aiRec

aiRec performs tomographic reconstruction using either SART or WBP.

aiRec needs a configuration file provided by the -u argument. Some options can be overwritten using command line arguments.

Options are:

CudaDeviceIDs

The deviceIDs of the GPUs to use.
Argument for command line: -d or –CudaDeviceIDs
Type: List<int>, a list of integer values
Option is mandatory: true

Input

The file to process.
Argument for command line: -i or –Input
Type: string
Option is mandatory: true

OutVolumeFile

Filename of the output volume.
Argument for command line: -o or –OutVolumeFile
Type: string
Option is mandatory: true

LP

Low pass filter value.
Argument for command line: -lp or –LP
Type: float
Option is mandatory: true

LPS

Low pass filter sigma value.
Argument for command line: -lps or –LPS
Type: float
Option is mandatory: true

HP

High pass filter value.
Argument for command line: -hp or –HP
Type: float
Option is mandatory: false
Default value if not set: 0

HPS

High pass filter sigma value.
Argument for command line: -hps or –HPS
Type: float
Option is mandatory: false
Default value if not set: 0

DeadPixelRemoval

Enables removal of dead pixels based on thresholding. If set to ‘relative’, the threshold is X times the STD + MEAN of the image.
Argument for command line: -deadPixel or –DeadPixelRemoval
Type: one of [ABSOLUTE, NONE, RELATIVE]
Option is mandatory: false
Default value if not set: NONE
Possible notations:

  • ABSOLUTE: ABSOLUTE, Absolute, absolute
  • NONE: NONE, None, none
  • RELATIVE: RELATIVE, Relative, relative

DeadPixelThreshold

Threshold above which a pixel is considered invalid.
Argument for command line: -threshold or –DeadPixelThreshold
Type: float
Option is mandatory: true
Only applicable if

  • DeadPixelRemoval = ABSOLUTE or
  • DeadPixelRemoval = RELATIVE

ReconstructionSettings

The file name for the file with reconstruction settings.
Argument for command line: -rec or –ReconstructionSettings
Type: string
Option is mandatory: true

ReconstructionMethod

The reconstruction method to use: SART or WBP.
Argument for command line: -m or –ReconstructionMethod
Type: one of [SART, WBP]
Option is mandatory: true
Possible notations:

  • SART: SART, Sart, sart
  • WBP: WBP, Wbp, wbp

Lambda

Relaxation factor used for SART back projection, usually = 1.
Type: float
Option is mandatory: false
Default value if not set: 1
Only applicable if ReconstructionMethod = SART.

LongObjectCompensation

The method to use for compensating the long object effect.
Type: one of [COMPENSATED, CONSTANT, MEASURED, MIXTURE]
Option is mandatory: true
Possible notations:

  • COMPENSATED: COMPENSATED, Compensated, compensated
  • CONSTANT: CONSTANT, Constant, constant
  • MEASURED: MEASURED, Measured, measured
  • MIXTURE: MIXTURE, Mixture, mixture

Only applicable if ReconstructionMethod = SART.

LongObjectCompensationRatio

The mixture ratio that combines ‘ratio * COMPENSATED + (1-ratio) * MEASURED’.
Type: float
Option is mandatory: true
Only applicable if LongObjectCompensation = MIXTURE.

DimLength

Dim the image borders over X pixels along the projected volume borders, for volume x and y axis.
Type: float2, two float values
Option is mandatory: false
Default value if not set: (50, 50)

CutLength

Crop the projected image along the projected volume borders, for volume x and y axis.
Type: float2, two float values
Option is mandatory: false
Default value if not set: (10, 10)

Iterations

The number of SART iterations to perform.
Type: int
Option is mandatory: true
Only applicable if ReconstructionMethod = SART.

OverSampling

The amount of over-sampling used for back-projection (relative to binned tilt series).
Type: int
Option is mandatory: true

VolumeBinning

Binning ratio of the reconstruction volume (relative to unbinned tilt series).
Type: float or float3, one or three float values
Option is mandatory: true

DoFourierFilter

Perform fourier space filtering on the tilt series before reconstruction.
Type: bool
Option is mandatory: true

SIRTCount

Size of the ordered subsets for contrast enhancement.
Type: int
Option is mandatory: true
Only applicable if ReconstructionMethod = SART.

CtfCorrectionType

The type of CTF correction to perform.
Type: one of [NONE, PHASE_FLIP, WIENER_FILTER]
Option is mandatory: true
Possible notations:

  • NONE: NONE, None, none, FALSE, false, False, NO, No, no
  • PHASE_FLIP: PHASEFLIP, PhaseFlip, phaseflip, PHASE_FLIP, Phase_Flip, phase_flip
  • WIENER_FILTER: WIENERFILTER, WienerFilter, wienerfilter, WIENER_FILTER, Wiener_Filter, wiener_filter

CTFSliceThickness

The thickness of a CTF slice for 3D-CTF-Correction in nanometer.
Type: float
Option is mandatory: true
Only applicable if

