Ghostbuster: A phase retrieval diffraction tomography algorithm for cryo-EM
Ultramicroscopy. 2024 Apr 12;262:113962. doi: 10.1016/j.ultramic.2024.113962. Online ahead of print.ABSTRACTEwald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how ...
Source: Ultramicroscopy - April 20, 2024 Category: Laboratory Medicine Authors: Joel Yeo Benedikt J Daurer Dari Kimanius Deepan Balakrishnan Tristan Bepler Yong Zi Tan N Duane Loh Source Type: research
Ghostbuster: A phase retrieval diffraction tomography algorithm for cryo-EM
Ultramicroscopy. 2024 Apr 12;262:113962. doi: 10.1016/j.ultramic.2024.113962. Online ahead of print.ABSTRACTEwald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how ...
Source: Ultramicroscopy - April 20, 2024 Category: Laboratory Medicine Authors: Joel Yeo Benedikt J Daurer Dari Kimanius Deepan Balakrishnan Tristan Bepler Yong Zi Tan N Duane Loh Source Type: research
Ghostbuster: A phase retrieval diffraction tomography algorithm for cryo-EM
Ultramicroscopy. 2024 Apr 12;262:113962. doi: 10.1016/j.ultramic.2024.113962. Online ahead of print.ABSTRACTEwald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how ...
Source: Ultramicroscopy - April 20, 2024 Category: Laboratory Medicine Authors: Joel Yeo Benedikt J Daurer Dari Kimanius Deepan Balakrishnan Tristan Bepler Yong Zi Tan N Duane Loh Source Type: research
A soft touch with electron beams: Digging out structural information of nanomaterials with advanced scanning low energy electron microscopy coupled with deep learning
In this report, we show how clearer structural and surface information at nanoscale can be obtained by SLEEM, coupled with deep learning. The method is demonstrated using Au nanoparticles-loaded mesoporous silica as a model system. Moreover, unlike conventional scanning electron microscopy (SEM), SLEEM does not require the samples to be coated with conductive films for analysis; thus, not only it is convenient to use but it also does not give artifacts. The results further reveal that SLEEM and deep learning can serve as great tools to analyze materials at nanoscale well. The biggest advantage of the presented method is it...
Source: Ultramicroscopy - April 19, 2024 Category: Laboratory Medicine Authors: Eli ška Materna Mikmeková Ji ří Materna Ivo Konvalina Šárka Mikmeková Ilona M üllerová Tewodros Asefa Source Type: research
Strain visualization using large-angle convergent-beam electron diffraction
In this study, we report a strain visualization method using large-angle convergent-beam electron diffraction (LACBED).1 We compare the proposed method with the strain maps acquired via STEM-NBD, a combination of scanning transmission electron microscopy (STEM) and nanobeam electron diffraction (NBD). Although STEM-NBD can precisely measure the lattice parameters, it requires a large amount of data and personal computer (PC) resources to obtain a two-dimensional strain map. Deficiency lines in the transmitted disk of LACBED reflect the crystalline structure information and move, curve, or disappear in the deformed area. Pr...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Fumihiko Uesugi Chiaki Tanii Naoyuki Sugiyama Masaki Takeguchi Source Type: research
Secondary-electron imaging of bulk crystalline specimens in an aberration corrected STEM
In this study, we explore the practicality of scanning transmission electron microscope (STEM) imaging with secondary electrons (SE), using a silicon-wedge specimen having a maximum thickness of 18 μm. We find that the atomic structure is present in the entire thickness range of the SE images although the background intensity increases moderately with thickness. The consistent intensity of secondary electron (SE) images at atomic positions and the modest increase in background intensity observed in silicon suggest a limited contribution from SEs generated by backscattered electrons, a conclusion supported by our multislic...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Sooyeon Hwang Lijun Wu Kim Kisslinger Judith Yang Ray Egerton Yimei Zhu Source Type: research
Strain visualization using large-angle convergent-beam electron diffraction
In this study, we report a strain visualization method using large-angle convergent-beam electron diffraction (LACBED).1 We compare the proposed method with the strain maps acquired via STEM-NBD, a combination of scanning transmission electron microscopy (STEM) and nanobeam electron diffraction (NBD). Although STEM-NBD can precisely measure the lattice parameters, it requires a large amount of data and personal computer (PC) resources to obtain a two-dimensional strain map. Deficiency lines in the transmitted disk of LACBED reflect the crystalline structure information and move, curve, or disappear in the deformed area. Pr...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Fumihiko Uesugi Chiaki Tanii Naoyuki Sugiyama Masaki Takeguchi Source Type: research
Secondary-electron imaging of bulk crystalline specimens in an aberration corrected STEM
In this study, we explore the practicality of scanning transmission electron microscope (STEM) imaging with secondary electrons (SE), using a silicon-wedge specimen having a maximum thickness of 18 μm. We find that the atomic structure is present in the entire thickness range of the SE images although the background intensity increases moderately with thickness. The consistent intensity of secondary electron (SE) images at atomic positions and the modest increase in background intensity observed in silicon suggest a limited contribution from SEs generated by backscattered electrons, a conclusion supported by our multislic...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Sooyeon Hwang Lijun Wu Kim Kisslinger Judith Yang Ray Egerton Yimei Zhu Source Type: research
Strain visualization using large-angle convergent-beam electron diffraction
