Cryo-tomography tilt-series alignment and tomographic reconstruction with motion compensation

J.J. Fernández (1), S. Li (2), T.A.M. Bharat (3,4), D.A. Agard (2)

(1) Spanish National Research Council (CSIC). Madrid. Spain.
(2) Dept. Biochemistry and Biophysics. UCSF. USA.
(3) MRC Laboratory of Molecular Biology. Cambridge. UK.
(4) University of Oxford. Oxford, UK.

Contact: @


The package TomoAlign contains the programs for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take the beam-induced sample motion into consideration.  Sample motion is modelled by means of either (1) polynomial surfaces or (2) interpolation splines from the residuals from the standard alignment. And the motion model is then integrated in the tomographic reconstruction. 

The package is structured into several programs. First, tomoalign carries out the alignment, which determines the basic parameters of the images (rotation, magnification, tilt) along with the polynomial/spline coefficients that model the motion. Then, the program tomorec calculates the tomogram from the tilt-series and takes into account the motion estimated during the alignment. Auxiliary programs are also provided to analyze, transform or scale the motion parameters.

The package also contains another alternative approach that consists in non-rigid tilt-series alignment. Here, the images of the tilt-series are warped to compensate for the motion. As a result, a pseudo-perfectly aligned tilt-series is produced, thereby enabling the use of standard programs for the subsequent tomographic reconstruction. This strategy, implemented in the program tomowarpalign, is valid only for thin samples.

 A detailed description of the procedures implemented in the package can be found in the following articles:

Primary publications to cite:

Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion
Journal of Structural Biology  202:200-209, 2018. [PDF] [Supplementary Material]

Consideration of sample motion in cryo-tomography based on alignment residual interpolation
Journal of Structural Biology  205:1-6, 2019.  [PDF] [Supplementary Material]

SBGrid Webinar:

Current version: January 2019

Available material:
  • Documentation in PDF:  tomoalign.pdf

  • Binaries for x86-based platforms under Linux
  • Binaries for x86-based platforms under OSX/macOS

The development of TomoAlign has been supported by Fundación Ramon Areces, Spanish Ministry of Science, MRC and NIH.

Copyright by the authors.