Real space iterative reconstruction for vector tomography (RESIRE-V).

Tomography has had an important impact on the physical, biological, and medical sciences. To date, most tomographic applications have been focused on 3D scalar reconstructions. However, in some crucial applications, vector tomography is required to reconstruct 3D vector fields such as the electric and magnetic fields. Over the years, several vector tomography methods have been developed. Here, we present the mathematical foundation and algorithmic implementation of REal Space Iterative REconstruction for Vector tomography, termed RESIRE-V. RESIRE-V uses multiple tilt series of projections and iterates between the projections and a 3D reconstruction. Each iteration consists of a forward step using the Radon transform and a backward step using its transpose, then updates the object via gradient descent. Incorporating with a 3D support constraint, the algorithm iteratively minimizes an error metric, defined as the difference between the measured and calculated projections. The algorithm can also be used to refine the tilt angles and further improve the 3D reconstruction. To validate RESIRE-V, we first apply it to a simulated data set of the 3D magnetization vector field, consisting of two orthogonal tilt series, each with a missing wedge. Our quantitative analysis shows that the three components of the reconstructed magnetization vector field agree well with the ground-truth counterparts. We then use RESIRE-V to reconstruct the 3D magnetization vector field of a ferromagnetic meta-lattice consisting of three tilt series. Our 3D vector reconstruction reveals the existence of topological magnetic defects with positive and negative charges. We expect that RESIRE-V can be incorporated into different imaging modalities as a general vector tomography method. To make the algorithm accessible to a broad user community, we have made our RESIRE-V MATLAB source codes and the data freely available at https://github.com/minhpham0309/RESIRE-V .

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography.

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at  https://zenodo.org/record/7273314 .

Three-dimensional topological magnetic monopoles and their interactions in a ferromagnetic meta-lattice.

Topological magnetic monopoles (TMMs), also known as hedgehogs or Bloch points, are three-dimensional (3D) non-local spin textures that are robust to thermal and quantum fluctuations due to the topology protection1-4. Although TMMs have been observed in skyrmion lattices1,5, spinor Bose-Einstein condensates6,7, chiral magnets8, vortex rings2,9 and vortex cores10, it has been difficult to directly measure the 3D magnetization vector field of TMMs and probe their interactions at the nanoscale. Here we report the creation of 138 stable TMMs at the specific sites of a ferromagnetic meta-lattice at room temperature. We further develop soft X-ray vector ptycho-tomography to determine the magnetization vector and emergent magnetic field of the TMMs with a 3D spatial resolution of 10 nm. This spatial resolution is comparable to the magnetic exchange length of transition metals11, enabling us to probe monopole-monopole interactions. We find that the TMM and anti-TMM pairs are separated by 18.3 ± 1.6 nm, while the TMM and TMM, and anti-TMM and anti-TMM pairs are stabilized at comparatively longer distances of 36.1 ± 2.4 nm and 43.1 ± 2.0 nm, respectively. We also observe virtual TMMs created by magnetic voids in the meta-lattice. This work demonstrates that ferromagnetic meta-lattices could be used as a platform to create and investigate the interactions and dynamics of TMMs. Furthermore, we expect that soft X-ray vector ptycho-tomography can be broadly applied to quantitatively image 3D vector fields in magnetic and anisotropic materials at the nanoscale.

5-Formylcytosine weakens the G-C pair and imparts local conformational fluctuations to DNA duplexes.

