Xmipp

xmipp_tomo_align_tilt_series (v3.0)

Usage

Align a single-axis tilt series without any marker.

See also
tomo_align_dual_tilt_series

Parameters

General Options

-i <metadatafile>
Input images The selfile must contain the list of micrographs and its tilt angles
--iorig <metadatafile=>
Metadata with images at original scale
--oroot <fn_out=>
Output alignment If not given, the input selfile without extension
--thr <num=1>
Parallel processing using "num" threads
--lastStep <step=-1>
Last step to perform Step -1 -> Perform all steps Step 0 -> Determination of affine transformations Step 1 -> Determination of landmark chains Step 2 -> Determination of alignment parameters Step 3 -> Writing aligned images

Step 0 (Affine alignment) Options

--maxShiftPercentage <p=0.2>
Maximum shift as percentage of image size
--thresholdAffine <th=0.85>
Threshold affine
--globalAffine
Look globally for affine transformations
--difficult
Apply some filters before affine alignment
--maxIterDE <n=30>
Maximum number of iteration in Differential Evolution
--showAffine
Show affine transformations as PPP*
--identifyOutliers <z=5>
Z-score to be an outlier
--noOutliers
Do not identify outliers
--pyramid <level=1>
Multiresolution for affine transformations

Step 1 (Landmark chain) Options

--seqLength <n=5>
Sequence length
--localSize <size=0.04>
In percentage
--useCriticalPoints <n=0>
Use critical points instead of a grid n is the number of critical points to choose in each image
--threshold <th=-1>
Correlation threshold
--blindSeqLength <n=-1>
Blind sequence length, -1=No blind landmarks
--maxStep <step=4>
Maximum step for chain refinement
--gridSamples <n=40>
Total number of samples=n*n
--isCapillar
Set this flag if the tilt series is of a capillar

Step 2 (Determination of alignment parameters) Options

--psiMax <psi=-1>
Maximum psi in absolute value (degrees) -1 -> do not optimize for psi
--deltaRot <rot=5>
In degrees. For the first optimization stage
--optimizeTiltAngle
Optimize tilt angle

Step 3 (Produce aligned images) Options

--dontNormalize
Don't normalize the output images

Examples and notes

Typical run
xmipp_tomo_align_tilt_series -i tiltseries.sel --thr 8
If there are image with large shifts
xmipp_tomo_align_tilt_series -i tiltseries.sel --thr 8 --globalAffine
If there are clear landmarks that can be tracked
xmipp_tomo_align_tilt_series -i tiltseries.sel --thr 8 --criticalPoints

User's comments

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