Tomo_align_tilt_series_v3

!xmipp_tomo_align_tilt_series (v3.0)

Usage

Align a single-axis tilt series without any marker.

See also Tomo_align_dual_tilt_series_v3

Parameters

General Options $``: Input images The selfile must contain the list of micrographs and its tilt angles $--iorig <metadatafile> $`--oroot &lt;fn_out`&gt; $`--thr <num`1> $`--lastStep <step`-1>

Step 0 (Affine alignment) Options $--maxShiftPercentage <p0.2> $--thresholdAffine <th0.85> $: Look globally for affine transformations $: Apply some filters before affine alignment $--maxIterDE <n30> $: Show affine transformations as PPP* $`--identifyOutliers <z`5> $: Do not identify outliers $--pyramid <level1>

Step 1 (Landmark chain) Options $--seqLength <n5> $--localSize <size0.04> $--useCriticalPoints <n0> $--threshold <th-1> $--blindSeqLength <n-1> $--maxStep <step4> $--gridSamples <n40> $``: Set this flag if the tilt series is of a capillar

Step 2 (Determination of alignment parameters) Options $--psiMax <psi-1> $--deltaRot <rot5> $``: Optimize tilt angle

Step 3 (Produce aligned images) Options $``: 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

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