Directive | Definition | Type | Batch | Tmplt | Etomo | Notes |
---|---|---|---|---|---|---|
Arguments to Copytomocoms | ||||||
setupset.copyarg.name | Root name of data set | String | Y | |||
setupset.copyarg.dual | Dual-axis data set | Bool | Y | Y | SO | |
setupset.copyarg.montage | Data are montaged | Bool | Y | Y | SD | |
setupset.copyarg.pixel | Pixel size of images in nanometers | Float | Y | Y | Overrides value from scanHeader | |
setupset.copyarg.gold | Size of gold beads in nanometers | Float | Y | Y | SD | |
setupset.copyarg.rotation | Angle from the vertical to the tilt axis in raw images | Float | Y | Y | Overrides value from scanHeader | |
setupset.copyarg.brotation | Angle from the vertical to the tilt axis for B axis | Float | Y | Y | Overrides value from scanHeader | |
setupset.copyarg.firstinc | First tilt angle and tilt angle increment | 2 Float | Y | |||
setupset.copyarg.bfirstinc | First tilt angle and tilt angle increment for B axis | 2 Float | Y | |||
setupset.copyarg.userawtlt | Take tilt angle from a .rawtlt file for A or only axis | Bool | Y | Y | SO | |
setupset.copyarg.buserawtlt | Take tilt angle from a .rawtlt file for B axis | Bool | Y | Y | SO | |
setupset.copyarg.extract | Extract tilt angles from data file for A or only axis | Bool | Y | Y | SO | |
setupset.copyarg.bextract | Extract tilt angles from data file for B axis | Bool | Y | Y | SO | |
setupset.copyarg.twodir | Starting angle of bi-directional series for A or only axis | Float | Y | Y | SO | |
setupset.copyarg.btwodir | Starting angle of bi-directional series for B axis | Float | Y | Y | SO | |
setupset.copyarg.skip | List of views to exclude from processing for A or only axis | List | Y | |||
setupset.copyarg.bskip | List of views to exclude from processing for B axis | List | Y | |||
setupset.copyarg.distort | Correct image distortion with the given .idf file | File | Y | Y | SO | |
setupset.copyarg.binning | Binning of raw images | Float | Y | Y | ||
setupset.copyarg.gradient | Correct for magnification gradients using the given .mgt file | File | Y | Y | SO | |
setupset.copyarg.focus | Focus was adjusted between frames when acquiring montage | Bool | Y | Y | SO | |
setupset.copyarg.bfocus | Focus was adjusted between montage frames for the B axis | Bool | Y | Y | SO | |
setupset.copyarg.defocus | Defocus in nanometers (underfocus positive) | Float | Y | Y | SO | |
setupset.copyarg.voltage | Microscope voltage in kV | Int | Y | Y | SO | |
setupset.copyarg.Cs | Spherical aberration in mm | Float | Y | Y | SO | |
setupset.copyarg.ctfnoise | Configuration file listing noise files for ctfplotter | File | Y | Y | SD | |
Other Setup Parameters | ||||||
setupset.scopeTemplate | Name of scope template file to use | String | Y | See notes at end | ||
setupset.systemTemplate | Name of system template file | String | Y | See notes at end | ||
setupset.userTemplate | Name of user template file | String | Y | See notes at end | ||
setupset.scanHeader | Whether to scan image file header | Bool | Y | Y | Etomo batch default is 1 | |
setupset.datasetDirectory | Full path to directory | String | Y | |||
Preprocessing | ||||||
runtime.Preprocessing.any.removeExcludedViews | Run excludeviews to remove and archive views to exclude | Bool | Y | Y | SD | Not available until IMOD 4.8.47 |
runtime.Excludeviews.any.deleteOldFiles | Remove the original stack when excluding views | Bool | Y | Y | SD | |
runtime.Preprocessing.any.removeXrays | Run ccderaser to remove X rays and other artifacts | Bool | Y | Y | NE | |
