aiImageStackAlignator aligns either a single movie stack to a single image or a set of movie stacks to a tilt series. For latter, input is either a text file listing all needed parameters or a MDOC file.
For tilt series, aiImageStackAlignator also performs the initial data import to the Artiatomi package setting microscope dependent parameters. Theses values are either provided in a microscope specific configuration in ‘artiatomi.settings’ (ARTIATOMI_PATH env. variable must be set), in a microscope settings file or in case of a text file, which lists all input images with associated parameters.
aiImageStackAlignator can be used without a configuration file and all parameters can be provided by command line arguments. For convenience, parameters can also be given using a configuration file with the -u command line argument. Note: If a parameter is passed by file and by command line, the command line overrides the file.
Options are:
CudaDeviceID
The deviceID of the GPU to use.
Argument for command line: -d or –CudaDeviceID
Type: int
Option is mandatory: false
Default value if not set: 0
Input
The file to process.
Argument for command line: -i or –Input
Type: string
Option is mandatory: true
Interpolation
Interpolation method to use.
Argument for command line: -interp or –Interpolation
Type: one of [CUBIC, LINEAR, NN]
Option is mandatory: false
Default value if not set: NN
Possible notations:
- CUBIC: CUBIC, cubic, Cubic
- LINEAR: LINEAR, linear, Linear
- NN: NN, nn, NearestNeighbor
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
MicroscopeID
Numeric identifier for the microscope used.
Argument for command line: -scopeID or –MicroscopeID
Type: int
Option is mandatory: false
Default value if not set: -1
MicroscopeName
Name identifier for the microscope used.
Argument for command line: -scopeName or –MicroscopeName
Type: string
Option is mandatory: false
Default value if not set: ’’
MicroscopeSettings
Use this additional settings file for this dataset.
Argument for command line: -settings or –MicroscopeSettings
Type: string
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
Output
The file to write the result to. If not provided the input file is appended by ‘Alig’
Argument for command line: -o or –Output
Type: string
Option is mandatory: false
Default value if not set: ’’
MaxShift
Maximum allowed shift.
Argument for command line: -m or –MaxShift
Type: int
Option is mandatory: false
Default value if not set: 0
AlignmentMethod
Either full alignment or blockwise alignment. When using global alignment, the number of correlations to compute can be reduced by only filling blocks of the CC-matrix.
Argument for command line: -method or –AlignmentMethod
Type: one of [BLOCK, FULL]
Option is mandatory: false
Default value if not set: FULL
Possible notations:
- BLOCK: BLOCK, block, Block
- FULL: FULL, full, Full
BlockSize
The block size to use for blocked alignment (only for global alignment).
Argument for command line: -bs or –BlockSize
Type: int
Option is mandatory: true
Only applicable if AlignmentMethod = BLOCK.
OutputDataType
The datatype of the aligned image.
Argument for command line: -dt or –OutputDataType
Type: one of [FLOAT, SHORT, UCHAR, USHORT]
Option is mandatory: false
Default value if not set: USHORT
Possible notations:
- FLOAT: FLOAT, float, Float
- SHORT: SHORT, short, Short
- UCHAR: UCHAR, uchar, Uchar, UChar
- USHORT: USHORT, ushort, Ushort, UShort
Algorithm
The algorithm to use: Global alignment (as in doi:10.1038/nmeth.2472), Refine (One-To-All approach), both, or skip alignment summing up with previously determined shifts.
Argument for command line: -algo or –Algorithm
Type: one of [BOTH, GLOBAL, REFINE, SKIP]
Option is mandatory: false
Default value if not set: BOTH
Possible notations:
- BOTH: BOTH, both, Both
- GLOBAL: GLOBAL, global, Global
- REFINE: REFINE, refine, Refine
- SKIP: SKIP, skip, Skip
CorrectMissingStripes
It can happen that K2 images have stripes with missing data. Enable this option if the dataset contains such stripes.
Argument for command line: -stripes or –CorrectMissingStripes
Type: bool
Option is mandatory: false
Default value if not set: false
SubpixelPrecision
Amount of sub-pixel precision: 2 is half pixel, 4 is a quarter pixel, etc. <= 1 to disable.
Argument for command line: -subpix or –SubpixelPrecision
Type: int
Option is mandatory: false
Default value if not set: 0
OutputScaling
Factor to apply to the output image before potential conversion to integer.
Argument for command line: -scaling or –OutputScaling
Type: float
Option is mandatory: false
Default value if not set: 1
OutputOffset
Offset to add to the output image before potential conversion to integer.
Argument for command line: -offset or –OutputOffset
Type: float
Option is mandatory: false
Default value if not set: 0
RefineThreshold
Maximal shift allowed for refined alignment.
Argument for command line: -rt or –RefineThreshold
Type: float
Option is mandatory: true
Only applicable if
- Algorithm = BOTH or
- Algorithm = REFINE
DeadPixelMap
An image indicating defective pixels (same size as movie frames).
Argument for command line: -deadPixelMap or –DeadPixelMap
Type: string
Option is mandatory: false
Default value if not set: ’’
GainReference
An image for gain reference (same size as movie frames).
Argument for command line: -gainRef or –GainReference
Type: string
Option is mandatory: false
Default value if not set: ’’
Skip
Skip the X first frames of a stack (they still get aligned, but not stacked in the final step).
Argument for command line: -skip or –Skip
Type: int
Option is mandatory: false
Default value if not set: 0
SkipShift
Skip frames with an incremental shift larger than the given limit (in pixels). The frames still get aligned, but not stacked in the final step.
Argument for command line: -skipShift or –SkipShift
Type: float
Option is mandatory: false
Default value if not set: 0
DosePerTilt
The exposed dose of each tilt. Value to be written in the metadata file for tilt series.
Argument for command line: -dose or –DosePerTilt
Type: float
Option is mandatory: false
Default value if not set: 0
AdditionalDoseFirstTilt
Additional dose for the first tilt due to extra measurements or longer exposure. Value to be written in the metadata file for tilt series.
Argument for command line: -extradose or –AdditionalDoseFirstTilt
Type: float
Option is mandatory: false
Default value if not set: 0
FrameMetadata
Frame metadata for a tilt series can be stored inside the tilt series metadata file or in an additional file. Only used if output is a tilt series.
Argument for command line: -meta or –FrameMetadata
Type: string
Option is mandatory: false
Default value if not set: ’’
TomogramNumber
The number of this tilt series / tomogram in a dataset.
Argument for command line: -tomo or –TomogramNumber
Type: int
Option is mandatory: false
Default value if not set: -1