AuTom: A novel automatic platform for electron tomography reconstruction.

We have developed a software package towards automatic electron tomography (ET): Automatic Tomography (AuTom). The presented package has the following characteristics: accurate alignment modules for marker-free datasets containing substantial biological structures; fully automatic alignment modules for datasets with fiducial markers; wide coverage of reconstruction methods including a new iterative method based on the compressed-sensing theory that suppresses the "missing wedge" effect; and multi-platform acceleration solutions that support faster iterative algebraic reconstruction. AuTom aims to achieve fully automatic alignment and reconstruction for electron tomography and has already been successful for a variety of datasets. AuTom also offers user-friendly interface and auxiliary designs for file management and workflow management, in which fiducial marker-based datasets and marker-free datasets are addressed with totally different subprocesses. With all of these features, AuTom can serve as a convenient and effective tool for processing in electron tomography.

[1]  J M Carazo,et al.  The effect of overabundant projection directions on 3D reconstruction algorithms. , 2001, Journal of structural biology.

[2]  Friedrich Förster,et al.  TOM software toolbox: acquisition and analysis for electron tomography. , 2005, Journal of structural biology.

[3]  M. van Heel,et al.  Fourier shell correlation threshold criteria. , 2005, Journal of structural biology.

[4]  Giovanni Cardone,et al.  A resolution criterion for electron tomography based on cross-validation. , 2005, Journal of structural biology.

[5]  Marek Malac,et al.  Practical electron tomography guide: Recent progress and future opportunities. , 2016, Micron.

[6]  Mark H Ellisman,et al.  Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. , 2006, Journal of structural biology.

[7]  Christopher Irving,et al.  Appion: an integrated, database-driven pipeline to facilitate EM image processing. , 2009, Journal of structural biology.

[8]  Jose-Jesus Fernandez,et al.  Computational methods for electron tomography. , 2012, Micron.

[9]  J M Carazo,et al.  3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). , 1998, Ultramicroscopy.

[10]  Albert F. Lawrence,et al.  Non-linear Bundle Adjustment for Electron Tomography , 2009, 2009 WRI World Congress on Computer Science and Information Engineering.

[11]  Yu Chen,et al.  A Fully Automatic Geometric Parameters Determining Method for Electron Tomography , 2017, ISBRA.

[12]  David N. Mastronarde,et al.  Automated tilt series alignment and tomographic reconstruction in IMOD. , 2017, Journal of structural biology.

[13]  Yu Chen,et al.  Accelerating Electron Tomography Reconstruction Algorithm ICON Using the Intel Xeon Phi Coprocessor on Tianhe-2 Supercomputer , 2017, ISBRA.

[14]  Mark Horowitz,et al.  Alignment of cryo-electron tomography datasets. , 2010, Methods in enzymology.

[15]  David N. Mastronarde,et al.  Fiducial Marker and Hybrid Alignment Methods for Single- and Double-axis Tomography , 2007 .

[16]  M. Fukushima,et al.  Levenberg–Marquardt methods with strong local convergence properties for solving nonlinear equations with convex constraints , 2004 .

[17]  K. Taylor,et al.  Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. , 2006, Ultramicroscopy.

[18]  Kai Zhang,et al.  FIRT: Filtered iterative reconstruction technique with information restoration. , 2016, Journal of structural biology.

[19]  J R Kremer,et al.  Computer visualization of three-dimensional image data using IMOD. , 1996, Journal of structural biology.

[20]  J Frank,et al.  A marker-free alignment method for electron tomography. , 1995, Ultramicroscopy.

[21]  J Heikkonen,et al.  Automatic alignment of transmission electron microscope tilt series without fiducial markers. , 2001, Journal of structural biology.

[22]  Hanspeter Winkler,et al.  Marker-free dual-axis tilt series alignment. , 2013, Journal of structural biology.

[23]  D. J. De Rosier,et al.  Reconstruction of Three Dimensional Structures from Electron Micrographs , 1968, Nature.

[24]  W Wan,et al.  Cryo-Electron Tomography and Subtomogram Averaging. , 2016, Methods in enzymology.

[25]  R. Guckenberger.  Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy , 1982 .

[26]  P. Gilbert.  Iterative methods for the three-dimensional reconstruction of an object from projections. , 1972, Journal of theoretical biology.

[27]  J Bernard Heymann,et al.  Bsoft: image processing and molecular modeling for electron microscopy. , 2007, Journal of structural biology.

[28]  Achilleas S Frangakis,et al.  Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series. , 2010, Journal of structural biology.

[29]  José María Carazo,et al.  Marker-free image registration of electron tomography tilt-series , 2009, BMC Bioinformatics.

[30]  Fa Zhang,et al.  ICON: 3D reconstruction with 'missing-information' restoration in biological electron tomography. , 2016, Journal of structural biology.

[31]  Jun Liu,et al.  Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography. , 2016, Journal of visualized experiments : JoVE.

[32]  G. Herman,et al.  Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and x-ray photography. , 1970, Journal of theoretical biology.

[33]  Renmin Han,et al.  A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. , 2015, Journal of structural biology.

[34]  S. Stagg,et al.  Automated batch fiducial-less tilt-series alignment in Appion using Protomo. , 2015, Journal of structural biology.

[35]  Michael C. Lawrence,et al.  Least-Squares Method of Alignment Using Markers , 1992 .

[36]  N. Grigorieff,et al.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs , 2015, bioRxiv.

[37]  Renmin Han,et al.  A marker-free automatic alignment method based on scale-invariant features. , 2014, Journal of structural biology.

[38]  S S Brandt,et al.  Automatic TEM image alignment by trifocal geometry , 2006, Journal of microscopy.

[39]  A. Kak,et al.  Simultaneous Algebraic Reconstruction Technique (SART): A Superior Implementation of the Art Algorithm , 1984, Ultrasonic imaging.

[40]  John W Sedat,et al.  UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. , 2007, Journal of structural biology.

[41]  D. Mastronarde.  Dual-axis tomography: an approach with alignment methods that preserve resolution. , 1997, Journal of structural biology.

[42]  J. Frank.  Electron tomography : methods for three-dimensional visualization of structures in the cell , 2005 .

[43]  C. Kanzow.  Levenberg-Marquardt methods for constrained nonlinear equations with strong local convergence properties , 2004 .

[44]  Gabor T. Herman,et al.  Algorithms for Three-dimensional Reconstruction From the Imperfect Projection Data Provided by Electron Microscopy , 2007 .

[45]  Yair Censor,et al.  Component averaging: An efficient iterative parallel algorithm for large and sparse unstructured problems , 2001, Parallel Comput..

[46]  Achilleas S Frangakis,et al.  Implementation and performance evaluation of reconstruction algorithms on graphics processors. , 2007, Journal of structural biology.

[47]  Inmaculada García,et al.  High-performance electron tomography of complex biological specimens. , 2002, Journal of structural biology.

[48]  Anja Seybert,et al.  Fiducial-less alignment of cryo-sections. , 2007, Journal of structural biology.