[3dem] TomoAlign - cryoET alignment/reconstruction with sample motion

[Jose-Jesus Fernandez]

Dear colleagues,

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  
tomographic reconstruction.

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  
low/mid tilts.

TomoAlign is compatible with IMOD and is available for Linux and for  
OSX. Anyone interested can visit the following link:

    http://www.cnb.csic.es/~jjfernandez/tomoalign

where the software, documentation, and a detailed description of the  
methods and their evaluation are available.

We hope the package may be useful.

Best regards,
    

TomoAlign team
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