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Nanofabrication of a gold fiducial array on specimen support for electron tomography.

ABSTRACT: Here we describe the production, using lithography and micro-engineering technologies, of patterned arrays of nanofabricated gold dots on a thin Si3N4 electron transparent layer, supported by silicon. We illustrate that the support with a patterned structure of nanosized gold can be exploited for (cryo) electron tomography application as a specimen support with predefined alignment markers. This nanogold patterned support has several advantages. The Si3N4 window provides a 50 nm thin, strong and flat support with a ~0.7 mm(2) large electron-beam transparent window. The nanogold pattern has a user-defined size and density, is highly regular and stable. This facilitates accurate tracking during tilt series acquisition, provides sufficient contrast for accurate alignment during the image reconstruction step and avoids an uneven lateral distribution and movement of individual fiducials. We showed that the support is suitable for electron tomography on plastic sections.

SUBMITTER: Koning RI

PROVIDER: S-EPMC7111319 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Nanofabrication of a gold fiducial array on specimen support for electron tomography.

Koning Roman I RI Kutchoukov Vladimir G VG Hagen Cornelis W CW Koster Abraham J AJ

Ultramicroscopy 20130716

Here we describe the production, using lithography and micro-engineering technologies, of patterned arrays of nanofabricated gold dots on a thin Si3N4 electron transparent layer, supported by silicon. We illustrate that the support with a patterned structure of nanosized gold can be exploited for (cryo) electron tomography application as a specimen support with predefined alignment markers. This nanogold patterned support has several advantages. The Si3N4 window provides a 50 nm thin, strong and ...[more]

PMID: 23954496

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Project description:MotivationElectron 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 toward 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.ResultsIn this article, 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 ⩽ 100 ms per image, even for micrographs with hundreds of fiducial markers, which makes the real-time ET data processing possible.Availability and implementationThe 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.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

Nanofabrication of a gold fiducial array on specimen support for electron tomography.

Publications

Nanofabrication of a gold fiducial array on specimen support for electron tomography.

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