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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

AutoPhaseNN: unsupervised physics-aware deep learning of 3D nanoscale Bragg coherent diffraction imaging

Abstract The problem of phase retrieval underlies various imaging methods from astronomy to nanoscale imaging. Traditional phase retrieval methods are iterative and are therefore computationally expensive. Deep learning (DL) models have been developed to either provide learned priors or completely replace phase retrieval. However, such models require vast amounts of labeled data, which can only be obtained through simulation or performing computationally prohibitive phase retrieval on experimental datasets. Using 3D X-ray Bragg coherent diffraction imaging (BCDI) as a representative technique, we demonstrate AutoPhaseNN, a DL-based approach which learns to solve the phase problem without labeled data. By incorporating the imaging physics into the DL model during training, AutoPhaseNN learns to invert 3D BCDI data in a single shot without ever being shown real space images. Once trained, AutoPhaseNN can be effectively used in the 3D BCDI data inversion about 100× faster than iterative phase retrieval methods while providing comparable image quality.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Real-time coherent diffraction inversion using deep generative networks

Abstract Phase retrieval, or the process of recovering phase information in reciprocal space to reconstruct images from measured intensity alone, is the underlying basis to a variety of imaging applications including coherent diffraction imaging (CDI). Typical phase retrieval algorithms are iterative in nature, and hence, are time-consuming and computationally expensive, making real-time imaging a challenge. Furthermore, iterative phase retrieval algorithms struggle to converge to the correct solution especially in the presence of strong phase structures. In this work, we demonstrate the training and testing of CDI NN, a pair of deep deconvolutional networks trained to predict structure and phase in real space of a 2D object from its corresponding far-field diffraction intensities alone. Once trained, CDI NN can invert a diffraction pattern to an image within a few milliseconds of compute time on a standard desktop machine, opening the door to real-time imaging.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2010

Hybrid Architecture Active Wavefront Sensing and Control

A method was developed for performing relatively high-speed wavefront sensing and control to overcome thermal instabilities in a segmented primary mirror telescope [e.g., James Webb Space Telescope (JWST) at L2], by using the onboard fine guidance sensor (FGS) to minimize expense and complexity. This FGS performs centroiding on a bright star to feed the information to the pointing and control system. The proposed concept is to beam split the image of the guide star (or use a single defocused guide star image) to perform wavefront sensing using phase retrieval techniques. Using the fine guidance sensor star image for guiding and fine phasing eliminates the need for other, more complex ways of achieving very accurate sensing and control that is needed for UV-optical applications. The phase retrieval occurs nearly constantly, so passive thermal stability over fourteen days is not required. Using the FGS as the sensor, one can feed segment update information to actuators on the primary mirror that can update the primary mirror segment fine phasing with this frequency. Because the thermal time constants of the primary mirror are very slow compared to this duration, the mirror will appear extremely stable during observations (to the level of accuracy of the sensing and control). The sensing can use the same phase retrieval techniques as the JWST by employing an additional beam splitter, and having each channel go through a weak lens (one positive and one negative). The channels can use common or separate detectors. Phase retrieval can be performed onboard. The actuation scheme would include a coarse stage able to achieve initial alignment of several millimeters of range (similar to JWST and can use a JWST heritage sensing approach in the science camera) and a fine stage capable of continual updates.

Feinberg, Lee↗
DOE OSTI2014

Moiré deflectometry using the Talbot-Lau interferometer as refraction diagnostic for High Energy Density plasmas at energies below 10 keV

The highly localized density gradients expected in High Energy Density (HED) plasma experiments can be characterized by x-ray phase-contrast imaging in addition to conventional attenuation radiography. Moiré deflectometry using the Talbot-Lau grating interferometer setup is an attractive HED diagnostic due to its high sensitivity to refraction induced phase shifts. We report on the adaptation of such a system for operation in the sub-10 keV range by using a combination of free standing and ultrathin Talbot gratings. This new x-ray energy explored matches well the current x-ray backlighters used for HED experiments, while also enhancing phase effects at lower electron densities. We studied the performance of the high magnification, low energy Talbot-Lau interferometer, for single image phase retrieval using Moiré fringe deflectometry. Our laboratory and simulation studies indicate that such a device is able to retrieve object electron densities from phase shift measurements. Using laboratory x-ray sources from 7 to 15 μm size we obtained accurate simultaneous measurements of refraction and attenuation for both sharp and mild electron density gradients.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Penalized maximum likelihood reconstruction for x-ray differential phase-contrast tomography