runtime.Preprocessing.any.archiveOriginal | Run archiveorig and delete original stack | Bool | Y | Y | NE | Etomo batch default is 1 |
comparam.eraser.ccderaser.PeakCriterion | Peak criterion # of SDs | Float | Y | Y | SD | |
comparam.eraser.ccderaser.DiffCriterion | Difference criterion # of SDs | Float | Y | Y | SD | |
comparam.eraser.ccderaser.MaximumRadius | Maximum radius of peak area | Float | Y | Y | SD | |
comparam.eraser.ccderaser.ModelFile | Manual replacement model | File | Y | Y | SO | |
comparam.eraser.ccderaser.LineObjects | Objects with lines to remove | List | Y | Y | SO | Etomo batch default is 2 |
comparam.eraser.ccderaser.BoundaryObjects | Objects with contours around areas to erase | List | Y | Y | SO | Etomo batch default is 3 |
comparam.eraser.ccderaser.AllSectionObjects | Objects to erase on all sections | List | Y | Y | SO | Etomo batch default is 1-3 |
runtime.Preprocessing.any.endExcludeCriterion | Exclude views from end of tilt series with SD below nearby SD times criterion | Float | Y | Y | NE | |
runtime.Preprocessing.any.darkExcludeRatio | Exclude high tilt views with region darker by this ratio than lighter regions | Float | Y | Y | NE | BRT default is 0.17 relative to light regions |
runtime.Preprocessing.any.darkExcludeFraction | Exclude high tilt views with dark region occupying this fraction of area | Float | Y | Y | NE | BRT default is 0.33 |
Coarse Alignment | ||||||
comparam.xcorr.tiltxcorr.FilterRadius2 | High frequency filter cutoff | Float | Y | Y | SD | |
comparam.xcorr.tiltxcorr.FilterSigma2 | High frequency filter falloff | Float | Y | Y | SD | |
comparam.xcorr.tiltxcorr.SearchMagChanges | Search for size changes at a list of views | Bool | Y | Y | SD | Useful only for bidirectional series |
comparam.xcorr.tiltxcorr.ExcludeCentralPeak | Exclude peak at 0 shift due to fixed pattern noise | Bool | Y | Y | SD | |
runtime.Fiducials.any.fiducialless | Choice to use fiducialless alignment | Bool | Y | Y | SO | |
comparam.prenewst.newstack.BinByFactor | Coarse aligned stack binning | Int | Y | Y | SD | |
comparam.prenewst.newstack.AntialiasFilter | Filter to use for antialiased size reduction (-1 for default) | Int | Y | Y | SD | |
comparam.prenewst.newstack.ModeToOutput | 0 to convert to bytes; empty not to | Int | Y | Y | SO | |
comparam.preblend.blendmont.BinByFactor | Coarse aligned stack binning | Int | Y | Y | SD | |
Tracking Choices | ||||||
runtime.Fiducials.any.trackingMethod | Choice of seed and track (0); patch track (1); or RAPTOR (2) | Int | Y | Y | SD | |
runtime.Fiducials.any.seedingMethod | Choice of manual (0); autofidseed (1); transferfid (2); both (3) | Int | Y | Y | SD | Need .b.seedingMethod = 2 to do just transferfid on second axis |
Beadtracking | ||||||
comparam.track.beadtrack.LightBeads | Whether beads are light | Bool | Y | Y | SO | |
comparam.track.beadtrack.LocalAreaTracking | Whether to do local | Bool | Y | Y | SD | |
comparam.track.beadtrack.LocalAreaTargetSize | Size of local areas | 2 Int | Y | Y | SD | |
comparam.track.beadtrack.SobelFilterCentering | Whether to use Sobel filter | Bool | Y | Y | SD | |
comparam.track.beadtrack.KernelSigmaForSobel | Sigma for Sobel filter | Float | Y | Y | SD | Needs to be 1.5 for cryo data |
comparam.track.beadtrack.RoundsOfTracking | Number of rounds of tracking in run | Int | Y | Y | SD | Etomo batch default is 4 |
runtime.BeadTracking.any.numberOfRuns | Number of times to run beadtrack (fiducial as seed) | Int | Y | Y | NE | Etomo batch default is 2 |
Auto Seed Finding | ||||||
