Ptychographic Dataset Research Articles

Ptychographic phase retrieval via a deep-learning-assisted iterative algorithm.

Ptychography is a powerful computational imaging technique with microscopic imaging capability and adaptability to various specimens. To obtain an imaging result, it requires a phase-retrieval algorithm whose performance directly determines the imaging quality. Recently, deep neural network (DNN)-based phase retrieval has been proposed to improve the imaging quality from the ordinary model-based iterative algorithms. However, the DNN-based methods have some limitations because of the sensitivity to changes in experimental conditions and the difficulty of collecting enough measured specimen images for training the DNN. To overcome these limitations, a ptychographic phase-retrieval algorithm that combines model-based and DNN-based approaches is proposed. This method exploits a DNN-based denoiser to assist an iterative algorithm like ePIE in finding better reconstruction images. This combination of DNN and iterative algorithms allows the measurement model to be explicitly incorporated into the DNN-based approach, improving its robustness to changes in experimental conditions. Furthermore, to circumvent the difficulty of collecting the training data, it is proposed that the DNN-based denoiser be trained without using actual measured specimen images but using a formula-driven supervised approach that systemically generates synthetic images. In experiments using simulation based on a hard X-ray ptychographic measurement system, the imaging capability of the proposed method was evaluated by comparing it with ePIE and rPIE. These results demonstrated that the proposed method was able to reconstruct higher-spatial-resolution images with half the number of iterations required by ePIE and rPIE, even for data with low illumination intensity. Also, the proposed method was shown to be robust to its hyperparameters. In addition, the proposed method was applied to ptychographic datasets of a Simens star chart and ink toner particles measured at SPring-8 BL24XU, which confirmed that it can successfully reconstruct images from measurement scans with a lower overlap ratio of the illumination regions than is required by ePIE and rPIE.

ProSPyX: software for post-processing images of X-ray ptychography with spectral capabilities.

X-ray ptychography is a coherent diffraction imaging technique based on acquiring multiple diffraction patterns obtained through the illumination of the sample at different partially overlapping probe positions. The diffraction patterns collected are used to retrieve the complex transmittivity function of the sample and the probe using a phase retrieval algorithm. Absorption or phase contrast images of the sample as well as the real and imaginary parts of the probe function can be obtained. Furthermore, X-ray ptychography can also provide spectral information of the sample from absorption or phase shift images by capturing multiple ptychographic projections at varying energies around the resonant energy of the element of interest. However, post-processing of the images is required to extract the spectra. To facilitate this, ProSPyX, a Python package that offers the analysis tools and a graphical user interface required to process spectral ptychography datasets, is presented. Using the PyQt5 Python open-source module for development and design, the software facilitates extraction of absorption and phase spectral information from spectral ptychographic datasets. It also saves the spectra in file formats compatible with other X-ray absorption spectroscopy data analysis software tools, streamlining integration into existing spectroscopic data analysis pipelines. To illustrate its capabilities, ProSPyX was applied to process the spectral ptychography dataset recently acquired on a nickel wire at the SWING beamline of the SOLEIL synchrotron.

Exact inversion of partially coherent dynamical electron scattering for picometric structure retrieval

The greatly nonlinear diffraction of high-energy electron probes focused to subatomic diameters frustrates the direct inversion of ptychographic data sets to decipher the atomic structure. Several iterative algorithms have been proposed to yield atomically-resolved phase distributions within slices of a 3D specimen, corresponding to the scattering centers of the electron wave. By pixelwise phase retrieval, current approaches do not only involve orders of magnitude more free parameters than necessary, but also neglect essential details of scattering physics such as the atomistic nature of the specimen and thermal effects. Here, we introduce a parametrized, fully differentiable scheme employing neural network concepts which allows the inversion of ptychographic data by means of entirely physical quantities. Omnipresent thermal diffuse scattering in thick specimens is treated accurately using frozen phonons, and atom types, positions and partial coherence are accounted for in the inverse model as relativistic scattering theory demands. Our approach exploits 4D experimental data collected in an aberration-corrected momentum-resolved scanning transmission electron microscopy setup. Atom positions in a 20 nm thick PbZr0.2Ti0.8O3 ferroelectric are measured with picometer precision, including the discrimination of different atom types and positions in mixed columns.

