scholarly journals Rapid Tilt-Series Method for Cryo-Electron Tomography: Characterizing Stage Behavior During FISE Acquisition

2020 ◽  
Author(s):  
Georges Chreifi ◽  
Songye Chen ◽  
Grant J. Jensen
Keyword(s):  
Data Quality ◽  
Electron Tomography ◽  
Series Method ◽  
Single Exposure ◽  
Traditional Methods ◽  
Electron Detector ◽  
Cryo Electron Tomography ◽  
Tilt Series

ABSTRACTWe and others recently developed rapid tilt-series acquisition methods for cryo-electron tomography on a Titan Krios G3i equipped with a single axis holder and a K-series direct electron detector and showed that one of these, the fast-incremental single exposure (FISE) method, significantly accelerates tilt-series acquisition when compared to traditional methods while preserving the quality of the images. Here, we characterize the behavior of our single axis holder in detail during a FISE experiment to optimally balance data quality with speed. We explain our methodology in detail so others can characterize their own stages, and conclude with recommendations for projects with different resolution goals.

scholarly journals Endocytosed nanogold fiducials for improved in-situ cryo–electron tomography tilt-series alignment

2021 ◽  
Vol 213 (1) ◽  
pp. 107698
Author(s):  
Casper Berger ◽  
Raimond B.G. Ravelli ◽  
Carmen López-Iglesias ◽  
Peter J. Peters
Keyword(s):  
Electron Tomography ◽  
Cryo Electron Tomography ◽  
Tilt Series

scholarly journals Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

Open Biology ◽  
2021 ◽  
Vol 11 (10) ◽  
Author(s):  
James M. Parkhurst ◽  
Maud Dumoux ◽  
Mark Basham ◽  
Daniel Clare ◽  
C. Alistair Siebert ◽  
...  
Keyword(s):  
Data Acquisition ◽  
Biological Samples ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
Software Pipeline ◽  
Digital Twin ◽  
Cryo Electron Tomography ◽  
The Impact

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.

scholarly journals Assessment of scoring functions to rank the quality of 3D subtomogram clusters from cryo-electron tomography

2020 ◽  
Author(s):  
Jitin Singla ◽  
Kate L. White ◽  
Raymond C. Stevens ◽  
Frank Alber
Keyword(s):  
Electron Tomography ◽  
Pearson Correlation ◽  
Scoring Function ◽  
Ground Truth ◽  
Scoring Functions ◽  
Ground Truth Data ◽  
Heterogeneous Samples ◽  
Cryo Electron Tomography ◽  
Template Free

AbstractCryo-electron tomography provides the opportunity for unsupervised discovery of endogenous complexes in situ. This process usually requires particle picking, clustering and alignment of subtomograms to produce an average structure of the complex. When applied to heterogeneous samples, template-free clustering and alignment of subtomograms can potentially lead to the discovery of structures for unknown endogenous complexes. However, such methods require useful scoring functions to measure the quality of aligned subtomogram clusters, which can be compromised by contaminations from misclassified complexes and alignment errors. To our knowledge, a comprehensive survey to assess the effectiveness of scoring functions for ranking the quality of subtomogram clusters does not exist yet. Here, we provide such a study and assess a total of 15 scoring functions for evaluating the quality of the subtomogram clusters, which differ in the amount of structural misalignments and contaminations due to misclassified complexes. We assessed both experimental and simulated subtomograms as ground truth data sets. Our analysis shows that the robustness of scoring functions varies largely. Most scores are sensitive to the signal-to-noise ratio of subtomograms and often require Gaussian filtering as preprocessing for improved performance. Two scoring functions, Spectral SNR-based Fourier Shell Correlation and Pearson Correlation in the Fourier domain with missing wedge correction, show a robust ranking of subtomogram clusters even without any preprocessing and irrespective of SNR levels of subtomograms. Of these two scoring functions, Spectral SNR-based Fourier Shell Correlation was fastest to compute and is a better choice for handling large numbers of subtomograms. Our results provide a guidance for choosing a scoring function for template-free approaches to detect complexes from heterogeneous samples.