comparam.autofidseed.autofidseed.TwoSurfaces | Whether beads on 2 surfaces | Bool | Y | Y | SD | Needed only if different from tiltalign |
comparam.autofidseed.autofidseed.TargetNumberOfBeads | # of beads to find | Int | Y | Y | SO | |
comparam.autofidseed.autofidseed.TargetDensityOfBeads | Density of beads to find per megapixel | Float | Y | Y | SD | |
runtime.SeedFinding.any.rawBoundaryModel | Model drawn on raw stack with areas to in/exclude | File | Y | NE | ||
comparam.autofidseed.autofidseed.ExcludeInsideAreas | Whether to exclude areas | Bool | Y | Y | SD | |
comparam.autofidseed.autofidseed.MinGuessNumBeads | Minimum beads present per section | Int | Y | SO | ||
comparam.autofidseed.autofidseed.AdjustSizes | Adjust parameters based on average bead size | Bool | Y | Y | SO | |
RAPTOR Parameters | ||||||
runtime.RAPTOR.any.useAlignedStack | Whether to use aligned stack in RAPTOR | Bool | Y | Y | SD | |
runtime.RAPTOR.any.numberOfMarkers | Number of markers to track | Int | Y | Y | SO | |
Patch Tracking | ||||||
comparam.xcorr_pt.tiltxcorr.SizeOfPatchesXandY | Size in X and Y of patches to track | 2 Int | Y | Y | SD | |
comparam.xcorr_pt.tiltxcorr.NumberOfPatchesXandY | Number of patches to track in X and Y | 2 Int | Y | Y | SD | May not be entered with OverlapOfPatchesXandY |
comparam.xcorr_pt.tiltxcorr.OverlapOfPatchesXandY | Overlap of patches in X and Y (negative allowed; default is 0.33 0.33) | 2 Float | Y | Y | SD | May not be entered with NumberOfPatchesXandY |
comparam.xcorr_pt.tiltxcorr.IterateCorrelations | Number of iterations | Int | Y | Y | SD | |
comparam.xcorr_pt.tiltxcorr.FilterRadius2 | Right cutoff radius for filter | Float | Y | Y | SD | |
comparam.xcorr_pt.tiltxcorr.FilterSigma2 | Sigma for Gaussian rolloff above radius2 | Float | Y | Y | SD | |
runtime.PatchTracking.any.rawBoundaryModel | Model file drawn on raw stack with boundary contours | File | Y | NE | ||
comparam.xcorr_pt.imodchopconts.LengthOfPieces | Contour length for breaking into pieces (-1 for default) | Int | Y | Y | SD | May not be entered with contourPieces |
comparam.xcorr_pt.imodchopconts.MinimumOverlap | Overlap if breaking contours | Int | Y | Y | SD | |
runtime.PatchTracking.any.contourPieces | Number of pieces to break contours into | Int | Y | NE | May not be entered with LengthOfPieces | |
runtime.PatchTracking.any.adjustTiltAngles | Run again with tilt angle offset from Tiltalign | Bool | Y | Y | NE | |
Alignment | ||||||
comparam.align.tiltalign.SurfacesToAnalyze | Analyze angles for 1 or 2 surfaces | Int | Y | Y | SO | Default in original com file is 2 |
comparam.align.tiltalign.LocalAlignments | Whether to do local alignments | Bool | Y | Y | SD | |
comparam.align.tiltalign.TargetPatchSizeXandY | Target minimum size for local patches | 2 Int | Y | Y | SO | |
comparam.align.tiltalign.MinFidsTotalAndEachSurface | Minimum fiducials in local area | 2 Int | Y | Y | SO | |
comparam.align.tiltalign.MagOption | Type of magnification solution (1 solve all; 3 group; 0 fix) | Int | Y | Y | SO | |
comparam.align.tiltalign.TiltOption | Type of tilt angle solution (1 solve all; 5 group; 0 fix) | Int | Y | Y | SO | |
comparam.align.tiltalign.RotOption | Type of rotation solution (1 solve all; 3 group; -1 solve one; 0 fix) | Int | Y | Y | SO | |
comparam.align.tiltalign.BeamTiltOption | Type of beam tilt solution (2 to search) | Int | Y | Y | SD | |
comparam.align.tiltalign.FixedOrInitialBeamTilt | Fixed beam tilt value or initial value for search | Float | Y | Y | SD | |
comparam.align.tiltalign.ProjectionStretch | Whether to solve for single stretch in all projections | Bool | Y | Y | SD | |
