When to use the projection assumption and the weak-phase object approximation in phase contrast cryo-EM

Vulović, Miloš; Voortman, Lenard M.; Vliet, Lucas J. van; Rieger, Bernd

doi:10.1016/j.ultramic.2013.08.002

Cited by 47 publications

(25 citation statements)

References 18 publications

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“…These models explore how electrons interact with matter (the macromolecule and its hydration layer [51]) and finally produce an image that is recorded by the device [52], [53]. For the moment, none of the previous advances in image formation has made its way into a 3D reconstruction algorithm, but certainly having a high-resolution model of how the image is formed in the microscope is a necessary step forward.…”

Section: ) High-resolution Electron Imaging: Direct Detection Devicementioning

confidence: 99%

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Kervrann

Sorzano

Acton

et al. 2016

IEEE J. Sel. Top. Signal Process.

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Abstract-Microscopy imaging, including fluorescence microscopy and electron microscopy, has taken a prominent role in life science research and medicine due to its ability to investigate the 3D interior of live cells and organisms. A long-term research in bio-imaging at the sub-cellular and cellular scales consists then in inferring the relationships between the dynamics of macromolecules and their functions. In this area, image processing and analysis methods are now essential to understand the dynamic organization of groups of interacting molecules inside molecular machineries and to address issues in fundamental biology driven by advances in molecular biology, optics and technology. In this paper, we present recent advances in fluorescence and electron microscopy and we focus on dedicated image processing and analysis methods required to quantify phenotypes for a limited number but typical studies in cell imaging.

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Section: ) High-resolution Electron Imaging: Direct Detection Devicementioning

confidence: 99%

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Kervrann

Sorzano

Acton

et al. 2016

IEEE J. Sel. Top. Signal Process.

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“…A weak phase (linear) approximation at each slice may also be assumed [31][32][33][34]. Scattering through a single slice is calculated by integration with the function,…”

Section: Accounting For Propagation Through the Specimen-the M-plamentioning

confidence: 99%

Structure retrieval with fast electrons using segmented detectors

et al. 2016

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We introduce an algorithm for the reconstruction of the complex transmission function of a specimen using segmented detectors in scanning transmission electron microscopy geometry. The phase of the transmission function can be related to magnetic and electric fields within the specimen and is sensitive to lighter elements. The technique is demonstrated for simulated data and also using experimental datasets taken from a MoS 2 monolayer and a SrTiO 3 crystal. We present an extension to the algorithm to account for uncertainties in the illuminating probe. The algorithm can be implemented using fast Fourier transforms, and this provides the possibility of reconstructing specimen transmission functions in real time.

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“…Under atomic-resolution imaging conditions, namely, zoneaxis orientation and evaluation of large scattering angles, the POA is usually no longer applicable for specimen thicknesses above a few nanometers for very light atomic species down to a few angstroms for medium and heavy elements [3,24,25], The wave function is modulated in amplitude and phase in a complicated manner referred to as dynamic scattering (e.g., Ref. [24]).…”

Section: B High Resolutionmentioning

confidence: 99%

“…[24]). For instance, the strong amplitude contrast of 88% is already obtained after a 4-nm-thick GaAs layer (i.e., not a particularly strong scatterer) aligned in the [110] direction at 200-kV acceleration voltage [24], A detailed study of the range of validity of the POA was published recently [25], and we discuss this crucial point further in the Appendix. Moreover, atomic electric fields strongly vary on length scales smaller than the Bohr radius, which are smaller than the electron probe sizes typically employed in hardware-corrected STEM.…”

Section: B High Resolutionmentioning

confidence: 99%

Differential phase contrast: An integral perspective

Lubk

Zweck

2015

Phys. Rev. A

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Differential phase contrast (DPC) in a scanning transmission electron microscope is a widely employed technique for probing electromagnetic fields on the nanoscale. We show that the DPC signal corresponds to the averaged lateral probability current of the scattered electron probe. Based on this result we discuss the interpretation of DPC in terms of the projected electric and magnetic fields and the influence of experimental parameters thereon. We further show that DPC can be interpreted as a quantum weak measurement and that the reciprocal broad beam illumination technique is given by an astigmatic transport of intensity reconstruction.

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When to use the projection assumption and the weak-phase object approximation in phase contrast cryo-EM

Cited by 47 publications

References 18 publications

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Structure retrieval with fast electrons using segmented detectors

Differential phase contrast: An integral perspective

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