aiBeadTracker finds gold beads in a tilt series and tracks them to individual markers.
It is important for aiBeadTracker to rely on the initial coarse alignments. The more precise image shifts and image rotation are determined before hand, the better are the results of aiBeadTracker. In case that markers in higher tilt angles are not well tracked, check for the image rotation value which should be known +/- 1 degree.
aiBeadTracker 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
AlignBeamDeclination
Align for beam declination.
Argument for command line: -aligBeamDecl or –AlignBeamDeclination
Type: bool
Option is mandatory: false
Default value if not set: true
AlignInPlaneRotation
Align for in plane rotation.
Argument for command line: -aligInPlaneRot or –AlignInPlaneRotation
Type: bool
Option is mandatory: false
Default value if not set: true
AlignFixedInPlaneRotation
Align for a fixed / constant in plane rotation.
Argument for command line: -aligFixedInPlaneRot or –AlignFixedInPlaneRotation
Type: bool
Option is mandatory: false
Default value if not set: false
Only applicable if AlignInPlaneRotation = true.
AlignTilt
Align for tilt angles
Argument for command line: -aligTilt or –AlignTilt
Type: bool
Option is mandatory: false
Default value if not set: true
AlignMagnification
Align for magnification change.
Argument for command line: -aligMag or –AlignMagnification
Type: bool
Option is mandatory: false
Default value if not set: true
FixMagnificationOnFirstTilt
Ensures that the magnification change on the first recorded tilt is 1.
Argument for command line: -fixMagInFirstTilt or –FixMagnificationOnFirstTilt
Type: bool
Option is mandatory: false
Default value if not set: true
Only applicable if AlignMagnification = true.
AlignMaxIterations
Maximum number of optimization iterations to perform.
Argument for command line: -aligIter or –AlignMaxIterations
Type: int
Option is mandatory: false
Default value if not set: 10000
AlignZShift
Z shift to apply during marker alignment.
Argument for command line: -aligZ or –AlignZShift
Type: float
Option is mandatory: false
Default value if not set: 0
FixLowerTiltAngles
Increases the costs for modifying lower tilt angles and avoids changes in these lower tilts.
Argument for command line: -fixTilt or –FixLowerTiltAngles
Type: bool
Option is mandatory: false
Default value if not set: false
LowPassImage
Low pass filter applied to the image for bead detection. Mainly to reduce noise.
Argument for command line: -lp1 or –LowPassImage
Type: float
Option is mandatory: false
Default value if not set: 400
LowPassEdge
Low pass filter applied to the image before edge detection. This value should be quite low.
Argument for command line: -lp2 or –LowPassEdge
Type: float
Option is mandatory: false
Default value if not set: 200
LowPassCCMap
Low pass filter applied to the CC map before peak detection to reduce false positives.
Argument for command line: -lp3 or –LowPassCCMap
Type: float
Option is mandatory: false
Default value if not set: 200
MinBeadSize
The smallest size of gold beads used in the sample in [nm].
Argument for command line: -minBead or –MinBeadSize
Type: float
Option is mandatory: false
Default value if not set: 5
MaxBeadSize
The largest size of gold beads used in the sample in [nm].
Argument for command line: -maxBead or –MaxBeadSize
Type: float
Option is mandatory: false
Default value if not set: 15
BeadIncrement
Speed up factor for scanning all bead sizes in the provided range.
Argument for command line: -beadIncr or –BeadIncrement
Type: int
Option is mandatory: false
Default value if not set: 2
MaxDistance
Theoretically, all gold beads remain on a line perpendicular to the tilt axis while going through all tilts of the tilt series. This parameter determines the maximum distance to that ideal line for a gold bead before being rejected. Note that this highly depends on the accuracy of the initial image rotation angles.
Argument for command line: -maxDist or –MaxDistance
Type: float
Option is mandatory: false
Default value if not set: 200
MaxCost
The maximum cost (summed distance of the reprojected bead) for a bead track during initialization.
Argument for command line: -cost or –MaxCost
Type: float
Option is mandatory: false
Default value if not set: 200
MaxDistanceBead
The maximum distance allowed for tracking on the non initialization tilts.
Argument for command line: -maxDistBead or –MaxDistanceBead
Type: float
Option is mandatory: false
Default value if not set: 200
InitTilts
The tilt indices used for marker initialization.
Argument for command line: -initTilts or –InitTilts
Type: List<int>, a list of integer values
Option is mandatory: false
Default value if not set: []
PreFilterLimit
The maximum reprojection error allowed per bead before alignment.
Argument for command line: -preFilter or –PreFilterLimit
Type: float
Option is mandatory: false
Default value if not set: 20
FilterLimit
The maximum reprojection error allowed per bead after initial alignment.
Argument for command line: -filter or –FilterLimit
Type: float
Option is mandatory: false
Default value if not set: 10
Sensitivity
The sensitivity for peak detection, i.e. how many times a peak must be above the STD of the CCMap in order to be accepted.
Argument for command line: -sens or –Sensitivity
Type: float
Option is mandatory: false
Default value if not set: 5
MinimumTiltCount
The minimum number of tilts a marker must appear or it is removed.
Argument for command line: -minTilts or –MinimumTiltCount
Type: int
Option is mandatory: false
Default value if not set: 5
GoldBeadFile
Save the detected gold beads in a seperate file.
Argument for command line: -beadFile or –GoldBeadFile
Type: string
Option is mandatory: false
Default value if not set: ‘goldbeads’
AlignmentFile
Save the tracked markers in a seperate file. If empty, markers are stored directly inside tilt series metadata.
Argument for command line: -aligFile or –AlignmentFile
Type: string
Option is mandatory: false
Default value if not set: ‘alignment’
AlignMarkers
Run marker alignment and filtering after marker detection.
Argument for command line: -align or –AlignMarkers
Type: bool
Option is mandatory: false
Default value if not set: false