The Laboratory of biological electron microscopy and structural biology

(dr. fei sun’s lab)

 
 

HOME     RESEARCH     PUBLICATIONS     MEMBERS     ALBUM     SOFTWARE     CONTACT     LINKS

1. ATOM 1.0: A GPU Powered Package for Electron Tomography Reconstruction.

Algebra tomography reconstruction package

Electron tomography (ET) has been developed rapidly and applied widely in the recent years, as it provides the prospects of reconstructing non-uniform cells or macromolecules in nano scale. To overcome the deficits of current ET reconstruction software packages, especially the large computations of ET iterative reconstruction algorithms, we have developed a Graphic Processor Unit (GPU) powered software, ATOM. Its main functions include: 2D alignment, reconstruction parameters estimation, 3D reconstruction, and 2D image visualization etc. In 2D alignment part, iterative fiducialess shift and rotation alignment methods are applied. In 3D reconstruction part, it supports Back Projection (BP), several iterative reconstruction methods, and their parallel versions on GPU platform. The speedups of parallel iterative reconstruction methods are appealing, e.g. parallel Simultaneous Iterative Reconstruction Techniques (SIRT) can achieve 47 times speedup in contrast to serial SIRT. ATOM is an open source software and can run on any platform that supports Qt and CUDA libraries. It has a friendly graphic user interface along with detailed manuals.

Reference:

Chu Q., Zhang K., Wan X., Zhang C., Zhang Y., Zhang G., Shen B., Lu X., Zhao K.,Chu X., Zhang F.*, Sun F.* (2011), ATOM1.0 : A GPU Powered Package for Electron Tomography Reconstruction. ACTA BIOPHYSICA SINICA, 27(3):231-241.

(In collaboration with Institute of Computation Technology, CAS, Center for Supercomputing, CAS and Inspur company)

2. AuTom (ATOM 2.0): An automatic platform for electron tomography reconstruction. See AuTom.