Philipp Pelz - Academia.edu (original) (raw)

Papers by Philipp Pelz

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information), Nov 15, 2020

Nature Communications, Jul 20, 2023

Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespre... more Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespread attention for its ability to image atomic electric fields with sub-Ångstrom spatial resolution. These electric field maps represent the integrated effect of the nucleus, core electrons and valence electrons, and separating their contributions is non-trivial. In this paper, we utilized simultaneously acquired 4D-STEM center of mass (CoM) images and annular dark field (ADF) images to determine the projected electron charge density in monolayer MoS 2. We evaluate the contributions of both the core electrons and the valence electrons to the derived electron charge density; however, due to blurring by the probe shape, the valence electron contribution forms a nearly featureless background while most of the spatial modulation comes from the core electrons. Our findings highlight the importance of probe shape in interpreting charge densities derived from 4D-STEM and the need for smaller electron probes. Four-dimensional scanning transmission electron microscopy (4D-STEM) has become a versatile tool in recent years with applications ranging from measuring nanoscale strain to uncovering thermal vibrations of atoms 1,2. One such 4D-STEM technique measures local electric fields by calculating the center of mass (CoM) of the diffraction pattern 3. In the past few years, sub-Ångstrom electric field and charge density mapping using 4D-STEM CoM imaging has become feasible due to aberration-corrected STEMs and fast pixelated detectors 4-9. Atomic electric fields emerge from a combination of strong nuclear effects and weak valence electrons that form chemical bonds. The ability to map valence electrons with high spatial resolution can potentially lead to new insights about chemical bonding, charge transfer effects, polarization, ferroelectricity, ion transport, and much more 10,11. Imaging valence electrons at the atomic scale is a non-trivial problem. Annular dark field (ADF) STEM, for example, images atom positions based on the high-angle scattering of incident electrons by the nucleus 12,13. Phase contrast high resolution (HR-) TEM can reveal chemical bonding effects due to charge redistribution, but electron orbital charge densities have not been explicitly imaged 14. Electron

arXiv (Cornell University), May 19, 2023

IEEE Signal Processing Magazine, 2022

The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning tra... more The arrival of direct electron detectors (DED) with high frame-rates in the field of scanning transmission electron microscopy has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four dimensional-scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed commonly available computing infrastructure. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis. The 4D Camera, a DED with 87 kHz frame-rate developed at Lawrence Berkeley National Laboratory, reduces the raw data to a linear-index encoded electron event representation (EER). Here we show with experimental data from the 4D Camera that linearindex encoded EER and its direct use in 4D-STEM phase contrast imaging methods enables real-time, interactive phase-contrast from large-area 4D-STEM datasets. We detail the computational complexity advantages of the EER and the necessary computational steps to achieve real-time interactive ptychography and center-of-mass differential phase contrast using commonly available hardware accelerators.

Microscopy and Microanalysis, Jul 12, 2023

One approach to three-dimensional structure determination using the wealth of scattering data in ... more One approach to three-dimensional structure determination using the wealth of scattering data in four-dimensional (4D) scanning transmission electron microscopy (STEM) is the parallax method proposed by Ophus et al. (2019. Advanced phase reconstruction methods enabled by 4D scanning transmission electron microscopy, Microsc Microanal 25, 10-11), which determines the scattering matrix and uses it to synthesize a virtual depth-sectioning reconstruction of the sample structure. Drawing on an equivalence with a hypothetical confocal imaging mode, we derive contrast transfer and point spread functions for this parallax method applied to weakly scattering objects, showing them identical to earlier depth-sectioning STEM modes when only bright field signal is used, but that improved depth resolution is possible if dark field signal can be used. Through a simulation-based study of doped Si, we show that this depth resolution is preserved for thicker samples, explore the impact of shot noise on the parallax reconstructions, discuss challenges to making use of dark field signal, and identify cases where the interpretation of the parallax reconstruction breaks down.

Microscopy and Microanalysis, Aug 1, 2022

arXiv (Cornell University), Nov 15, 2020

Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techn... more Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, Pb 2 Ir 2 O 7 , and yttrium-stabilized zirconia, Y 0.095 Zr 0.905 O 2 , heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb-Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.

$Research paper thumbnail of Reconstructing the Scattering Matrix from Scanning Electron Diffraction Measurements Alone$

arXiv (Cornell University), Aug 28, 2020

Three-dimensional phase-contrast imaging of multiply-scattering samples in x-ray and electron mic... more Three-dimensional phase-contrast imaging of multiply-scattering samples in x-ray and electron microscopy is challenging due to small numerical apertures, the unavailability of wave front shaping optics, and the highly nonlinear inversion required from intensity-only measurements. In this work, we present an algorithm using the scattering matrix formalism to solve the scattering from a noncrystalline medium from scanning diffraction measurements and simultaneously recover the illumination aberrations. We demonstrate our method experimentally in a scanning transmission electron microscope, recovering the scattering matrix of a heterogeneous sample with two layers of multiwall carbon nanotubes filled with TaTe 2 core-shell structures, spaced 10 nm apart in the axial direction. Our work enables phase contrast imaging and materials characterization in multiply-scattering samples at high resolution for a wide range of materials.

