ArticleBioinformatics (Oxford, England)2019
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.Bioinformatics (Oxford, England) · 2026Article
- Genetically encoded barcodes for correlative volume electron microscopy.Nature biotechnology · 2023Article
- HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing.Genome biology · 2023Article
- Computational methods forFrontiers in cellular and infection microbiology · 2023Review
- On the application, reporting, and sharing of in silico simulations for genetic studies.Genetic epidemiology · 2021Review
- DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM.BMC bioinformatics · 2020Article
- Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization.BMC bioinformatics · 2019Article
- A joint method for marker-free alignment of tilt series in electron tomography.Bioinformatics (Oxford, England) · 2019Article
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11 authors.
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Abstract
Motivation: Dual-axis electron tomography is an important 3 D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically; (ii) how to integrate the information from the two different tilt series; and (iii) how to cope with the inconsistency between the two different tilt series. Results: Here we develop a toolkit for fully automatic alignment of dual-axis electron tomography, with a simultaneous reconstruction procedure. The proposed toolkit and its workflow carries out the following solutions: (i) fully automatic detection and tracking of fiducial markers under large-field datasets; (ii) automatic combination of two different tilt series and global calibration of projection parameters; and (iii) inconsistency correction based on distortion correction parameters and the consequently simultaneous reconstruction. With all of these features, the presented toolkit can achieve accurate alignment and reconstruction simultaneously and conveniently under a single global coordinate system. Availability and implementation: The toolkit AuTom-dualx (alignment module dualxmauto and reconstruction module volrec_mltm) are accessible for general application at http://ear.ict.ac.cn, and the key source code is freely available under request. Supplementary information: Supplementary data are available at Bioinformatics online.
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