Inverse Multislice Ptychography by Layer-Wise Optimisation and Sparse Matrix Decomposition

Bangun, Arya; Melnyk, Oleh; März, Benjamin; Diederichs, Benedikt; Clausen, Alexander; Weber, Dieter; Filbir, Frank; Müller‐Caspary, Knut

doi:10.1109/tci.2022.3218993

Cited by 9 publications

(4 citation statements)

References 39 publications

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“…However, to our knowledge none of the methods for blind ptychography guarantees a sublinear convergence rate as in Theorem 3.4. The proofs presented in this paper can be extended for layerwise optimization algorithm for multislice ptychography [30]. While Algorithm 2 is supported by theoretical analysis, numerical examples point towards its underperformance in terms of computation time.…”

Section: Conclusion and Discussionmentioning

confidence: 94%

Image Recovery for Blind Polychromatic Ptychography

Filbir¹,

Melnyk²

2022

Preprint

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Ptychography is a lensless imaging technique, which considers reconstruction from a set of far-field diffraction patterns obtained by illuminating small overlapping regions of the specimen. In many cases, a distribution of light inside the illuminated region is unknown and has to be estimated along with the object of interest. This problem is referred to as blind ptychography. While in ptychography the illumination is commonly assumed to have a point spectrum, in this paper we consider an alternative scenario with non-trivial light spectrum known as blind polychromatic ptychography.Firstly, we show that non-blind polychromatic ptychography can be seen as a recovery from quadratic measurements. Then, a reconstruction from such measurements can be performed by a variant of Amplitude Flow algorithm, which has guaranteed sublinear convergence to a critical point. Secondly, we address recovery from blind polychromatic ptychographic measurements by devising an alternating minimization version of Amplitude Flow and showing that it converges to a critical point at a sublinear rate.

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Section: Conclusion and Discussionmentioning

confidence: 94%

Image Recovery for Blind Polychromatic Ptychography

Filbir¹,

Melnyk²

2022

Preprint

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“…Because at low-dose settings, single events at high angles dominate the whole COM calculation due to their weighting with the spatial frequency, determining the COM from diffraction within a cutoff spatial frequency typically improves the signal-to-noise ratio. A 4D-STEM setup also enables advanced processing, e.g., iterative ptychography as with the extended ptychographic iterative engine 11 (ePIE) or potentially inverse multislice 39 , 40 . For iterative 4D-STEM ptychography defocusing leads to a larger overlap of probe positions which is beneficial for the deconvolution of specimen and probe.…”

Section: Discussionmentioning

confidence: 99%

Imaging built-in electric fields and light matter by Fourier-precession TEM

Lorenzen,

März,

Xue

et al. 2024

Sci Rep

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We report the precise measurement of electric fields in nanostructures, and high-contrast imaging of soft matter at ultralow electron doses by transmission electron microscopy (TEM). In particular, a versatile method based on the theorem of reciprocity is introduced to enable differential phase contrast imaging and ptychography in conventional, plane-wave illumination TEM. This is realised by a series of TEM images acquired under different tilts, thereby introducing the sampling rate in reciprocal space as a tuneable parameter, in contrast to momentum-resolved scanning techniques. First, the electric field of a p–n junction in GaAs is imaged. Second, low-dose, in-focus ptychographic and DPC characterisation of Kagome pores in weakly scattering covalent organic frameworks is demonstrated by using a precessing electron beam in combination with a direct electron detector. The approach offers utmost flexibility to record relevant spatial frequencies selectively, while acquisition times and dose requirements are significantly reduced compared to the 4D-STEM counterpart.

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“…Conceptually, 4D STEM possesses the advantage of allowing an enormous flexibility for data processing, with current developments going far beyond direct inversion schemes and single-slice models. In particular, ptychographic iterative engine algorithms perform very well with regards to spatial resolution (Maiden et al, 2009) and developments for inverse multislice ptychography (Bangun et al, 2022;Chen et al, 2021;Maiden et al, 2012) provide solutions beyond the projection assumption. Overcoming the (W)PO limitations to CTEM by 2-3-slice phase retrieval in 4D STEM is thus a promising way to explore the opportunity of resolution and contrast enhancement in future cryo-EM.…”

Section: Discussionmentioning

confidence: 99%

Dynamical scattering in ice-embedded proteins in conventional and scanning transmission electron microscopy

Leidl

Sachse

Müller‐Caspary

2023

IUCrJ

Self Cite

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Structure determination of biological macromolecules using cryogenic electron microscopy is based on applying the phase object (PO) assumption and the weak phase object (WPO) approximation to reconstruct the 3D potential density of the molecule. To enhance the understanding of image formation of protein complexes embedded in glass-like ice in a transmission electron microscope, this study addresses multiple scattering in tobacco mosaic virus (TMV) specimens. This includes the propagation inside the molecule while also accounting for the effect of structural noise. The atoms in biological macromolecules are light but are distributed over several nanometres. Commonly, PO and WPO approximations are used in most simulations and reconstruction models. Therefore, dynamical multislice simulations of TMV specimens embedded in glass-like ice were performed based on fully atomistic molecular-dynamics simulations. In the first part, the impact of multiple scattering is studied using different numbers of slices. In the second part, different sample thicknesses of the ice-embedded TMV are considered in terms of additional ice layers. It is found that single-slice models yield full frequency transfer up to a resolution of 2.5 Å, followed by attenuation up to 1.4 Å. Three slices are sufficient to reach an information transfer up to 1.0 Å. In the third part, ptychographic reconstructions based on scanning transmission electron microscopy (STEM) and single-slice models are compared with conventional TEM simulations. The ptychographic reconstructions do not need the deliberate introduction of aberrations, are capable of post-acquisition aberration correction and promise benefits for information transfer, especially at resolutions beyond 1.8 Å.

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Inverse Multislice Ptychography by Layer-Wise Optimisation and Sparse Matrix Decomposition

Cited by 9 publications

References 39 publications

Image Recovery for Blind Polychromatic Ptychography

Image Recovery for Blind Polychromatic Ptychography

Imaging built-in electric fields and light matter by Fourier-precession TEM

Dynamical scattering in ice-embedded proteins in conventional and scanning transmission electron microscopy

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