Journal of the American Chemical Society, Aug 3, 2023

arXiv (Cornell University), Jun 17, 2022

Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimen... more Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimensional atomic scale structure of samples in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined using phase-contrast single-particle cryo-electron microscopy from thousands of identical proteins, and reconstructions have reached atomic resolution for specific proteins. In materials science, threedimensional atomic structures of complex nanomaterials have been determined using a combination of annular dark field (ADF) scanning transmission electron microscopic (STEM) tomography and subpixel localization of atomic peaks, in a method termed atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform mixed-state electron ptychography from 34.5 million diffraction patterns to reconstruct a high-resolution tilt series of a double wall-carbon nanotube (DW-CNT), encapsulating a complex ZrTe sandwich structure. Class averaging of the resulting reconstructions and subpixel localization of the atomic peaks in the reconstructed volume reveals the complex three-dimensional atomic structure of the core-shell heterostructure with 17 pm precision. From these measurements, we solve the full Zr11Te50 structure, which contains a previously unobserved ZrTe2 phase in the core. The experimental realization of ptychographic atomic electron tomography (PAET) will allow for structural determination of a wide range of nanomaterials which are beam-sensitive or contain light elements.

$Research paper thumbnail of Using a fast hybrid pixel detector for dose-efficient diffraction imaging beam-sensitive organic molecular thin films$

Journal of Physics: Materials

We discuss the benefits and showcase the applications of using a fast, Hybrid-Pixel Detector (HPD... more We discuss the benefits and showcase the applications of using a fast, Hybrid-Pixel Detector (HPD) for 4D-STEM experiments and emphasize that in dose-efficient diffraction imaging the structure of molecular nano-crystallites in an organic solar cell thin film with a recently proposed modality of 4D-Scanning Confocal Electron Diffraction (4D-SCED). With 4D-SCED, spot diffraction patterns form from an interaction area of a few nm while the electron beam rasters over the sample, resulting in high dose effectiveness yet highly demanding on the detector in frame speed, sensitivity, and single-pixel count rate. We compare the datasets acquired with 4D-SCED using a fast HPD with those using state-of-the-art CMOS cameras to map the in-plane orientation of π-stacking nano-crystallites of small molecule DRCN5T in a blend of DRCN5T: PC71BM after solvent vapor annealing. The high-speed CMOS camera, using a scintillator optimized for low doses, showed impressive results for single electron sensi...

Microscopy and Microanalysis

arXiv (Cornell University), Feb 19, 2017

Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic o... more Electron ptychography has seen a recent surge of interest for phase sensitive imaging at atomic or near-atomic resolution. However, applications are so far mainly limited to radiation-hard samples because the required doses are too high for imaging biological samples at high resolution. We propose the use of non-convex, Bayesian optimization to overcome this problem and reduce the dose required for successful reconstruction by two orders of magnitude compared to previous experiments. We suggest to use this method for imaging single biological macromolecules at cryogenic temperatures and demonstrate 2D single-particle reconstructions from simulated data with a resolution of 7.9Å at a dose of 20 e − /Å 2. When averaging over only 15 low-dose datasets, a resolution of 4Å is possible for large macromolecular complexes. With its independence from microscope transfer function, direct recovery of phase contrast and better scaling of signal-to-noise ratio, cryo-electron ptychography may become a promising alternative to Zernike phase-contrast microscopy.

Micron, 2021

Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned ove... more Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned over a sample's surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging methods have made STEM one of the most important tools for atomic-resolution materials science. Many of these imaging methods rely on accurate imaging and diffraction simulations in order to interpret experimental results. However, STEM simulations have traditionally required large calculation times, as modeling the electron scattering requires a separate simulation for each of the typically millions of probe positions. We have created the Prismatic simulation code for fast simulation of STEM experiments with support for multi-CPU and multi-GPU (graphics processing unit) systems, using both the conventional multislice and our recently-introduced PRISM method. In this paper, we introduce Prismatic version 2.0, which adds many new algorithmic improvements, an updated graphical user interface (GUI), post-processing of simulation data, and additional operating modes such as plane-wave TEM. We review various aspects of the simulation methods and codes in detail and provide various simulation examples. Prismatic 2.0 is freely available both as an open-source package that can be run using a C++ or Python command line interface, or GUI, as well within a Docker container environment.

In the recent years, cryo-electron microscopy (cryo-EM) has evolved into a main- stream technique... more In the recent years, cryo-electron microscopy (cryo-EM) has evolved into a main- stream technique to decipher the structure-function relationship of biological specimens from single molecules to whole cells. Cryo-EM relies on the strong interaction of high-energy electrons with matter, which causes a measurable phase shift of the electron wave even for single small macromolecules. Experi- mental methods to measure this phase shift effectively are therefore the key to obtaining higher spatial resolution images or even movies before radiation dam- age destroys the molecule, yet current phase contrast methods suffer several limitations for biological electron microscopy. They are either impractical to im- plement, do not allow to deconvolve the influence of microscope optics from the image, or involve inelastic scattering events after the electron wave has passed the sample, which scramble the acquired phase information. Ptychography creates a high-dimensional phase space map of the im...

Microscopy and Microanalysis

$Research paper thumbnail of Imaging the electron charge density in monolayer MoS2 at the {\AA}ngstrom scale$

arXiv (Cornell University), Oct 17, 2022

arXiv (Cornell University), Nov 15, 2020

Nature Communications

Metal-organic layers (MOLs) are highly attractive for application in catalysis, separation, sensi... more Metal-organic layers (MOLs) are highly attractive for application in catalysis, separation, sensing and biomedicine, owing to their tunable framework structure. However, it is challenging to obtain comprehensive information about the formation and local structures of MOLs using standard electron microscopy methods due to serious damage under electron beam irradiation. Here, we investigate the growth processes and local structures of MOLs utilizing a combination of liquid-phase transmission electron microscopy, cryogenic electron microscopy and electron ptychography. Our results show a multistep formation process, where precursor clusters first form in solution, then they are complexed with ligands to form non-crystalline solids, followed by the arrangement of the cluster-ligand complex into crystalline sheets, with additional possible growth by the addition of clusters to surface edges. Moreover, high-resolution imaging allows us to identify missing clusters, dislocations, loop and ...