xmipp_image_align_tilt_pairs (v3.0)


Center the tilted images of all tilted-untilted image pairs. This program receives as input a metadata with attwo sets of images, untilted and tilted. In the first one, a metadata is required with values for: angleRot,the angle between y-axis and tilt axis taken from micrographs. Also the in-plane translations (shiftX and shiftY) and rotation(anglePsi) are expected from a previous alignment step. In the tilted metadata should be provided the angle between y-axis and tilt axis, anglePsi and the tilt angle taken from the experiment. As output, the first euler angle angleRot of tilted images is set with anglePsi of untilted ones. The in-plane translations shiftX and shiftY of tilted images are calculated using cross-correlation yielding also the cross-correlation coeficient maxCC
  • If the particles under study are disc-shaped and lying flat on the micrograph (i.e. the have a relatively low height (Z) and are more-or-less spherically shaped in XY), this program is expected to give good results using the default options.
  • If the particles have a different shape, the centering may be poor, since especially in the X direction the shift becomes poorly defined. In these cases, three alternative options may be tried: --skip_stretching will skip the cosine-stretching prior to centering. --force_x_zero will force the shift in the X direction to be zero, and will only center the images in the Y direction --skip_centering will skip the entire centering, so that only the Psi angle of the tilted images will be modified.


-u <metadata>
Input metadata with untilted images
-t <metadata>
Input metadata with tilted images. Both metadatas should have same number of entries, and the same order is assumed for image pairs).
-o, --odoc <metadata>
Output metadata file with rotations & translations.
--max_shift <value=0.0>
Discard images which shift more (in pixels).
Force x-shift to be zero.
Default action is to stretch the tilted images in X direction by 1/cos(tilt_angle), before centering them. Use this option to skip it.
Default action is to center tilted images based on cross-correlation with the untilted pairs. Use this option to skip it.

Examples and notes

To center tilted images g0t.sel allowing a maximum shift of 10 pixels:
xmipp_align_tilt_pairs -u g0u.sel -t g0t.sel -o g0t_aligned.doc --max_shift 10

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