Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Atomic Resolution Defocused Electron Ptychography at Low Dose with a Fast, Direct Electron Detector.

ABSTRACT: Electron ptychography has recently attracted considerable interest for high resolution phase-sensitive imaging. However, to date studies have been mainly limited to radiation resistant samples as the electron dose required to record a ptychographic dataset is too high for use with beam-sensitive materials. Here we report defocused electron ptychography using a fast, direct-counting detector to reconstruct the transmission function, which is in turn related to the electrostatic potential of a two-dimensional material at atomic resolution under various low dose conditions.

SUBMITTER: Song J

PROVIDER: S-EPMC6408533 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Atomic Resolution Defocused Electron Ptychography at Low Dose with a Fast, Direct Electron Detector.

Song Jiamei J Allen Christopher S CS Gao Si S Huang Chen C Sawada Hidetaka H Pan Xiaoqing X Warner Jamie J Wang Peng P Kirkland Angus I AI

Scientific reports 20190308 1

Electron ptychography has recently attracted considerable interest for high resolution phase-sensitive imaging. However, to date studies have been mainly limited to radiation resistant samples as the electron dose required to record a ptychographic dataset is too high for use with beam-sensitive materials. Here we report defocused electron ptychography using a fast, direct-counting detector to reconstruct the transmission function, which is in turn related to the electrostatic potential of a two ...[more]

PMID: 30850641

Similar Datasets

Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose.

Project description:Both high resolution and high precision are required to quantitatively determine the atomic structure of complex nanostructured materials. However, for conventional imaging methods in scanning transmission electron microscopy (STEM), atomic resolution with picometer precision cannot usually be achieved for weakly-scattering samples or radiation-sensitive materials, such as 2D materials. Here, we demonstrate low-dose, sub-angstrom resolution imaging with picometer precision using mixed-state electron ptychography. We show that correctly accounting for the partial coherence of the electron beam is a prerequisite for high-quality structural reconstructions due to the intrinsic partial coherence of the electron beam. The mixed-state reconstruction gains importance especially when simultaneously pursuing high resolution, high precision and large field-of-view imaging. Compared with conventional atomic-resolution STEM imaging techniques, the mixed-state ptychographic approach simultaneously provides a four-times-faster acquisition, with double the information limit at the same dose, or up to a fifty-fold reduction in dose at the same resolution.

| S-EPMC7293311 | biostudies-literature

Low-dose cryo electron ptychography via non-convex Bayesian optimization.

Project description:Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic or near-atomic resolution. However, applications are so far mainly limited to radiation-hard samples, because the required doses are too high for imaging biological samples at high resolution. We propose the use of non-convex Bayesian optimization to overcome this problem, and show via numerical simulations that the dose required for successful reconstruction can be reduced by two orders of magnitude compared to previous experiments. As an important application we suggest to use this method for imaging single biological macromolecules at cryogenic temperatures and demonstrate 2D single-particle reconstructions from simulated data with a resolution up to 5.4?Å at a dose of 20e - /Å2. When averaging over only 30 low-dose datasets, a 2D resolution around 3.5?Å is possible for macromolecular complexes even below 100 kDa. With its independence from the microscope transfer function, direct recovery of phase contrast, and better scaling of signal-to-noise ratio, low-dose cryo electron ptychography may become a promising alternative to Zernike phase-contrast microscopy.

| S-EPMC5575234 | biostudies-literature

Low-dose phase retrieval of biological specimens using cryo-electron ptychography.

Project description:Cryo-electron microscopy is an essential tool for high-resolution structural studies of biological systems. This method relies on the use of phase contrast imaging at high defocus to improve information transfer at low spatial frequencies at the expense of higher spatial frequencies. Here we demonstrate that electron ptychography can recover the phase of the specimen with continuous information transfer across a wide range of the spatial frequency spectrum, with improved transfer at lower spatial frequencies, and as such is more efficient for phase recovery than conventional phase contrast imaging. We further show that the method can be used to study frozen-hydrated specimens of rotavirus double-layered particles and HIV-1 virus-like particles under low-dose conditions (5.7 e/Å2) and heterogeneous objects in an Adenovirus-infected cell over large fields of view (1.14 × 1.14 μm), thus making it suitable for studies of many biologically important structures.

| S-EPMC7265480 | biostudies-literature

Throughput and resolution with a next-generation direct electron detector.

