A joint method for marker-free alignment of tilt series in electron tomography
Item Type Article
Authors Han, Renmin;Bao, Zhipeng;Zeng, Xiangrui;Niu, Tongxin;Zhang, Fa;Xu, Min;Gao, Xin
Citation Han, R., Bao, Z., Zeng, X., Niu, T., Zhang, F., Xu, M., & Gao, X.
(2019). A joint method for marker-free alignment of tilt series in electron tomography. Bioinformatics, 35(14), i249–i259.
doi:10.1093/bioinformatics/btz323 Eprint version Post-print
DOI 10.1093/bioinformatics/btz323
Publisher Oxford University Press (OUP)
Journal Bioinformatics
Rights This is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The version of record is available online at: https://
academic.oup.com/bioinformatics/article/35/14/i249/5529170.
Download date 2023-12-24 21:51:40
Link to Item http://hdl.handle.net/10754/656169
A joint method for the marker-free alignment of tilt series in electron tomography
Renmin Han
1, Zhipeng Bao
2, Xiangrui Zeng
3, Tongxin Niu
4, Fa Zhang
5, Min Xu
3,∗, Xin Gao
1,∗1
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal,
23955-6900, Saudi Arabia
2
Department of Electronic Engineering, Tsinghua University, Beijing 100084, China
3
Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
4
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
5
High Performance Computer Research Center, Chinese Academy of Sciences, Beijing 100190, China
All correspondence should be addressed to Min Xu ([email protected]) and Xin Gao ([email protected]).
S1 Experimental results
Figure S1: The reconstructed tomograms of the filament dataset. The presented tomograms are reconstructed by SART with 40 iterations and 0.2 relaxation factor. (A)&(C) The middle and topx−yslices of the tomogram reconstructed from the result of IMOD’s fiducial marker-based alignment. (B)&(D) The middle and topx−yslices of the tomogram reconstructed from the result of our joint method.
Figure S2: The reconstructed tomograms of the mitochondria dataset (they−z slices). The presented tomograms are re- constructed by SART with 40 iterations and 0.2 relaxation factor. (A)&(C)&(E) The top, middle and bottomy−zslices of the tomogram reconstructed from the result of AuTom’s feature-based alignment. (B)&(D)&(F) The top, middle and bottom y−z slices of the tomogram reconstructed from the result of our joint method. By comparing the areas located in the red rectangle, we can find that the ultrastructure (membrane) details are much clearer by our joint method, as well as a clearer sample boundary and fewer artifects.