comparam.align.tiltalign.XtiltOption | Enter 4 to solve for X-axis tilt between separate groups | Int | Y | Y | SD | |
comparam.align.tiltalign.RobustFitting | Whether to use robust fitting to downweight some points | Bool | Y | Y | SD | Etomo batch default is 1 |
comparam.align.tiltalign.KFactorScaling | Factor that determines how many points are downweighted | Float | Y | Y | SD | |
comparam.align.tiltalign.WeightWholeTracks | Apply weighting to entire contours from patch tracking | Bool | Y | Y | SO | |
runtime.TiltAlignment.any.enableStretching | Allow stretching solution if bead number and distribution permit | Bool | Y | Y | NE | |
comparam.align.tiltalign.ResidualReportCriterion | Criterion # of SDs above mean residual error to report | Float | Y | SO | ||
runtime.RestrictAlign.any.targetMeasurementRatio | Target measurement/unknown ratio when there are few fiducials | Float | Y | Y | SD | |
runtime.RestrictAlign.any.minMeasurementRatio | Minimum measurement/unknown ratio when there are few fiducials | Float | Y | Y | SD | |
runtime.RestrictAlign.any.orderOfRestrictions | Ordered list of parameter restrictions when there are few fiducials | String | Y | Y | SO | |
runtime.RestrictAlign.any.skipBeamTiltWithOneRot | Whether to skip beam tilt solution when switching to one rotation | Bool | Y | Y | SO | |
Tomogram Positioning | ||||||
runtime.Positioning.any.sampleType | Do positioning for given sample type (0 none; 1 plastic section; 2 cryo) | Int | Y | Y | NE | |
runtime.Positioning.any.wholeTomogram | Whether to make a whole tomogram for positioning | Bool | Y | Y | SD | Has no effect in BRT currently |
runtime.Positioning.any.binByFactor | Binning for whole tomogram | Int | Y | Y | SD | BRT has size-based default up to 4 for plastic; No effect for cryo |
runtime.Positioning.any.thickness | Unbinned thickness (pixels) for samples or whole tomogram | Int | Y | Y | SD | Required for cryo; BRT has size-based defaults for plastic |
runtime.Positioning.any.hasGoldBeads | Cryopositioning needs to take gold beads into account | Bool | Y | Y | NE | Relevant only for cryo after patch tracking or fiducialless |
comparam.tomopitch.tomopitch.ExtraThickness | Unbinned pixels to add on each surface in positioning | Int | Y | Y | SD | BRT default is 25 for cryo |
comparam.cryoposition.cryoposition.BinningToApply | Binning to use in cryopositioning | Int | Y | Y | NE | |
runtime.Positioning.any.centerOnGold | Shift to center on gold if it is on two surfaces and not positioning | Bool | Y | Y | NE | Requires at least 4 fiducials on each surface |
Aligned Stack Choices | ||||||
runtime.AlignedStack.any.correctCTF | Whether to correct CTF | Bool | Y | Y | NE | |
runtime.AlignedStack.any.eraseGold | Whether to erase gold (1 for fid-based; 2 for 3d) | Int | Y | Y | NE | |
runtime.AlignedStack.any.filterStack | Whether to do 2D filtering | Bool | Y | Y | NE | |
Aligned Stack Parameters | ||||||
runtime.AlignedStack.any.linearInterpolation | Use linear interpolation | Bool | Y | Y | NES | |
runtime.AlignedStack.any.binByFactor | Binning to apply | Int | Y | Y | SD | |
comparam.newst.newstack.TaperAtFill | Extent to taper (1 for default) and 0 or 1 to taper outside or inside | 2 Int | Y | Y | ||
comparam.newst.newstack.AntialiasFilter | Filter to use for antialiased size reduction | Int | Y | Y | SD | |
runtime.AlignedStack.any.sizeInXandY | Unbinned size of output in X and Y | 2 Int | Y | Y | SD | |
runtime.CTFplotting.any.autoFitRangeAndStep | Range and step for autofitting | 2 Float | Y | Y | SO | Must be present for fitting to occur |
