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  1. Article ; Online: Sampling theory perspective on tomographic tilt increment schemes.

    Seifer, Shahar

    Ultramicroscopy

    2022  Volume 245, Page(s) 113669

    Abstract: Given a limited radiation exposure to be distributed over a discrete number of tilted projections in tomography, the optimal collection of information depends on the tilt increment scheme. Relying on principles of sampling theory, several tilt increment ... ...

    Abstract Given a limited radiation exposure to be distributed over a discrete number of tilted projections in tomography, the optimal collection of information depends on the tilt increment scheme. Relying on principles of sampling theory, several tilt increment schemes can be compared and quantified. Following reasoning of Saxton, a revised scheme is offered in which the tilt angle increments Δθ
    MeSH term(s) Image Processing, Computer-Assisted/methods ; Tomography/methods ; Tomography, X-Ray Computed/methods ; Computer Simulation ; Algorithms
    Language English
    Publishing date 2022-12-18
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479043-9
    ISSN 1879-2723 ; 0304-3991
    ISSN (online) 1879-2723
    ISSN 0304-3991
    DOI 10.1016/j.ultramic.2022.113669
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Quantitative atomic cross section analysis by 4D-STEM and EELS.

    Seifer, Shahar / Houben, Lothar / Elbaum, Michael

    Ultramicroscopy

    2024  Volume 259, Page(s) 113936

    Abstract: We demonstrate the use of a 4-dimensional scanning transmission electron microscope (4D-STEM) to extract atomic cross section information in amorphous materials. We measure the scattering amplitudes of 200 keV electrons in several representative ... ...

    Abstract We demonstrate the use of a 4-dimensional scanning transmission electron microscope (4D-STEM) to extract atomic cross section information in amorphous materials. We measure the scattering amplitudes of 200 keV electrons in several representative specimens: amorphous carbon, silica, amorphous ice of pure water, and vitrified phosphate buffer solution. Diffraction patterns are recorded by 4D-STEM with or without energy filter at the zero-loss peak. In addition, Electron Energy Loss Spectroscopy (EELS) data are acquired at several thicknesses and energies. Mixed elastic and inelastic contributions for thick samples can be decoupled based on a convolution model. Measured differential cross sections between 1 and 3 mrad are due primarily to plasmon excitations and follow precisely a 1/θ
    Language English
    Publishing date 2024-02-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1479043-9
    ISSN 1879-2723 ; 0304-3991
    ISSN (online) 1879-2723
    ISSN 0304-3991
    DOI 10.1016/j.ultramic.2024.113936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Synchronization of scanning probe and pixelated sensor for image-guided diffraction microscopy.

    Seifer, Shahar / Elbaum, Michael

    HardwareX

    2023  Volume 14, Page(s) e00431

    Abstract: A 4-dimensional modality of a scanning transmission electron microscope (4D-STEM) acquires diffraction images formed by a coherent and focused electron beam scanning the specimen. Newly developed ultrafast detectors offer a possibility to acquire high ... ...

    Abstract A 4-dimensional modality of a scanning transmission electron microscope (4D-STEM) acquires diffraction images formed by a coherent and focused electron beam scanning the specimen. Newly developed ultrafast detectors offer a possibility to acquire high throughput diffraction patterns at each pixel of the scan, enabling rapid tilt series acquisition for 4D-STEM tomography. Here we present a solution to the problem of synchronizing the electron probe scan with the diffraction image acquisition, and demonstrate on a fast hybrid-pixel detector camera (ARINA, DECTRIS). Image-guided tracking and autofocus corrections are handled by the freely-available microscope-control software SerialEM, in conjunction with a high angle annular dark field (HAADF) image acquired simultaneously. The open source SavvyScan system offers a versatile set of scanning patterns, operated by commercially available multi-channel acquisition and signal generator computer cards (Spectrum Instrumentation GmbH). Images are recorded only within a sub-region of the total field, so as to avoid spurious data collection during flyback and/or acceleration periods in the scan. Hence, the trigger of the fast camera follows selected pulses from the scan generator clock gated according to the chosen scan pattern. Software and protocol are provided for gating the trigger pulses via a microcontroller (ST Microelectronics ARM Cortex). We demonstrate the system on a standard replica grating and by diffraction imaging of a ferritin specimen.
    Language English
    Publishing date 2023-05-24
    Publishing country England
    Document type Journal Article
    ISSN 2468-0672
    ISSN (online) 2468-0672
    DOI 10.1016/j.ohx.2023.e00431
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  4. Article ; Online: ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography.