Project description:Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high-resolution image capture. A new-generation DED, the DE64, has been developed by Direct Electron that has good performance in both integrating and counting modes. The camera has been characterized in both modes in terms of image quality, throughput and resolution of cryo-EM reconstructions. The modulation transfer function, noise power spectrum and detective quantum efficiency (DQE) were determined for both modes, as well as the number of images per unit time. Although the DQE for counting mode was superior to that for integrating mode, the data-collection throughput for this mode was more than ten times slower. Since throughput and resolution are related in single-particle cryo-EM, data for apoferritin were collected and reconstructed using integrating mode, integrating mode in conjunction with a Volta phase plate (VPP) and counting mode. Only the counting-mode data resulted in a better than 3?Å resolution reconstruction with similar numbers of particles, and this increased performance could not be compensated for by the increased throughput of integrating mode or by the increased low-frequency contrast of integrating mode with the VPP. These data show that the superior image quality provided by counting mode is more important for high-resolution cryo-EM reconstructions than the superior throughput of integrating mode.

| S-EPMC6830211 | biostudies-literature

Low-dose cryo-electron ptychography of Apoferritin at 4.0 mrad

Project description: Not available

| EMPIAR-12236 | biostudies-other

Characterizing the resolution and throughput of the Apollo direct electron detector.

Project description:Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.

| S-EPMC9791170 | biostudies-literature

Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures.

Project description:The aberration-corrected scanning transmission electron microscope (STEM) has emerged as a key tool for atomic resolution characterization of materials, allowing the use of imaging modes such as Z-contrast and spectroscopic mapping. The STEM has not been regarded as optimal for the phase-contrast imaging necessary for efficient imaging of light materials. Here, recent developments in fast electron detectors and data processing capability is shown to enable electron ptychography, to extend the capability of the STEM by allowing quantitative phase images to be formed simultaneously with incoherent signals. We demonstrate this capability as a practical tool for imaging complex structures containing light and heavy elements, and use it to solve the structure of a beam-sensitive carbon nanostructure. The contrast of the phase image contrast is maximized through the post-acquisition correction of lens aberrations. The compensation of defocus aberrations is also used for the measurement of three-dimensional sample information through post-acquisition optical sectioning.

| S-EPMC5007440 | biostudies-literature

Low-dose cryo-electron ptychography of Phi-92 Bacteriophage at 5.1 mrad

Project description: Not available

| EMPIAR-12233 | biostudies-other

Low-dose cryo-electron ptychography of Tobacco Mosaic Virus at 6.1 mrad

Project description: Not available

| EMPIAR-12234 | biostudies-other

Atomic-Resolution Imaging of Fast Nanoscale Dynamics with Bright Microsecond Electron Pulses.

Project description:Atomic-resolution electron microscopy is a crucial tool to elucidate the structure of matter. Recently, fast electron cameras have added the time domain to high-resolution imaging, allowing static images to be acquired as movies from which sample drift can later be removed computationally and enabling real-time observations of atomic-scale dynamics on the millisecond time scale. Even higher time resolution can be achieved with short electron pulses, yet their potential for atomic-resolution imaging remains unexplored. Here, we generate high-brightness microsecond electron pulses from a Schottky emitter whose current we briefly drive to near its limit. We demonstrate that drift-corrected imaging with such pulses can achieve atomic resolution in the presence of much larger amounts of drift than with a continuous electron beam. Moreover, such pulses enable atomic-resolution observations on the microsecond time scale, which we employ to elucidate the crystallization pathways of individual metal nanoparticles as well as the high-temperature transformation of perovskite nanocrystals.

| S-EPMC7809695 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data