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dc.contributor.authorHan, Renmin
dc.contributor.authorLi, Guojun
dc.contributor.authorGao, Xin
dc.date.accessioned2021-02-03T08:20:06Z
dc.date.available2021-02-03T08:20:06Z
dc.date.issued2021-01-08
dc.date.submitted2020-07-02
dc.identifier.citationHan, R., Li, G., & Gao, X. (2021). Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints. Bioinformatics. doi:10.1093/bioinformatics/btaa1098
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.pmid33416867
dc.identifier.doi10.1093/bioinformatics/btaa1098
dc.identifier.urihttp://hdl.handle.net/10754/667204
dc.description.abstractAbstract Motivation Electron tomography (ET) has become an indispensable tool for structural biology studies. In ET, the tilt series alignment and the projection parameter calibration are the key steps towards high-resolution ultrastructure analysis. Usually, fiducial markers are embedded in the sample to aid the alignment. Despite the advances in developing algorithms to find correspondence of fiducial markers from different tilted micrographs, the error rate of the existing methods is still high such that manual correction has to be conducted. In addition, existing algorithms do not work well when the number of fiducial markers is high. Results In this paper, we try to completely solve the fiducial marker correspondence problem. We propose to divide the workflow of fiducial marker correspondence into two stages: (i) initial transformation determination, and (ii) local correspondence refinement. In the first stage, we model the transform estimation as a correspondence pair inquiry and verification problem. The local geometric constraints and invariant features are used to reduce the complexity of the problem. In the second stage, we encode the geometric distribution of the fiducial markers by a weighted Gaussian mixture model and introduce drift parameters to correct the effects of beam-induced motion and sample deformation. Comprehensive experiments on real-world datasets demonstrate the robustness, efficiency and effectiveness of the proposed algorithm. Especially, the proposed two-stage algorithm is able to produce an accurate tracking within an average of ≤ ms per image, even for micrographs with hundreds of fiducial markers, which makes the real-time ET data processing possible. Availability The code is available at https://github.com/icthrm/auto-tilt-pair . Additionally, the detailed original figures demonstrated in the experiments can be accessed at https://rb.gy/6adtk4.
dc.description.sponsorshipThis work was supported by the National Key Research and Development Program of China [2020YFA0712400], the National Natural Science Foundation of China [62072280, 11931008, 61771009], the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No. FCC/1/1976-17, FCC/1/1976-23, FCC/1/1976-26, URF/1/4098-01-01, URF/1/4352-01-01, URF/1/4379-01-01, REI/1/0018-01-01 and REI/1/4473-01-01.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa1098/6069572
dc.rightsThis 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/advance-article/doi/10.1093/bioinformatics/btaa1098/6069572.
dc.titleRobust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalBioinformatics
dc.rights.embargodate2022-01-08
dc.eprint.versionPost-print
dc.contributor.institutionResearch Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, PR China
kaust.personHan, Renmin
kaust.personGao, Xin
kaust.grant.numberFCC/1/1976-17
kaust.grant.numberFCC/1/1976-23
kaust.grant.numberFCC/1/1976-26
kaust.grant.numberREI/1/0018-01-01
dc.date.accepted2020-12-28
dc.relation.issupplementedbygithub:icthrm/auto-tilt-pair
refterms.dateFOA2021-02-03T08:39:03Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Software]</i> <br/> Title: icthrm/auto-tilt-pair:. Publication Date: 2020-01-18. github: <a href="https://github.com/icthrm/auto-tilt-pair" >icthrm/auto-tilt-pair</a> Handle: <a href="http://hdl.handle.net/10754/668077" >10754/668077</a></a></li></ul>
kaust.acknowledged.supportUnitOffice of Sponsored Research (OSR)


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