arXiv subjects

Jianwei Miao

Publications and source records attributed to Jianwei Miao.

48 records · Page 3Linked to original sources

arXiv2014

Three-dimensional coherent X-ray diffraction imaging of a whole, frozen-hydrated cell

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffraction imaging (cryo-CDI) could bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, we report for the first time 3D cryo-CDI of a whole, frozen-hydrated cell - in this case a Neospora caninum tachyzoite - using 8 keV X-rays. Our 3D reconstruction reveals the surface and internal morphology of the cell, including its complex, polarized sub-cellular architecture with a 3D resolution of ~75-100 nm, which is presently limited by the coherent X-ray flux and detector size. Given the imminent improvement in the coherent X-ray flux at the facilities worldwide, our work forecasts the possibility of routine 3D imaging of frozen-hydrated cells with spatial resolutions in the tens of nanometres.

physics.bio-ph↗

arXiv2014

Phase Retrieval with Application to Optical Imaging

This review article provides a contemporary overview of phase retrieval in optical imaging, linking the relevant optical physics to the information processing methods and algorithms. Its purpose is to describe the current state of the art in this area, identify challenges, and suggest vision and areas where signal processing methods can have a large impact on optical imaging and on the world of imaging at large, with applications in a variety of fields ranging from biology and chemistry to physics and engineering.

cs.IT↗

arXiv2013

Multi-Shell Ankylography

Three-dimensional (3D) imaging techniques appeal to a broad range of scientific and industrial applications. Typically, projection slice theorem enables multiple two-dimensional (2D) projections of an object to be combined in the Fourier domain to yield a 3D image. However, traditional techniques require a significant number of projections. The significant number of views required in conventional tomography not only complicates such imaging modalities, but also limits their ability to image samples that are sensitive to radiation dose or are otherwise unstable in time. In this work, we demonstrate through numerical simulations and an eigenvalue analysis that a recently developed technique called ankylography enables 3D image reconstruction using much fewer views than conventional tomography. Such a technique with the ability to obtain the 3D structure information from a few views is expected to find applications in both optical and x-ray imaging fields.

physics.optics↗

arXiv2013

Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D structure studies of such particles at nanometer resolution on femtosecond time scales.

physics.optics↗

arXiv2012

Oversampling smoothness (OSS): an effective algorithm for phase retrieval of noisy diffraction intensities

Coherent diffraction imaging (CDI) is high-resolution lensless microscopy that has been applied to image a wide range of specimens using synchrotron radiation, X-ray free electron lasers, high harmonic generation, soft X-ray laser and electrons. Despite these rapid advances, it remains a challenge to reconstruct fine features in weakly scattering objects such as biological specimens from noisy data. Here we present an effective iterative algorithm, termed oversampling smoothness (OSS), for phase retrieval of noisy diffraction intensities. OSS exploits the correlation information among the pixels or voxels in the region outside of a support in real space. By properly applying spatial frequency filters to the pixels or voxels outside the support at different stage of the iterative process (i.e. a smoothness constraint), OSS finds a balance between the hybrid input-output (HIO) and error reduction (ER) algorithms to search for a global minimum in solution space, while reducing the oscillations in the reconstruction. Both our numerical simulations with Poisson noise and experimental data from a biological cell indicate that OSS consistently outperforms the HIO, ER-HIO and noise robust (NR)-HIO algorithms at all noise levels in terms of accuracy and consistency of the reconstructions. We expect OSS to find application in the rapidly growing CDI field as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed.

physics.optics↗

arXiv2012

Electron tomography at 2.4 Å resolution

Transmission electron microscopy (TEM) is a powerful imaging tool that has found broad application in materials science, nanoscience and biology(1-3). With the introduction of aberration-corrected electron lenses, both the spatial resolution and image quality in TEM have been significantly improved(4,5) and resolution below 0.5 Å has been demonstrated(6). To reveal the 3D structure of thin samples, electron tomography is the method of choice(7-11), with resolutions of ~1 nm^3 currently achievable(10,11). Recently, discrete tomography has been used to generate a 3D atomic reconstruction of a silver nanoparticle 2-3 nm in diameter(12), but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of a ~10 nm gold nanoparticle at 2.4 Å resolution. While we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified at three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply-twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic scale resolution(13-15), but also to improve the spatial resolution and image quality in other tomography fields(7,9,16-20).

