Dataset Information

Improvements on marker-free images alignment for electron tomography.

ABSTRACT: Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.

SUBMITTER: Sorzano COS

PROVIDER: S-EPMC7527754 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Improvements on marker-free images alignment for electron tomography.

Sorzano C O S COS de Isidro-Gómez F F Fernández-Giménez E E Herreros D D Marco S S Carazo J M JM Messaoudi C C

Journal of structural biology: X 20200917

Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In ...[more]

PMID: 33024955

Similar Datasets

Project description:MOTIVATION:Electron tomography (ET) is a widely used technology for 3D macro-molecular structure reconstruction. To obtain a satisfiable tomogram reconstruction, several key processes are involved, one of which is the calibration of projection parameters of the tilt series. Although fiducial marker-based alignment for tilt series has been well studied, marker-free alignment remains a challenge, which requires identifying and tracking the identical objects (landmarks) through different projections. However, the tracking of these landmarks is usually affected by the pixel density (intensity) change caused by the geometry difference in different views. The tracked landmarks will be used to determine the projection parameters. Meanwhile, different projection parameters will also affect the localization of landmarks. Currently, there is no alignment method that takes interrelationship between the projection parameters and the landmarks. RESULTS:Here, we propose a novel, joint method for marker-free alignment of tilt series in ET, by utilizing the information underlying the interrelationship between the projection model and the landmarks. The proposed method is the first joint solution that combines the extrinsic (track-based) alignment and the intrinsic (intensity-based) alignment, in which the localization of landmarks and projection parameters keep refining each other until convergence. This iterative approach makes our solution robust to different initial parameters and extreme geometric changes, which ensures a better reconstruction for marker-free ET. Comprehensive experimental results on three real datasets show that our new method achieved a significant improvement in alignment accuracy and reconstruction quality, compared to the state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION:The main program is available at https://github.com/icthrm/joint-marker-free-alignment. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

Dataset Information

Improvements on marker-free images alignment for electron tomography.

Publications

Improvements on marker-free images alignment for electron tomography.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets