPassRadiusSigmaRadius and sigma for high-frequency Gaussian filter2 FloatY Cannot be used with DeconvolutionStretch
comparam.reducefiltvol.reducefiltvol.DeconvolutionStrengthStrength of deconvolution filter for boosting frequencies attenuated by CTFFloatY Cannot be used with LowPassRadiusSigma
comparam.reducefiltvol.reducefiltvol.SNRFalloffFalloff rate in the assumed SNR with frequency (default 0.7)FloatY  
comparam.reducefiltvol.reducefiltvol.HighPassNyquistCutoff for high-pass filter as fraction of Nyquist (default 0.02)FloatY  
comparam.reducefiltvol.reducefiltvol.DefocusInMicronsDefocus to assume for deconvolution instead of using Ctfplotter outputFloatY  
comparam.reducefiltvol.reducefiltvol.PhaseShiftPhase shift in degrees to use for deconvolutionFloatY  
comparam.reducefiltvol.reducefiltvol.ModeToOutputMode of Mtffilter output: 0 for byte; 1 or 6 for integer; 2 or 12 for floatIntY  
Data Set Cleanup     
runtime.Cleanup.any.doCleanupRun Tomocleanup on the data setBoolYNE 
runtime.Cleanup.any.keepAlignedKeep final aligned stack BoolYNE 
runtime.Cleanup.any.keepUntrimmedKeep untrimmed reconstruction even if Trimvol is runBoolYNE 
runtime.Cleanup.any.keepAxisKeep single axis reconstructions even if Combine finishedBoolYNE 
runtime.Cleanup.any.keepSIRTKeep SIRT or SIRT-like reconstructions when back-projection also doneBoolYNEBRT default is to keep these
External Commands     
runtime.ReplaceStep.any.9Command to run in place of CtfplotterStringYNE 
runtime.RunAfterStep.any.9Command to run after CtfplotterStringYNE 
runtime.ReplaceStep.any.13Command to run in place of MtffilterStringYNE 
runtime.RunAfterStep.any.13Command to run after MtffilterStringYNE 
runtime.ReplaceStep.any.20Command to run in place of TrimvolStringYNE 
runtime.RunAfterStep.any.20Command to run after TrimvolStringYNE 


  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 Tmplt column can be included in a template file. These and all other 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.
  6. The entry in the Etomo column has these meanings:
  7. "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.
  8. When doing dose weighting with an ".mdoc" file or an HDF file from SerialEM, no entry is needed for the dose information file except in one case: when processing in the old naming style with an original extension other than ".mrc". In that case, add the directive with just the extension before the ".mdoc" in the name, e.g., ".st".
  9. Directives to run a command in place of or after a given step have these rules:
  10. Until the dose-symmetric entry is supported in Etomo, the dose-symmetric directives cannot be used with tilt series having "bidir=" in the title line unless you turn off Scan Header and provide axis rotation and pixel size entries. Upgrade SerialEM to 3.8.15 or higher to avoid this problem.