X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning

Deng, Junjing; Vine, D. J.; Chen, Si; Jin, Qiaoling; Nashed, Youssef S. G.; Peterka, Tom; Vogt, Stefan; Jacobsen, Chris

doi:10.1038/s41598-017-00569-y

Cited by 97 publications

(67 citation statements)

References 79 publications

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“…The attraction of this technique comes from its capability of recovering both the complex-valued probe and object functions, a blind deconvolution, as well as its ability of breaking the resolution barrier set by the focusing optics. It gains increasing popularity in recent years for its robustness in practice and was used successfully for many imaging applications in different fields [4][5][6][7][8][9]. The major challenge of this technique resides in the fact that the mathematical problem is non-convex and ill posed.…”

Section: Introductionmentioning

confidence: 99%

Ptychographic phase retrieval by proximal algorithms

Yan

2020

New J. Phys.

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We derive a set of ptychography phase-retrieval iterative engines based on proximal algorithms originally developed in convex optimization theory, and discuss their connections with existing ones. The use of proximal operator creates a simple frame work that allows us to incorporate the effect of noise from a maximum-likelihood (ML) principle. We focus on three particular algorithms, namely proximal minimization, alternating direction method of multiplier and accelerated proximal gradient (APG). We benchmark their performance with numerical simulations, and discuss their optimal conditions for convergence and accuracy. An experimental dataset is used to demonstrate their effectiveness as well, in which case an array of cubic Au nanoparticles with a size of 50 nm is imaged. We show that with the presence of Poisson noise, a dataset with photon counts up to 10 4 at one detector pixel already requires ML-based methods to achieve a stable convergence. Among the three algorithms derived in this work, APG method is reported first time for its application in ptychographic reconstruction and shows superior performance in terms of both accuracy and convergence rate with a noisy dataset.

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Section: Introductionmentioning

confidence: 99%

Ptychographic phase retrieval by proximal algorithms

Yan

2020

New J. Phys.

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“…Images of 5-μm-thick cryogenically cooled cells were obtained by water-window absorption-based imaging at about 30 nm resolution [2,4] at about 1 GGy dose. Cryogenically cooled cells of 18 μm thickness were imaged by ptychography at 6.2 keV photon energy, achieving 180-nm resolution at 670 kGy [21], and a 5-μm-wide alga cell was imaged in a similar fashion at 5.2 keV photon energy to achieve 18-nm resolution at 29 MGy [22]. (In the latter case, high-resolution fluorescence maps were obtained simultaneously.)…”

Section: Introductionmentioning

confidence: 99%

Dose efficient Compton X-ray microscopy

Villanueva-Pérez¹,

Bajt²,

Chapman³

2018

Optica

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X-ray imaging techniques have proven invaluable to study biological systems at high resolution due to the penetration power and short wavelength of this radiation. In practice, the resolution and sensitivity of current X-ray imaging techniques are not limited by the performance of optics or image-recovery methods but by radiation damage. We propose the use of Compton (inelastic) X-ray scattering for high-resolution cellular imaging and provide a study of a scanning microscope geometry that requires a dose to achieve a given resolution that is three orders of magnitude lower than for coherent (elastic) scattering. We find that the dose per imaging signal is minimized at a photon energy of 64 keV. This corresponds to a short enough wavelength (0.02 nm) to provide nanometer transverse resolution and micrometer depth of field for tomographic imaging of whole cells. The microscope could be implemented at future high-energy and high-brightness synchrotron-radiation facilities to provide images of unsectioned and unlabeled cells in their native conditions at enough detail to bridge the techniques of super-resolution optical microscopy and cryo-electron microscopy. © 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement OCIS codes: (110.7440) X-ray imaging; (340.7460) X-ray microscopy; (170.3880) Medical and biological imaging.

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“…In x-ray ptychography experiments, this estimate has been found to agree within 20% of what is required for imaging integrated circuit features [14] and frozen hydrated biological specimens [56] using iterative phase retrieval algorithms. This indicates that the algorithms themselves can be robust to noise, and work at the limit of the minimally required photon exposure.…”

Section: Demonstrationmentioning

confidence: 93%

3D x-ray imaging of continuous objects beyond the depth of focus limit

Gilles¹,

Nashed²,

Du³

et al. 2018

Optica

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X-ray ptychography is becoming the standard method for sub-30 nm imaging of thick extended samples. Available algorithms and computing power have traditionally restricted sample reconstruction to 2D slices. We build on recent progress in optimization algorithms and high performance computing to solve the ptychographic phase retrieval problem directly in 3D. Our approach addresses samples that do not fit entirely within the depth of focus of the imaging system. Such samples pose additional challenges because of internal diffraction effects within the sample. We demonstrate our approach on a computational sample modeled with 17 million complex variables.

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X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning

Cited by 97 publications

References 79 publications

Ptychographic phase retrieval by proximal algorithms

Ptychographic phase retrieval by proximal algorithms

Dose efficient Compton X-ray microscopy

3D x-ray imaging of continuous objects beyond the depth of focus limit

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