Three-Dimensional Reconstruction of Two Forms of the Chaperonin GRO EL

1990 ◽  
Vol 48 (1) ◽  
pp. 258-259
Author(s):  
J.L. Carrascosa ◽  
G. Abella ◽  
S. Marco ◽  
M. Muyal ◽  
J.M. Carazo
Keyword(s):  
Three Dimensional ◽  
The Other ◽  
Two Dimensional ◽  
Series Method ◽  
Three Dimensional Reconstruction ◽  
Structural Components ◽  
E Coli ◽  
Dimensional Reconstruction ◽  
Morphogenetic Factors ◽  
Tilt Series

Chaperonins are a class of proteins characterized by their role as morphogenetic factors. They trantsiently interact with the structural components of certain biological aggregates (viruses, enzymes etc), promoting their correct folding, assembly and, eventually transport. The groEL factor from E. coli is a conspicuous member of the chaperonins, as it promotes the assembly and morphogenesis of bacterial oligomers and/viral structures.We have studied groEL-like factors from two different bacteria:E. coli and B.subtilis. These factors share common morphological features , showing two different views: one is 6-fold, while the other shows 7 morphological units. There is also a correlation between the presence of a dominant 6-fold view and the fact of both bacteria been grown at low temperature (32°C), while the 7-fold is the main view at higher temperatures (42°C). As the two-dimensional projections of groEL were difficult to interprete, we studied their three-dimensional reconstruction by the random conical tilt series method from negatively stained particles.

Embedded Gold Markers for Improved TEM/STEM Tomography Reconstruction

2008 ◽  
Author(s):  
Jian-Shing Luo ◽  
Chia-Chi Huang ◽  
Jeremy D. Russell
Keyword(s):  
3D Reconstruction ◽  
Feature Tracking ◽  
Semiconductor Device ◽  
Electron Tomography ◽  
Tracking Process ◽  
Carbon Coated ◽  
Novel Method ◽  
Tomography Reconstruction ◽  
Tilt Series ◽  
20 Nm

Abstract Electron tomography includes four main steps: tomography data acquisition, image processing, 3D reconstruction, and visualization. After acquisition, tilt-series alignments are performed. Two methods are used to align the tilt-series: cross-correlation and feature tracking. Normally, about 10-20 nm of fiducial markers, such as gold beads, are deposited onto one side of 100 mesh carbon-coated grids during the feature-tracking process. This paper presents a novel method for preparing electron tomography samples with gold beads inside to improve the feature tracking process and quality of 3D reconstruction. Results show that the novel electron tomography sample preparation method improves image alignment, which is essential for successful tomography in many contemporary semiconductor device structures.

Designing Information Product (IP) Maps On the Process of Data Processing and Academic Information

2017 ◽  
Vol 4 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Diana Effendi
Keyword(s):  
Data Quality ◽  
Data Management ◽  
Information Management ◽  
Information Quality ◽  
Quality Data ◽  
Management Approach ◽  
Quality Of Data ◽  
Information Product ◽  
Academic Activities

Information Product Approach (IP Approach) is an information management approach. It can be used to manage product information and data quality analysis. IP-Map can be used by organizations to facilitate the management of knowledge in collecting, storing, maintaining, and using the data in an organized. The  process of data management of academic activities in X University has not yet used the IP approach. X University has not given attention to the management of information quality of its. During this time X University just concern to system applications used to support the automation of data management in the process of academic activities. IP-Map that made in this paper can be used as a basis for analyzing the quality of data and information. By the IP-MAP, X University is expected to know which parts of the process that need improvement in the quality of data and information management.   Index term: IP Approach, IP-Map, information quality, data quality. REFERENCES[1] H. Zhu, S. Madnick, Y. Lee, and R. Wang, “Data and Information Quality Research: Its Evolution and Future,” Working Paper, MIT, USA, 2012.[2] Lee, Yang W; at al, Journey To Data Quality, MIT Press: Cambridge, 2006.[3] L. Al-Hakim, Information Quality Management: Theory and Applications. Idea Group Inc (IGI), 2007.[4] “Access : A semiotic information quality framework: development and comparative analysis : Journal ofInformation Technology.” [Online]. Available: http://www.palgravejournals.com/jit/journal/v20/n2/full/2000038a.html. [Accessed: 18-Sep-2015].[5] Effendi, Diana, Pengukuran Dan Perbaikan Kualitas Data Dan Informasi Di Perguruan Tinggi MenggunakanCALDEA Dan EVAMECAL (Studi Kasus X University), Proceeding Seminar Nasional RESASTEK, 2012, pp.TIG.1-TI-G.6.

Sign in / Sign up

Export Citation Format

Share Document