In this study, we report a strain visualization method using large-angle convergent-beam electron diffraction (LACBED).1 We compare the proposed method with the strain maps acquired via STEM-NBD, a combination of scanning transmission electron microscopy (STEM) and nanobeam electron diffraction (NBD). Although STEM-NBD can precisely measure the lattice parameters, it requires a large amount of data and personal computer (PC) resources to obtain a two-dimensional strain map. Deficiency lines in the transmitted disk of LACBED reflect the crystalline structure information and move, curve, or disappear in the deformed area. Pr...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Fumihiko Uesugi Chiaki Tanii Naoyuki Sugiyama Masaki Takeguchi Source Type: research
Secondary-electron imaging of bulk crystalline specimens in an aberration corrected STEM
In this study, we explore the practicality of scanning transmission electron microscope (STEM) imaging with secondary electrons (SE), using a silicon-wedge specimen having a maximum thickness of 18 μm. We find that the atomic structure is present in the entire thickness range of the SE images although the background intensity increases moderately with thickness. The consistent intensity of secondary electron (SE) images at atomic positions and the modest increase in background intensity observed in silicon suggest a limited contribution from SEs generated by backscattered electrons, a conclusion supported by our multislic...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Sooyeon Hwang Lijun Wu Kim Kisslinger Judith Yang Ray Egerton Yimei Zhu Source Type: research
Strain visualization using large-angle convergent-beam electron diffraction
In this study, we report a strain visualization method using large-angle convergent-beam electron diffraction (LACBED).1 We compare the proposed method with the strain maps acquired via STEM-NBD, a combination of scanning transmission electron microscopy (STEM) and nanobeam electron diffraction (NBD). Although STEM-NBD can precisely measure the lattice parameters, it requires a large amount of data and personal computer (PC) resources to obtain a two-dimensional strain map. Deficiency lines in the transmitted disk of LACBED reflect the crystalline structure information and move, curve, or disappear in the deformed area. Pr...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Fumihiko Uesugi Chiaki Tanii Naoyuki Sugiyama Masaki Takeguchi Source Type: research
Secondary-electron imaging of bulk crystalline specimens in an aberration corrected STEM
In this study, we explore the practicality of scanning transmission electron microscope (STEM) imaging with secondary electrons (SE), using a silicon-wedge specimen having a maximum thickness of 18 μm. We find that the atomic structure is present in the entire thickness range of the SE images although the background intensity increases moderately with thickness. The consistent intensity of secondary electron (SE) images at atomic positions and the modest increase in background intensity observed in silicon suggest a limited contribution from SEs generated by backscattered electrons, a conclusion supported by our multislic...
Source: Ultramicroscopy - April 14, 2024 Category: Laboratory Medicine Authors: Sooyeon Hwang Lijun Wu Kim Kisslinger Judith Yang Ray Egerton Yimei Zhu Source Type: research
High-resolution scanning tunneling microscope and its adaptation for local thermopower measurements in 2D materials
We present the design, fabrication and discuss the performance of a new combined high-resolution Scanning Tunneling and Thermopower Microscope (STM/SThEM). We also describe the development of the electronic control, the user interface, the vacuum system, and arrangements to reduce acoustical noise and vibrations. We demonstrate the microscope's performance with atomic-resolution topographic images of highly oriented pyrolytic graphite (HOPG) and local thermopower measurements in the semimetal Bi2Te3. Our system offers a tool to investigate the relationship between electronic structure and thermoelectric properties at the n...
Source: Ultramicroscopy - April 13, 2024 Category: Laboratory Medicine Authors: Jose D Berm údez-Perez Edwin Herrera-Vasco Javier Casas-Salgado Hector A Castelblanco Karen Vega-Bustos Gabriel Cardenas-Chirivi Oscar L Herrera-Sandoval Hermann Suderow Paula Giraldo-Gallo Jose Augusto Galvis Source Type: research
High-resolution scanning tunneling microscope and its adaptation for local thermopower measurements in 2D materials
We present the design, fabrication and discuss the performance of a new combined high-resolution Scanning Tunneling and Thermopower Microscope (STM/SThEM). We also describe the development of the electronic control, the user interface, the vacuum system, and arrangements to reduce acoustical noise and vibrations. We demonstrate the microscope's performance with atomic-resolution topographic images of highly oriented pyrolytic graphite (HOPG) and local thermopower measurements in the semimetal Bi2Te3. Our system offers a tool to investigate the relationship between electronic structure and thermoelectric properties at the n...
Source: Ultramicroscopy - April 13, 2024 Category: Laboratory Medicine Authors: Jose D Berm údez-Perez Edwin Herrera-Vasco Javier Casas-Salgado Hector A Castelblanco Karen Vega-Bustos Gabriel Cardenas-Chirivi Oscar L Herrera-Sandoval Hermann Suderow Paula Giraldo-Gallo Jose Augusto Galvis Source Type: research
Reflection imaging with a helium zone plate microscope
Ultramicroscopy. 2024 Mar 25;261:113961. doi: 10.1016/j.ultramic.2024.113961. Online ahead of print.ABSTRACTNeutral helium atom microscopy is a novel microscopy technique which offers strictly surface-sensitive, non-destructive imaging. Several experiments have been published in recent years where images are obtained by scanning a helium beam spot across a surface and recording the variation in scattered intensity at a fixed total scattering angle θSD and fixed incident angle θi relative to the overall surface normal. These experiments used a spot obtained by collimating the beam (referred to as helium pinhole microscopy...
Source: Ultramicroscopy - April 6, 2024 Category: Laboratory Medicine Authors: Ranveig Flatab ø Sabrina D Eder Thomas Reisinger Gianangelo Bracco Peter Baltzer Bj örn Samelin Bodil Holst Source Type: research