DNA epigenetic modifications such as 5-methyl (5mC), 5-hydroxymethyl (5hmC), 5-formyl (5fC) and 5-carboxyl (5caC) cytosine have unique and specific biological roles. Crystallographic studies of 5mC containing duplexes were conducted in the A-, B- or the intermediate E-DNA polymorphic forms. 5fC-modified duplexes initially observed in the disputed F-DNA architecture were subsequently crystallized in the A-form, suggesting that epigenetic modifications enable DNA sequences to adopt diverse conformational states that plausibly contribute to their function. Solution-state studies of these modifications were found in the B-DNA form, with marked differences in the conformational flexibility of 5fC containing duplexes in comparison to C/5mC containing duplexes, compromising the DNA duplex's stability. Herein, we systematically evaluate sensitive and commonly inaccessible NMR parameters to map the subtle differences between C, 5mC, and their oxidized (5hmC/5fC) counterparts. We observe that 15N/1H chemical shifts effectively report on the weakening of 5fC-G Watson-Crick base-pair H-bonding, extending the instability beyond any achievable within the sequence-specific changes in DNA. Triple 5fC containing sequences propagate the destabilization farther from the site of modifications, explaining reduced duplex stability upon multiple modifications. Additionally, scalar and residual dipolar coupling measurements unravel local sugar pucker fluctuations. One-bond 13C-1H scalar coupling measurements point towards a significant deviation away from the anticipated C2'-endo pucker for the 5fC modified nucleotide. Structural models obtained employing 13C-1H residual dipolar couplings and inter-proton distances corroborate the sugar pucker's deviation for 5fC modified DNA duplexes. The changes in the sugar pucker equilibria remain local to the 5fC modified nucleotide sans additive/long-range effects arising from multiple contiguous modifications. These observations highlight the impact of a major groove modification that alters the physical properties of DNA duplex without disturbing the Watson-Crick face. The changes observed in our studies for the 5fC containing DNA contrast with the perturbations induced by damage/lesion highlight the varied conformational preferences that modified nucleobases impart to the DNA duplex. As sequence-specific DNA transactions are rooted in the base-pair stability and pucker deviations, the observed structural perturbations for 5fC-modified DNA potentially play critical functional roles, such as protein-DNA recognition and interactions.

Determining the three-dimensional atomic structure of an amorphous solid.

Amorphous solids such as glass, plastics and amorphous thin films are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells1-4. However, owing to the lack of long-range order, the three-dimensional (3D) atomic structure of amorphous solids has so far eluded direct experimental determination5-15. Here we develop an atomic electron tomography reconstruction method to experimentally determine the 3D atomic positions of an amorphous solid. Using a multi-component glass-forming alloy as proof of principle, we quantitatively characterize the short- and medium-range order of the 3D atomic arrangement. We observe that, although the 3D atomic packing of the short-range order is geometrically disordered, some short-range-order structures connect with each other to form crystal-like superclusters and give rise to medium-range order. We identify four types of crystal-like medium-range order-face-centred cubic, hexagonal close-packed, body-centred cubic and simple cubic-coexisting in the amorphous sample, showing translational but not orientational order. These observations provide direct experimental evidence to support the general framework of the efficient cluster packing model for metallic glasses10,12-14,16. We expect that this work will pave the way for the determination of the 3D structure of a wide range of amorphous solids, which could transform our fundamental understanding of non-crystalline materials and related phenomena.

X-ray linear dichroic ptychography.

Biominerals such as seashells, coral skeletons, bone, and tooth enamel are optically anisotropic crystalline materials with unique nanoscale and microscale organization that translates into exceptional macroscopic mechanical properties, providing inspiration for engineering new and superior biomimetic structures. Using Seriatopora aculeata coral skeleton as a model, here, we experimentally demonstrate X-ray linear dichroic ptychography and map the c-axis orientations of the aragonite (CaCO3) crystals. Linear dichroic phase imaging at the oxygen K-edge energy shows strong polarization-dependent contrast and reveals the presence of both narrow (<35°) and wide (>35°) c-axis angular spread in the coral samples. These X-ray ptychography results are corroborated by four-dimensional (4D) scanning transmission electron microscopy (STEM) on the same samples. Evidence of co-oriented, but disconnected, corallite subdomains indicates jagged crystal boundaries consistent with formation by amorphous nanoparticle attachment. We expect that the combination of X-ray linear dichroic ptychography and 4D STEM could be an important multimodal tool to study nano-crystallites, interfaces, nucleation, and mineral growth of optically anisotropic materials at multiple length scales.