cond-mat.mtrl-sci↗

arXiv2011

Potential and Challenge of Ankylography

The concept of ankylography, which under certain circumstances enables 3D structure determination from a single view [1], had ignited a lively debate even before its publication [2,3]. Since then, a number of readers requested the ankylographic reconstruction codes from us. To facilitate a better understanding of ankylography, we posted the source codes of the ankylographic reconstruction on a public website and encouraged interested readers to download the codes and test the method [4]. Those who have tested our codes confirm that the principle of ankylography works. Furthermore, our mathematical analysis and numerical simulations suggest that, for a continuous object with array size of 14x14x14 voxels, its 3D structure can usually be reconstructed from the diffraction intensities sampled on a spherical shell of 1 voxel thick [4]. In some cases where the object does not have very dense structure, ankylography can be applied to reconstruct its 3D image with array size of 25x25x25 voxels [4]. What remains to be elucidated is how to extend ankylography to the reconstruction of larger objects, and what further theoretical, experimental and algorithm developments will be necessary to make ankylography a practical and useful imaging tool. Here we present our up-to-date understanding of the potential and challenge of ankylography. Further, we clarify some misconceptions on ankylography, and respond to technical comments raised by Wei [5] and Wang et al. [6] Finally, it is worthwhile to point out that the potential for recovering 3D information from the Fourier coefficients within a spherical shell may also find application in other fields.

physics.optics↗

arXiv2011

3D Imaging of a Phase Object from a Single Sample Orientation Using an Optical Laser

Ankylography is a new 3D imaging technique, which, under certain circumstances, enables reconstruction of a 3D object from a single sample orientation. Here, we provide a matrix rank analysis to explain the principle of ankylography. We then present an ankylography experiment on a microscale phase object using an optical laser. Coherent diffraction patterns are acquired from the phase object using a planar CCD detector and are projected onto a spherical shell. The 3D structure of the object is directly reconstructed from the spherical diffraction pattern. This work may potentially open the door to a new method for 3D imaging of phase objects in the visible light region. Finally, the extension of ankylography to more complicated and larger objects is suggested.

physics.optics↗

arXiv2009

2nd Response to "Feasibility of 3D reconstruction from a single 2D diffraction measurement"

We present our 2nd response to Thibault's commentary article [1] and his reply [2], in which he commented upon our ankylography paper [3] and our 1st response [4]. In this article, we further explain why we think Thibault's theoretical analysis is flawed and his interpretation of our experiment is incorrect. Furthermore, we provide a quantitative analysis and a numerical experiment to illustrate why ankylography can in principle be applicable to general samples. Finally, we present detailed procedures for our numerical experiment on ankylographic reconstructions, which uses the traditional HIO algorithm only with the positivity constraint [5]. We welcome anyone (including Thibault) interested in ankylography to perform numerical experiments and verify our results. We will be very happy to provide any help if needed.

physics.optics↗

arXiv2009

Response to "Feasibility of 3D reconstruction from a single 2D diffraction measurement"

We present our response to Pierre Thibault's article, titled "Feasibility of 3D reconstruction from a single 2D diffraction measurement" [1], in which he commented upon our recent ankylography paper [2]. While we appreciate Thibault's efforts in promoting further reflection on our paper, we found serious errors both in his understanding and analysis of ankylography: he inaccurately presented the oversampling scheme in ankylography, incorrectly described our reconstruction algorithm and our experiment, and formulated arguments based upon a flawed and overly-restrictive theoretical analysis. Therefore, we conclude that his main claims are either scientifically invalid or a misrepresentation of our claims about ankylography. Below is our detailed point-by-point response to his criticisms.

physics.optics↗

arXiv2009

Three-dimensional structure determination from a single view

The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for 3D structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography (1,2), or by scanning a series of thin sections through the sample, as in confocal microscopy (3). Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 Angstrom resolution and a single poliovirus at 2 - 3 nm resolution from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we demonstrate that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. This approach of obtaining complete 3D structure information from a single view is anticipated to find broad applications in the physical and life sciences. As X-ray free electron lasers (X-FEL) and other coherent X-ray sources are under rapid development worldwide, ankylography potentially opens a door to determining the 3D structure of a biological specimen in a single pulse and allowing for time-resolved 3D structure determination of disordered materials.

cond-mat.mtrl-sci↗

arXiv2008

Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays

Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and myoglobin based on X-ray diffraction analysis in the 1950s, X-ray crystallography has become the primary methodology used to determine the 3D structure of macromolecules. However, biological specimens such as cells, organelles, viruses and many important macromolecules are difficult or impossible to crystallize, and hence their structures are not accessible by crystallography. Here we report, for the first time, the recording and reconstruction of X-ray diffraction patterns from single, unstained viruses. The structure of the viral capsid inside a virion was visualized. This work opens the door for quantitative X-ray imaging of a broad range of specimens from protein machineries, viruses and organelles to whole cells. Moreover, our experiment is directly transferable to the use of X-ray free electron lasers, and represents a major experimental milestone towards the X-ray imaging of single macromolecules.

physics.bio-ph↗