Super-resolution electron ptychography of low dimensional materials at 30 keV: Beyond the detector limit

We demonstrate that electron ptychographic phase reconstruction can recover spatial frequencies higher than those directly recorded in the experimental electron diffraction patterns. This ability to recover high angle information from the oversampled low angle information allows an annular detector to be inserted which partially shadows a lower pixelated detector to simultaneously record a conventional annular dark field image and a ptychographic dataset. We apply this approach to 30 keV imaging of monolayer molybdenum disulfide and achieve an Abbe limited resolution of 1.2 ± 0.1Å in our reconstructions.

High-speed X-ray ptychographic tomography

X-ray ptychography is a coherent scanning imaging technique widely used at synchrotron facilities for producing quantitative phase images beyond the resolution limit of conventional x-ray optics. The scanning nature of the technique introduces an inherent overhead to the collection at every scan position and limits the acquisition time of each 2D projection. The overhead associated with motion can be minimised with a continuous-scanning approach. Here we present an acquisition architecture based on continuous-scanning and up-triggering which allows to record ptychographic datasets at up to 9 kHz. We demonstrate the method by applying it to record 2D scans at up to 273 µm2/s and 3D scans of a (20 µm)3 volume in less than three hours. We discuss the current limitations and the outlook toward the development of sub-second 2D acquisition and minutes-long 3D ptychographic tomograms.

Reconstruction method of a ptychographic dataset with unknown positions.

Wavefield drift or wobbling occurs quite often in coherent scanning systems such as satellite laser communication, laser pointing of high-power lasers, or microscopy. The uncertainty of wavefront positions might result in blurred images or large measurement errors. Here we propose an iterative approach that can retrieve both the drift positions and complex-valued distribution of the wavefield from a ptychographic diffraction intensity dataset. We demonstrate the feasibility and effectiveness of the method in numerical simulation and an optical experiment. The method requires little a priori knowledge and thus would open up new opportunities in many fields.

General method for complex-wave fields registration with high fidelity.

In the field of optical imaging, the image registration method could be applied to realize a large field of view along with high resolution. The traditional image registration methods are mostly conceived for intensity images and might fail for complex-valued images. Especially, those methods do not account for the random phase offset associated with phase. In this paper, we proposed a general method for complex-wave field registration. A similar procedure has been proposed for the reconstruction of the ptychographic dataset, but here is modified for the registration of general wave fields. The method can efficiently separate the illumination and object function, refine the positions of each wavefront, and thus provide a stitched wide-field object wave with high fidelity. Simulation and experimental results applied to register the wave fields obtained from digital holographic microscopy are given to verify the feasibility of the method. This method would have potential applications in large-field high-resolution microscopy, adaptive imaging, remote sensing and the measurement of structured optical fields.

Atomic Resolution Defocused Electron Ptychography at Low Dose with a Fast, Direct Electron Detector

Electron ptychography has recently attracted considerable interest for high resolution phase-sensitive imaging. However, to date studies have been mainly limited to radiation resistant samples as the electron dose required to record a ptychographic dataset is too high for use with beam-sensitive materials. Here we report defocused electron ptychography using a fast, direct-counting detector to reconstruct the transmission function, which is in turn related to the electrostatic potential of a two-dimensional material at atomic resolution under various low dose conditions.

High dose efficiency atomic resolution imaging via electron ptychography

Radiation damage places a fundamental limitation on the ability of microscopy to resolve many types of materials at high resolution. Here we evaluate the dose efficiency of phase contrast imaging with electron ptychography. The method is found to be far more resilient to temporal incoherence than conventional and spherical aberration optimized phase contrast imaging, resulting in significantly greater clarity at a given dose. This robustness is explained by the presence of achromatic lines in the four dimensional ptychographic dataset.

Data compression strategies for ptychographic diffraction imaging

Abstract Ptychography is a computational imaging method for solving inverse scattering problems. To date, the high amount of redundancy present in ptychographic data sets requires computer memory that is orders of magnitude larger than the retrieved information. Here, we propose and compare data compression strategies that significantly reduce the amount of data required for wavefield inversion. Information metrics are used to measure the amount of data redundancy present in ptychographic data. Experimental results demonstrate the technique to be memory efficient and stable in the presence of systematic errors such as partial coherence and noise.

Divide and update: towards single-shot object and probe retrieval for near-field holography.

