aiCTFRefine

After a first round of sub-tomogram averaging, aiCTFRefine refines the CTF parameters for every tilt in a tilt series by projecting each particle on each micrograph. Searching for the CTF parameters only based on the real particle position allows for precise defocus and astigmatism determination.

aiCTFRefine 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 additional particle shifts.
Argument for command line: -o or –ExtraShifts
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

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

DefocusMin

Begin of search range in [nm] for each iteration. The value is added to the initial defocus value.
Argument for command line: -defMin or –DefocusMin
Type: List<float>, a list of floating point values
Option is mandatory: true

DefocusMax

End of search range in [nm] for each iteration. The value is added to the initial defocus value.
Argument for command line: -defMax or –DefocusMax
Type: List<float>, a list of floating point values
Option is mandatory: true

DefocusStep

Search step in [nm] for defocus in each iteration.
Argument for command line: -defStep or –DefocusStep
Type: List<float>, a list of floating point values
Option is mandatory: true

Astigmatism

If true, the astigmatism parameters are included in the search.
Argument for command line: -astig or –Astigmatism
Type: bool
Option is mandatory: false
Default value if not set: false

AstigmatismMin

Begin of search range for astigmatism in [nm] for each iteration. The value is added to the initial value.
Argument for command line: -astigMin or –AstigmatismMin
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

AstigmatismMax

End of search range for astigmatism in [nm] for each iteration. The value is added to the initial value.
Argument for command line: -astigMax or –AstigmatismMax
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

AstigmatismStep

Search step for astigmatism in each iteration.
Argument for command line: -astigStep or –AstigmatismStep
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

AstigmatismAngleMin

Begin of search range for astigmatism angle in [degree] for each iteration. The value is added to the initial value.
Argument for command line: -astigAngMin or –AstigmatismAngleMin
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

AstigmatismAngleMax

End of search range for astigmatism in [degree] for each iteration. The value is added to the initial value.
Argument for command line: -astigAngMax or –AstigmatismAngleMax
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

AstigmatismAngleStep

Search step for astigmatism angle in each iteration.
Argument for command line: -astigAngStep or –AstigmatismAngleStep
Type: List<float>, a list of floating point values
Option is mandatory: true
Only applicable if Astigmatism = true.

FrameMetadata

Frame metadata for a tilt series can be stored inside the tilt series metadata file or in an additional file.
Argument for command line: -meta or –FrameMetadata
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.

DoseLimit

Only tilt with a total dose lower than this limit are refined.
Type: float
Option is mandatory: false
Default value if not set: 0