    Seifer, Shahar / Elbaum, Michael

    Biological imaging

    2022  Volume 2, Page(s) e7

    Abstract: Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly ...

    Abstract Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required in order to produce a successful alignment. Information from highly tilted views must often be excluded to the detriment of axial resolution in the reconstruction. We introduce here an approach to tilt series alignment based on identification of fiducial particle clusters that transform coherently in rotation, essentially those that lie at similar depth. Clusters are identified by comparison of tilted views with a single untilted reference, rather than with adjacent tilts. The software, called ClusterAlign, proves robust to poor signal to noise ratio and varying visibility of the individual fiducials and is successful in carrying the alignment to the ends of the tilt series where other methods tend to fail. ClusterAlign may be used to generate a list of tracked fiducials, to align a tilt series, or to perform a complete 3D reconstruction. Tools to evaluate alignment error by projection matching are included. Execution involves no manual intervention, and adherence to standard file formats facilitates an interface with other software, particularly IMOD/etomo, tomo3d, and tomoalign.
    Language English
    Publishing date 2022-08-05
    Publishing country England
    Document type Journal Article
    ISSN 2633-903X
    ISSN (online) 2633-903X
    DOI 10.1017/S2633903X22000071
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  5. Article ; Online: Thermal inactivation scaling applied for SARS-CoV-2.

    Seifer, Shahar / Elbaum, Michael

    Biophysical journal

    2020  Volume 120, Issue 6, Page(s) 1054–1059

    Abstract: Based on a model of protein denaturation rate limited by an entropy-related barrier, we derive a simple formula for virus inactivation time as a function of temperature. Loss of protein structure is described by two reaction coordinates: conformational ... ...

    Abstract Based on a model of protein denaturation rate limited by an entropy-related barrier, we derive a simple formula for virus inactivation time as a function of temperature. Loss of protein structure is described by two reaction coordinates: conformational disorder of the polymer and wetting by the solvent. These establish a competition between conformational entropy and hydrophobic interaction favoring random coil or globular states, respectively. Based on the Landau theory of phase transition, the resulting free energy barrier is found to decrease linearly with the temperature difference T - T
    MeSH term(s) COVID-19/complications ; Fever/virology ; Humans ; SARS-CoV-2/physiology ; Temperature ; Virus Inactivation
    Language English
    Publishing date 2020-11-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.11.2259
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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: Flexible STEM with Simultaneous Phase and Depth Contrast.

    Seifer, Shahar / Houben, Lothar / Elbaum, Michael

    Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

    2021  , Page(s) 1–12

    Abstract: Recent advances in scanning transmission electron microscopy (STEM) have rekindled interest in multi-channel detectors and prompted the exploration of unconventional scan patterns. These emerging needs are not yet addressed by standard commercial ... ...

    Abstract Recent advances in scanning transmission electron microscopy (STEM) have rekindled interest in multi-channel detectors and prompted the exploration of unconventional scan patterns. These emerging needs are not yet addressed by standard commercial hardware. The system described here incorporates a flexible scan generator that enables exploration of low-acceleration scan patterns, while data are recorded by a scalable eight-channel array of nonmultiplexed analog-to-digital converters. System integration with SerialEM provides a flexible route for automated acquisition protocols including tomography. Using a solid-state quadrant detector with additional annular rings, we explore the generation and detection of various STEM contrast modes. Through-focus bright-field scans relate to phase contrast, similarly to wide-field TEM. More strikingly, comparing images acquired from different off-axis detector elements reveals lateral shifts dependent on defocus. Compensation of this parallax effect leads to decomposition of integrated differential phase contrast (iDPC) to separable contributions relating to projected electric potential and to defocus. Thus, a single scan provides both a computationally refocused phase contrast image and a second image in which the signed intensity, bright or dark, represents the degree of defocus.
    Language English
    Publishing date 2021-10-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1385710-1
    ISSN 1435-8115 ; 1431-9276
    ISSN (online) 1435-8115
    ISSN 1431-9276
    DOI 10.1017/S1431927621012861
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  7. Article ; Online: Toward Compositional Contrast by Cryo-STEM.