We present a phase reconstruction scheme for X-ray near-field holographic imaging based on a separability constraint for probe and object. In order to achieve this, we have devised an algorithm which requires only two measurements - with and without an object in the beam. This scheme is advantageous if the standard flat-field correction fails and a full ptychographic dataset can not be acquired, since either object or probe are dynamic. The scheme is validated by numerical simulations and by a proof-of-concept experiment using highly focused undulator radiation of the beamline ID16a of the European Synchrotron Radiation Facility (ESRF).

Background noise removal in x-ray ptychography

Ptychography is a diffraction-based x-ray microscopy method that removes the resolution limit imposed by image-forming optical elements. However, background noise in the recorded diffraction patterns will degrade the reconstructed images and may cause reconstruction failure. Removal of the background noise from a ptychography dataset is an important but rather ambiguous prereconstruction data processing step because high-spatial-frequency diffraction signals are inevitably partly wiped out along with the noise. In this paper, several newly designed techniques for removing background noise from experimental ptychographic datasets are provided. Meanwhile, effects of residual background noise and high-frequency signal loss on reconstructed image quality are discussed in detail. The image quality is assessed quantitatively by the power spectral density analysis method and spatial resolution calculation. Both the simulated and experimental results indicate that the positive effect of noise removal by these methods clearly exceeds the negative effect of the accompanied high-spatial-frequency signal loss because part of the lost signals can be recovered by the improved consistencies between neighboring diffraction patterns by the noise removal.

Denoised Wigner distribution deconvolution via low-rank matrix completion.

Wigner distribution deconvolution (WDD) is a decades-old method for recovering phase from intensity measurements. Although the technique offers an elegant linear solution to the quadratic phase retrieval problem, it has seen limited adoption due to its high computational/memory requirements and the fact that the technique often exhibits high noise sensitivity. Here, we propose a method for noise suppression in WDD via low-rank noisy matrix completion. Our technique exploits the redundancy of an object's phase space to denoise its WDD reconstruction. We show in model calculations that our technique outperforms other WDD algorithms as well as modern iterative methods for phase retrieval such as ptychography. Our results suggest that a class of phase retrieval techniques relying on regularized direct inversion of ptychographic datasets (instead of iterative reconstruction techniques) can provide accurate quantitative phase information in the presence of high levels of noise.

Ptychographic microscope for three-dimensional imaging.

Ptychography is a coherent imaging technique that enables an image of a specimen to be generated from a set of diffraction patterns. One limitation of the technique is the assumption of a multiplicative interaction between the illuminating coherent beam and the specimen, which restricts ptychography to samples no thicker than a few tens of micrometers in the case of visible-light imaging at micron-scale resolution. By splitting a sample into axial sections, we demonstrated in recent work that this thickness restriction can be relaxed and whats-more, that coarse optical sectioning can be realized using a single ptychographic data set. Here we apply our technique to data collected from a modified optical microscope to realize a reduction in the optical sectioning depth to 2 μm in the axial direction for samples up to 150 μm thick. Furthermore, we increase the number of sections that are imaged from 5 in our previous work to 34 here. Our results compare well with sectioned images collected from a confocal microscope but have the added advantage of strong phase contrast, which removes the need for sample staining.

Coherent laser scanning diffraction microscopy

Coherent diffractive imaging (CDI) is a promising approach to high-resolution x-ray microscopy. While CDI typically has a rather limited field of view, this problem can be solved by ptychography, a technique for which an extended object is raster scanned by a compact coherent illumination probe. Significant overlap of illumination for adjacent scan points allows then a self-consistent reconstruction from the entirety of collected coherent diffraction patterns. However, current reconstruction schemes require accurate a priori knowledge of the probe. Our recently developed new algorithm for ptychographic data sets allows us to simultaneously reconstruct both object and illuminating probe. We demonstrate the application of the new method in a test experiment with visible laser light showing that intricate illumination functions can be retrieved reliably.

Probe retrieval in ptychographic coherent diffractive imaging

Ptychography is a coherent diffractive imaging method that uses multiple diffraction patterns obtained through the scan of a localized illumination on the specimen. Until recently, reconstruction algorithms for ptychographic datasets needed the a priori knowledge of the incident illumination. A new reconstruction procedure that retrieves both the specimen's image and the illumination profile was recently demonstrated with hard X-ray data. We present here the algorithm in greater details and illustrate its practical applicability with a visible light dataset. Improvements in the quality of the reconstruction are shown and compared to previous reconstruction techniques. Implications for future applications with other types of radiation are discussed.