aiShiftRefine determines an indivual shift for each particle and each projection in a tilt series to compensate for alignment inaccuracies.
aiShiftRefine 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
ExtraShifts
The file name for the detected shifts.
Argument for command line: -o or –ExtraShifts
Type: string
Option is mandatory: true
ExtraShiftsIn
A shift file with shifts that are to be used as start values.
Type: string
Option is mandatory: true
LP
Low pass filter value.
Argument for command line: -lp or –LP
Type: List<float>, a list of floating point values
Option is mandatory: true
LPS
Low pass filter sigma value.
Argument for command line: -lps or –LPS
Type: List<float>, a list of floating point values
Option is mandatory: true
HP
High pass filter value.
Argument for command line: -hp or –HP
Type: List<float>, a list of floating point values
Option is mandatory: false
Default value if not set: []
HPS
High pass filter sigma value.
Argument for command line: -hps or –HPS
Type: List<float>, a list of floating point values
Option is mandatory: false
Default value if not set: []
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
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
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
DebugImages
Save temporary images to disk for debugging.
Type: bool
Option is mandatory: false
Default value if not set: false
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
MotiveList
The motive list with alignment information for each particle.
Type: string
Option is mandatory: true
References
Reference filename. Naming convention: filename_RefNr_IterationNr.em/mrc.
Type: string
Option is mandatory: true
Masks
Mask filename. Naming convention: filename_MaskNr.em/mrc.
Type: string
Option is mandatory: true
GroupMode
Grouping method for particle projection.
Type: one of [BY_GROUP, MAX_COUNT, MAX_DISTANCE]
Option is mandatory: true
Possible notations:
- BY_GROUP: ByGroup, BY_GROUP, by_group
- MAX_COUNT: MaxCount, MAX_COUNT, max_count
- MAX_DISTANCE: MaxDistance, MAX_DISTANCE, max_distance
MaxShift
Maximum shift allowed.
Type: int
Option is mandatory: true
MaxDist
Maximum distance inbetween particles to form a group.
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if GroupMode = MAX_DISTANCE.
GroupSize
Number of particles to form a group.
Type: List<int>, a list of integer values
Option is mandatory: true
Only applicable if GroupMode = MAX_COUNT.
SpeedupDistance
Assign the same shift to particles in a radius (in unbinned pixels) of this distance instead of computing it individually.
Type: float
Option is mandatory: false
Default value if not set: 0
ProjectionMode
Compare the projected reference with the original micrograph or with the particles.
Type: one of [ORIGINAL, PARTICLE]
Option is mandatory: true
Possible notations:
- ORIGINAL: Original, ORIGINAL, original
- PARTICLE: Particle, PARTICLE, particle
Particles
Filename for the reconstructed particles.
Type: string
Option is mandatory: true
Only applicable if ProjectionMode = PARTICLE.
AveragingMode
Defines how to average the group particles: as an entire image or by averaging the CC image.
Type: one of [CC, IMAGE]
Option is mandatory: true
Possible notations:
- CC: Cc, CC, cc
- IMAGE: Image, IMAGE, image
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.