    Elbaum, Michael / Seifer, Shahar / Houben, Lothar / Wolf, Sharon G / Rez, Peter

    Accounts of chemical research

    2021  Volume 54, Issue 19, Page(s) 3621–3631

    Abstract: Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological ... ...

    Abstract Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological samples are particularly sensitive due to their composition of light elements suspended in an aqueous medium. Early investigators developed techniques of embedding and staining with heavy metal salts for contrast enhancement. Indeed, the Nobel Prize in 1974 recognized Claude, de Duve, and Palade for establishment of the field of cell biology, largely due to their developments in separation and preservation of cellular components for electron microscopy. A decade later, cryogenic fixation was introduced. Vitrification of the water avoids the need for dehydration and provides an ideal matrix in which the organic macromolecules are suspended; the specimen represents a native state, suddenly frozen in time at temperatures below -150 °C. The low temperature maintains a low vapor pressure for the electron microscope, and the amorphous nature of the medium avoids diffraction contrast from crystalline ice. Such samples are extremely delicate, however, and cryo-EM imaging is a race for information in the face of ongoing damage by electron irradiation. Through this journey, cryo-EM enhanced the resolution scale from membranes to molecules and most recently to atoms. Cryo-EM pioneers, Dubochet, Frank, and Henderson, were awarded the Nobel Prize in 2017 for high resolution structure determination of biological macromolecules.A relatively untapped feature of cryo-EM is its preservation of composition. Nothing is added and nothing removed. Analytical spectroscopies based on electron energy loss or X-ray emission can be applied, but the very small interaction cross sections conflict with the weak exposures required to preserve sample integrity. To what extent can we interpret quantitatively the pixel intensities in images themselves? Conventional cryo-transmission electron microscopy (TEM) is limited in this respect, due to the strong dependence of the contrast transfer on defocus and the absence of contrast at low spatial frequencies.Inspiration comes largely from a different modality for cryo-tomography, using soft X-rays. Contrast depends on the difference in atomic absorption between carbon and oxygen in a region of the spectrum between their core level ionization energies, the so-called water window. Three dimensional (3D) reconstruction provides a map of the local X-ray absorption coefficient. The quantitative contrast enables the visualization of organic materials without stain and measurement of their concentration quantitatively. We asked, what aspects of the quantitative contrast might be transferred to cryo-electron microscopy?Compositional contrast is accessible in scanning transmission EM (STEM) via incoherent elastic scattering, which is sensitive to the atomic number
    MeSH term(s) Cryoelectron Microscopy ; Macromolecular Substances/chemistry ; Microscopy, Electron, Scanning Transmission
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2021-09-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1483291-4
    ISSN 1520-4898 ; 0001-4842
    ISSN (online) 1520-4898
    ISSN 0001-4842
    DOI 10.1021/acs.accounts.1c00279
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  8. Article: Spatial and temporal turbulent velocity and vorticity power spectra from sound scattering.

    Seifer, Shahar / Steinberg, Victor

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2005  Volume 71, Issue 4 Pt 2, Page(s) 45601

    Abstract: By performing sound-scattering measurements with a detector array consisting of 62 elements in a flow between two counter-rotating disks we obtain the energy and vorticity power spectra directly in both spatial and temporal domains. Fast-accumulated ... ...

    Abstract By performing sound-scattering measurements with a detector array consisting of 62 elements in a flow between two counter-rotating disks we obtain the energy and vorticity power spectra directly in both spatial and temporal domains. Fast-accumulated statistics and a large signal-to-noise ratio allow us to get high-quality data rather effectively and to test scaling laws in details.
    Language English
    Publishing date 2005-04
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.71.045601
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