ICON : 3D reconstruction with ‘missing-information’ restoration in biological electron tomography
(In collaboration with Prof. Fa Zhang, Institute of Computation Technology, CAS)
Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the ‘missing wedge’ artifacts, thus severely weakens the further biological interpretation. We developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of non-negativity density of biological specimen. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we also provided a practical method to verify the validity of these restored information. We expect a great potential of ICON in the future application of high-resolution structural determination of macromolecules in situ.
Reference:
Deng Y., Chen Y., Zhang Y., Wang S., Zhang F.* and Sun F.* (2016), ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography. Journal of Structural Biology 195(1) : 100-112. doi: 10.1016/j.jsb.2016.04.004.
Chen Y., Wang Z., Zhang J., Li L., Wan X., Sun F.*, and Zhang F.* (2017), Accelerating electron tomography reconstruction algorithm ICON with GPU. Biophysics Reports, 3: 36-42. doi: 10.1007/s41048-017-0041-z
(In this version, the cross-validation procedure is further improved with an automatic determination of the verification resolution. In addition, a program for preprocessing and another program for verification filtering are added.)
(In this version, a thickness-related normalization procedure was added in the preprocessing step. And the default threshold in ICON reconstruction has been set as 0.3, which is defined for cryo-electron tomography. In addition, some bugs were fixed in the verification filtering procedure, especially when dealing with large size (e.g. 2048*2048*2048) of tomogram.)
(In this version, a dose dependent filtering procedure was added in the preprocessing step. In addition, some bugs were fixed in the previous verification filtering procedure ICONMask1. More importantly, a new verification filtering program ICONMask2 was added in the package to perform better verification filtering and reduce the needs of large memory.)
The dataset (ICON_testdata.tar.gz) for learning and testing ICON can be downloaded in the appendix.
附件下载：
Workshops
Workshops
International Workshop of 3D Molecular Imaging by Cryo-Electron Microscopy, Third K. H. Kuo Summer School of Electron Microscopy and Crystallography in 2010.
International Workshop of Advanced Image Processing of Cryo-Electron Microscopy, 2013
Get acquainted with Cryo-Electron Microscopy: First Chinese Workshop for Structural Biologists, 2015
International Workshop of Advanced Image Processing of Cryo-Electron Microscopy, 2015
Instutions
Instutions
Institute of Biophysics, Chinese Academy of Sciences
The Scripps Research Institute
Max Planck Institute of Biochemistry
Database
Database
National Center for Biotechnology Information(NCBI)
Protein Data Bank
The Electron Microscopy Data Bank
ExPASy Proteomics Server
Pfam
3D EM
3DEM
Tools and Softwars
Tools and Softwars
CCP4
CCP-EM
MOLE 2.0 (characterization of channels and pores in protein complex)