Potential of Attosecond Coherent Diffractive Imaging.

Attosecond science has been transforming our understanding of electron dynamics in atoms, molecules, and solids. However, to date almost all of the attoscience experiments have been based on spectroscopic measurements because attosecond pulses have intrinsically very broad spectra due to the uncertainty principle and are incompatible with conventional imaging systems. Here we report an important advance towards achieving attosecond coherent diffractive imaging. Using simulated attosecond pulses, we simultaneously reconstruct the spectrum, 17 probes, and 17 spectral images of extended objects from a set of ptychographic diffraction patterns. We further confirm the principle and feasibility of this method by successfully performing a ptychographic coherent diffractive imaging experiment using a light-emitting diode with a broad spectrum. We believe this work clears the way to an unexplored domain of attosecond imaging science, which could have a far-reaching impact across different disciplines.

Semi-implicit relaxed Douglas-Rachford algorithm (sDR) for ptychography.

Alternating projection based methods, such as ePIE and rPIE, have been used widely in ptychography. However, they only work well if there are adequate measurements (diffraction patterns); in the case of sparse data (i.e. fewer measurements) alternating projection underperforms and might not even converge. In this paper, we propose semi-implicit relaxed Douglas-Rachford (sDR), an accelerated iterative method, to solve the classical ptychography problem. Using both simulated and experimental data, we show that sDR improves the convergence speed and the reconstruction quality relative to extended ptychographic iterative engine (ePIE) and regularized ptychographic iterative engine (rPIE). Furthermore, in certain cases when sparsity is high, sDR converges while ePIE and rPIE fail or encounter slow convergence. To facilitate others to use the algorithm, we post the Matlab source code of sDR on a public website (www.physics.ucla.edu/research/imaging/sDR/index.html). We anticipate that this algorithm can be generally applied to the ptychographic reconstruction of a wide range of samples in the physical and biological sciences.

Multimodal x-ray and electron microscopy of the Allende meteorite.

Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems.

Generalized proximal smoothing (GPS) for phase retrieval.

In this paper, we report the development of the generalized proximal smoothing (GPS) algorithm for phase retrieval of noisy data. GPS is a optimization-based algorithm, in which we relax both the Fourier magnitudes and support constraint. We relax the support constraint by incorporating the Moreau-Yosida regularization and heat kernel smoothing, and derive the associated proximal mapping. We also relax the magnitude constraint into a least squares fidelity term, whose proximal mapping is available as well. GPS alternatively iterates between the two proximal mappings in primal and dual spaces, respectively. Using both numerical simulation and experimental data, we show that GPS algorithm consistently outperforms the classical phase retrieval algorithms such as hybrid input-output (HIO) and oversampling smoothness (OSS), in terms of the convergence speed, consistency of the phase retrieval, and robustness to noise.

In situ coherent diffractive imaging.

Coherent diffractive imaging (CDI) has been widely applied in the physical and biological sciences using synchrotron radiation, X-ray free-electron laser, high harmonic generation, electrons, and optical lasers. One of CDI's important applications is to probe dynamic phenomena with high spatiotemporal resolution. Here, we report the development of a general in situ CDI method for real-time imaging of dynamic processes in solution. By introducing a time-invariant overlapping region as real-space constraint, we simultaneously reconstructed a time series of complex exit wave of dynamic processes with robust and fast convergence. We validated this method using optical laser experiments and numerical simulations with coherent X-rays. Our numerical simulations further indicated that in situ CDI can potentially reduce radiation dose by more than an order of magnitude relative to conventional CDI. With further development, we envision in situ CDI could be applied to probe a range of dynamic phenomena in the future.

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity.

We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 ± 1.0 nm and 4.0 ± 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity.

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging.

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.