comparam.ctfplotter.ctfplotter.InvertTiltAngles | Invert the sign of the tilt angles | Bool | Y | Y | SD | |
comparam.ctfplotter.ctfplotter.FrequencyRangeToFit | Starting and ending frequencies of range to fit | 2 Float | Y | Y | SO | |
comparam.ctfplotter.ctfplotter.ExtraZerosToFit | Extent to fit past 2nd zero as multiple of interzero distance | 2 Float | Y | Y | SO | |
comparam.ctfplotter.ctfplotter.VaryExponentInFit | Vary exponent of CTF function when fitting | Bool | Y | Y | SO | |
comparam.ctfplotter.ctfplotter.BaselineFittingOrder | Order for polynomial fit to flatten baseline | Int | Y | Y | SO | |
comparam.ctfcorrection.ctfphaseflip.InvertTiltAngles | Invert the sign of the tilt angles | Bool | Y | Y | SD | |
comparam.mtffilter.mtffilter.LowPassRadiusSigma | Radius and sigma for 2D filtering | 2 Float | Y | Y | SO | |
runtime.GoldErasing.any.binning | Binning to use in finding gold | Int | Y | Y | SO | BRT default: bead size / 5 rounded to integer |
runtime.GoldErasing.any.extraDiameter | Extra (binned) pixels of diameter to erase | Float | Y | Y | NE | |
runtime.GoldErasing.any.thickness | Unbinned reconstruction thickness | Int | Y | Y | SO | Required if there are not fiducials on two surfaces |
comparam.golderaser.ccderaser.ExpandCircleIterations | Iterations for expanding patches around circles | Int | Y | Y | SD | BRT default 2 |
Reconstruction | ||||||
comparam.tilt.tilt.THICKNESS | Thickness for reconstruction | Int | Y | Y | SO | |
runtime.Reconstruction.any.binnedThickness | Thickness in binned pixels | Int | Y | Y | NE | May not be entered with THICKNESS |
runtime.Reconstruction.any.fallbackThickness | Unbinned thickness if computed distance non-existent or too small | Int | Y | Y | NE | May not be entered with THICKNESS or binnedThickness |
runtime.Reconstruction.any.extraThickness | Added thickness if derived from align.log or positioning | Int | Y | Y | NE | |
comparam.tilt.tilt.RADIAL | Radius and sigma for 1D filter | 2 Float | Y | Y | SO | |
comparam.tilt.tilt.LOG | Different log base or empty for no log | Float | Y | Y | SD | |
comparam.tilt.tilt.SCALE | Scaling values to add and multiply by | 2 Float | Y | Y | SO | |
comparam.tilt.tilt.FakeSIRTiterations | Use SIRT-like radial filter equivalent to given # of SIRT iterations | Int | Y | Y | SO | May not be entered with useSIRT |
runtime.Reconstruction.any.useSirt | Whether to do SIRT | Bool | Y | Y | SO | |
runtime.Reconstruction.any.doBackprojAlso | Whether to do BP in addition to SIRT | Bool | Y | Y | NE | |
SIRT Parameters | ||||||
comparam.sirtsetup.sirtsetup.LeaveIterations | Iterations to leave | List | Y | Y | SD | |
comparam.sirtsetup.sirtsetup.ScaleToInteger | Scaling to integer min/max | 2 Int | Y | Y | SD | Use -20000 20000 |
comparam.sirtsetup.sirtsetup.RadiusAndSigma | Radius and sigma for radial filter | 2 Float | Y | Y | SD | |
Tomogram Combination | ||||||
runtime.Combine.any.matchAtoBThickRatio | Criterion ratio of B to A thickness for matching A to B | Float | Y | Y | NE | Default 0.9; use < 0.2 to match B to A or > 5 for A to B |
runtime.Combine.any.findSecBoxSize | Box size for running Findsection on tomograms | Int | Y | Y | NE | BRT default 32 |
runtime.Combine.any.findSecNumScales | Number of scales to analyze when running Findsection | Int | Y | Y | NE | BRT default 4 |
runtime.Combine.any.patchSize | Starting patch size for patch correlations | String | Y | Y | Use single letter (S M L E); avoid size (default M) | |
