The Laboratory of biological electron microscopy and structural biology

(dr. fei sun’s lab)

 
 

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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


The program of ICON can be obtained here.


Version 1.0

ICON_v1.0_CentOS64.tar.gz (CentOS x64_86 system)

ICON_v1.0_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.5

(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.)

ICON_v1.5_CentOS64.tar.gz (CentOS x64_86 system)

ICON_v1.5_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.6.1

(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.)

ICON_v1.6.1_CentOS64.tar.gz (CentOS x64_86 system)

ICON_v1.6.1_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.7.2

(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.)

ICON_v1.7.2_CentOS64.tar.gz (CentOS x64_86 system)

ICON_v1.7.2_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


GPU accelerated ICON (ICON-GPU)

Version 1.0

ICON-GPU_v1.0_CentOS64.tar.gz (CentOS x64_86 system)

ICON-GPU_v1.0_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.2.5

ICON-GPU_v1.2.5_CentOS64.tar.gz (CentOS x64_86 system)

ICON-GPU_v1.2.5_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.2.6

ICON-GPU_v1.2.6_CentOS64.tar.gz (CentOS x64_86 system)

ICON-GPU_v1.2.6_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.2.7

(In this version, ICONMask2 is accelerated with one bug fixed.)

ICON-GPU_v1.2.7_CentOS64.tar.gz (CentOS x64_86 system)

ICON-GPU_v1.2.7_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Version 1.2.9

(In this version, a new ICONMask3 is provided to perform accurate weighting and masking, which can prevent the blurring artifacts in ICONMask2.)

ICON-GPU_v1.2.9_CentOS64.tar.gz (CentOS x64_86 system)

ICON-GPU_v1.2.9_Ubuntu64.tar.gz (Ubuntu x64_86 system)

The user guide of ICON could be found here.


Test dataset

The dataset for learning and testing ICON can be downloaded below:

ICON_testdata.tar.gz