  • CtfCorrectionType = PHASE_FLIP or
  • CtfCorrectionType = WIENER_FILTER

SwitchCTFDirection

Inverses the defocus offset value (experimental, do not use).
Type: bool
Option is mandatory: false
Default value if not set: false
Only applicable if

  • CtfCorrectionType = PHASE_FLIP or
  • CtfCorrectionType = WIENER_FILTER

IgnoreZShiftForCTF

Ignore possible Z-Shift of the reconstruction volume for defocus offset.
Type: bool
Option is mandatory: false
Default value if not set: true
Only applicable if

  • CtfCorrectionType = PHASE_FLIP or
  • CtfCorrectionType = WIENER_FILTER

FP16Volume

Use float16 as internal volume storage format.
Type: bool
Option is mandatory: false
Default value if not set: false

ProjectionScaleFactor

Scale values in case of float16 as internal volume storage format to compensate for accuracy loss.
Type: float
Option is mandatory: true
Only applicable if FP16Volume = true.

ProjectionNormalization

Projection normalization method to use before reconstruction.
Type: one of [MEAN, NONE, STANDARD_DEV]
Option is mandatory: true
Possible notations:

  • MEAN: MEAN, Mean, mean
  • NONE: NONE, none, None
  • STANDARD_DEV: STD, std, StandardDeviation, STANDARD_DEV

WBPFilter

WBP filter to use.
Type: one of [EXACT, NONE, RAMP]
Option is mandatory: true
Possible notations:

  • EXACT: Exact, EXACT, exact
  • NONE: None, NONE, none
  • RAMP: Ramp, RAMP, ramp

Only applicable if ReconstructionMethod = WBP.

DebugImages

Save temporary images to disk for debugging.
Type: bool
Option is mandatory: false
Default value if not set: false

CosineWeighting

Apply cosine weighting to tilted projections.
Type: bool
Option is mandatory: true
Only applicable if ReconstructionMethod = WBP.

DoseWeighting

Apply dose weighting to tilts before reconstruction.
Type: bool
Option is mandatory: false
Default value if not set: false
Only applicable if ReconstructionMethod = WBP.

MissingFrameWeighting

If set to ‘true’ and when frames from a dose fractionation stack were excluded, the projection is downweighted accordingly. If set to ‘false’ no additional weighting occurs.
Type: bool
Option is mandatory: true

LimitToNyquist

Fourier filter the result of forward projection to limit the signal to nyquist limit of the volume.
Type: bool
Option is mandatory: false
Default value if not set: true

ProjectionOrder

The order in which the tilt series is reconstructed.
Type: one of [AS_FILE, AS_RECORDED, INVERSE_AS_RECORDED, RANDOM, RANDOM_ZERO_TILT_FIRST, RANDOM_ZERO_TILT_LAST]
Option is mandatory: true
Possible notations:

  • AS_FILE: AS_FILE, As_File, as_file, ASFILE, AsFile, asfile
  • AS_RECORDED: AS_RECORDED, As_Recorded, as_recorded, ASRECORDED, AsRecorded, asrecorded
  • INVERSE_AS_RECORDED: INVERSE_AS_RECORDED, Inverse_As_Recorded, inverse_as_recorded, INVERSEASRECORDED, InverseAsRecorded, inverseasrecorded
  • RANDOM: RANDOM, Random, random
  • RANDOM_ZERO_TILT_FIRST: RANDOM_ZERO_TILT_FIRST, Random_Zero_Tilt_First, random_zero_tilt_first, RANDOMZEROTILTFIRST, RandomZeroTiltFirst, randomzerotiltfirst
  • RANDOM_ZERO_TILT_LAST: RANDOM_ZERO_TILT_LAST, Random_Zero_Tilt_Last, random_zero_tilt_last, RANDOMZEROTILTLAST, RandomZeroTiltLast, randomzerotiltlast

Only applicable if ReconstructionMethod = SART.

Binning

Bin the tilt series images prior to reconstruction.
Type: float
Option is mandatory: false
Default value if not set: 1

CompensateImageRotation

Rotate the image before applying the WBP filter so that the WBP is not interpolated.
Type: bool
Option is mandatory: false
Default value if not set: false

SampleThickness

Overrides the sample thickness value in the reconstruction settings to allow the reconstruction with improved contrast.
Argument for command line: -thickness or –SampleThickness
Type: int
Option is mandatory: false
Default value if not set: -1

ReduceGoldBeadArtifacts

Reduces artifacts due to the high contrast of gold beads in the tomogram.
Type: bool
Option is mandatory: false
Default value if not set: false

ReduceGoldBeadArtifactStrength

The strength factor for gold bead artifact reduction. The value has to be in range [0..1] and is usually > 0.5.
Type: float
Option is mandatory: true
Only applicable if ReduceGoldBeadArtifacts = true.

GoldBeadSize

The size of the goldbeads used in the tilt series in nm. (With a small additional margin of 1 to 2 nm and if multiple sizes are used, the larger one.)
Type: float
Option is mandatory: true
Only applicable if ReduceGoldBeadArtifacts = true.