aiRecSubvol performs tomographic reconstruction of individual particles using WBP (or without any weighting at all). aiRecSubvol can also directly compute the average of the indiviual particles.
aiRecSubvol 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
The file base name of the reconstructed volumes.
Argument for command line: -o or –OutVolumeFile
Type: string
Option is mandatory: true
OutWedgeFile
The file base name for the summed wedges corresponding to the reconstructed volumes.
Type: string
Option is mandatory: true
Only applicable if
- WBPFilter = NONE and
- SubVolumeRecMode = REFERENCE
ReconstructionSettings
The file name for the file with reconstruction settings.
Argument for command line: -rec or –ReconstructionSettings
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
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)
OverSampling
The amount of over-sampling used for back-projection (relative to binned tilt series).
Type: int
Option is mandatory: true
RecDimensions
Size of the reconstructed sub-volume in unbinned voxels.
Type: int3, three integer values
Option is mandatory: true
VolumeBinning
Binning ratio of the reconstruction volume (relative to unbinned tilt series).
Type: float
Option is mandatory: true
DoFourierFilter
Perform fourier space filtering on the tilt series before reconstruction.
Type: bool
Option is mandatory: true
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
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
DoseWeighting
Apply dose weighting to tilts before reconstruction.
Type: bool
Option is mandatory: false
Default value if not set: false
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
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
SubVolumeRecMode
Define if sub-volumes are reconstructed individually or directly accumulated per reference.
Type: one of [PARTICLE, REFERENCE]
Option is mandatory: true
Possible notations:
- PARTICLE: Particle, PARTICLE, particle
- REFERENCE: Reference, REFERENCE, reference
BatchSize
The number of particles reconstructed in parallel (per GPU).
Type: int
Option is mandatory: true
Only applicable if SubVolumeRecMode = PARTICLE.
MotiveList
The motive list with alignment information for each particle.
Type: string
Option is mandatory: true
ExtraShifts
Additional projection shift information for each particle (from shift refinement).
Type: string
Option is mandatory: false
Default value if not set: ’’
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.