runtime.Combine.any.finalPatchSize | Final size for patch correlations | String | Y | Y | Use single letter (S M L E) or size in X-Y-Z (default E) | |
runtime.Combine.any.extraTargets | Extra residual targets for final trial | String | Y | Y | BRT default 0.4 0.45 (with a comma!) | |
runtime.Combine.any.wedgeReduction | Fraction to reduce amplitudes in missing wedge regions | Float | Y | Y | ||
runtime.Combine.any.lowFromBothRadius | Fourier radius below which to take components from both tomograms | Float | Y | Y | ||
runtime.Combine.any.doSIRTifBoth | 1 to combine SIRT reconstructions if BP was done also | Int | Y | Y | NE | |
comparam.solvematch.solvematch.MaximumResidual | Maximum error when fitting to corresponding points | Float | Y | Y | ||
comparam.dualvolmatch.dualvolmatch.MaximumResidual | Error in fit to patch vectors that makes it fall back to preliminary transform | Float | Y | Y | ||
comparam.patchcorr.corrsearch3d.KernelSigma | Sigma for kernel filter in patch correlations | Float | Y | Y | BRT default 1.45 | |
comparam.matchorwarp.matchorwarp.RefineLimit | Mean residual limit for using linear fit and transformation | Float | Y | Y | ||
comparam.matchorwarp.matchorwarp.WarpLimits | Series of mean residual limits for Findwarp try to reach with warping | String | Y | Y | ||
Postprocessing | ||||||
runtime.Postprocess.any.doTrimvol | Run Trimvol on the reconstruction | Bool | Y | Y | NE | runtime.Trimvol directives are ignored if this is 0 |
runtime.Trimvol.any.findSecAddThickness | Fraction or # of pixels to add to Findsection Z extent | Float | Y | Y | NE | For plastic sections only |
runtime.Trimvol.any.reorient | Reorientation in trimvol (0 none; 1 flip; 2 rotate) | Int | Y | Y | NE | BRT default is 2 |
runtime.Trimvol.any.thickness | Fraction or # of slices to trim thickness to | Float | Y | Y | NE | May not be entered with findSecAddThickness |
runtime.Trimvol.any.sizeInX | Fraction or # of pixels to trim to in X | Float | Y | Y | NE | |
runtime.Trimvol.any.sizeInY | Fraction or # of pixels to trim to in Y | Float | Y | Y | NE | |
runtime.Trimvol.any.scaleFromX | Fraction or # of pixels in X to use to set scaling to bytes | Float | Y | Y | NE | BRT default is 0.8 |
runtime.Trimvol.any.scaleFromY | Fraction or # of pixels in Y to use to set scaling to bytes | Float | Y | Y | NE | BRT default is 0.8 |
runtime.Trimvol.any.scaleFromZ | Fraction or # of slices in Z to use to set scaling to bytes | Float | Y | Y | NE | BRT default is 0.33 |
runtime.Trimvol.any.scaleToMeanSD | Mean and standard deviation to scale to for converting to bytes | 2 Float | Y | Y | NE | Scale to given mean/SD instead of using Findcontrast |
runtime.Trimvol.any.doAorBofDualAxis | Trim a/b.rec of dual axis set | Bool | Y | Y | NE | |
runtime.Trimvol.any.doSIRTifBoth | 1 to trim SIRT or 2 to trim both if BP done also | Int | Y | Y | NE | |
runtime.NAD.any.iterations | Number of iterations for running NAD | Int | Y | Y | NE | Both iterations and Kvalue must be entered |
runtime.NAD.any.Kvalue | K value to use when running NAD | Float | Y | Y | NE | |
runtime.NAD.any.chunkMemoryMB | Memory available for each chunk in MB | Int | Y | Y | NE | BRT default 512 |
External Commands | ||||||
runtime.ReplaceStep.any.9 | Command to run in place of Ctfplotter | String | Y | Y | NE | |
runtime.RunAfterStep.any.9 | Command to run after Ctfplotter | String | Y | Y | NE | |
runtime.ReplaceStep.any.13 | Command to run in place of Mtffilter | String | Y | Y | NE | |
runtime.RunAfterStep.any.13 | Command to run after Mtffilter | String | Y | Y | NE |
Notes: