[3dem] TomoAlign - cryoET alignment/reconstruction with sample motion
JJ.Fernandez at csic.es
Mon Feb 18 07:35:20 PST 2019
We have developed TomoAlign, a software package that implements
several approaches to deal with the sample motion in cryoET
tilt-series alignment and tomographic reconstruction.
The general strategy consists of two steps. First, the sample motion
is modelled during fiducial-based tilt-series alignment. Second, the
resulting model is used to compensate for the motion during
TomoAlign includes the following approaches:
1. THE SAMPLE MOTION IS MODELLED WITH POLYNOMIALS.
The polynomials are determined by an optimization process aiming to
minimize the alignment residual.
2. THE SAMPLE MOTION IS MODELLED WITH INTERPOLATING SPLINES.
The residuals from the standard alignment (i.e. with no motion) are
interpreted as local estimates of the motion at the sparse 3D fiducial
positions. A continuous sample motion model is then obtained by
scattered data interpolation.
3. NON-RIGID TILT-SERIES ALIGNMENT.
Here, the sample motion model is also obtained by residual
interpolation, as above. And motion correction is applied directly at
the image level by warping the images of the tilt-series. As a result,
the standard cryoET workflow can follow (e.g. IMOD, tomo3d). This
strategy is valid only for thin samples, and even restricted to the
TomoAlign is compatible with IMOD and is available for Linux and for
OSX. Anyone interested can visit the following link:
where the software, documentation, and a detailed description of the
methods and their evaluation are available.
We hope the package may be useful.
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