Purpose: The purpose of this work is to propose a cost function with regularization to iteratively reconstruct attenuation, phase, and scatter images simultaneously from differential phase contrast (DPC) acquisitions, without the need of phase retrieval, and examine its properties. Furthermore this reconstruction method is applied to an acquisition pattern that is suitable for a DPC tomographic system with continuously rotating gantry (sliding window acquisition), overcoming the severe smearing in noniterative reconstruction. Methods: We derive a penalized maximum likelihood reconstruction algorithm to directly reconstruct attenuation, phase, and scatter image from the measured detector values of a DPC acquisition. The proposed penalty comprises, for each of the three images, an independent smoothing prior. Image quality of the proposed reconstruction is compared to images generated with FBP and iterative reconstruction after phase retrieval. Furthermore, the influence between the priors is analyzed. Finally, the proposed reconstruction algorithm is applied to experimental sliding window data acquired at a synchrotron and results are compared to reconstructions based on phase retrieval. Results: The results show that the proposed algorithm significantly increases image quality in comparison to reconstructions based on phase retrieval. No significant mutual influence between the proposed independent priors could be observed. Further it could be illustrated that the iterative reconstruction of a sliding window acquisition results in images with substantially reduced smearing artifacts. Conclusions: Although the proposed cost function is inherently nonconvex, it can be used to reconstruct images with less aliasing artifacts and less streak artifacts than reconstruction methods based on phase retrieval. Furthermore, the proposed method can be used to reconstruct images of sliding window acquisitions with negligible smearing artifacts.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

Assimilating compact phase space retrievals of atmospheric composition with WRF-Chem/DART: a regional chemical transport/ensemble Kalman filter data assimilation system

This study introduces the Weather Research and Forecasting Model with chemistry/Data Assimilation Research Testbed (WRF-Chem/DART) chemical transport forecasting/data assimilation system together with the assimilation of ''compact phase space retrievals'' of satellite-derived atmospheric composition products. WRF-Chem is a state-of-the-art chemical transport model. DART is a flexible software environment for researching ensemble data assimilation with different assimilation and forecast model options. DART's primary assimilation tool is the ensemble adjustment Kalman filter. WRF-Chem/DART is applied to the assimilation of Terra/Measurement of Pollution in the Troposphere (MOPITT) carbon monoxide (CO) trace gas retrieval profiles. Those CO observations are first assimilated as quasi-optimal retrievals (QORs). Our results show that assimilation of the CO retrievals (i) reduced WRF-Chem's CO bias in retrieval and state space, and (ii) improved the CO forecast skill by reducing the Root Mean Square Error (RMSE) and increasing the Coefficient of Determination ($R^2$). Those CO forecast improvements were significant at the 95 % level. Trace gas retrieval data sets contain (i) large amounts of data with limited information content per observation, (ii) error covariance cross-correlations, and (iii) contributions from the retrieval prior profile that should be removed before assimilation. Those characteristics present challenges to the assimilation of retrievals. This paper addresses those challenges by introducing the assimilation of compact phase space retrievals (CPSRs). CPSRs are obtained by preprocessing retrieval data sets with an algorithm that (i) compresses the retrieval data, (ii) diagonalizes the error covariance, and (iii) removes the retrieval prior profile contribution. Most modern ensemble assimilation algorithms can efficiently assimilate CPSRs. Our results show that assimilation of MOPITT CO CPSRs reduced the number of observations (and assimilation computation costs) by ~ 35 %, while providing CO forecast improvements comparable to or better than with the assimilation of MOPITT CO QORs.

58 GEOSCIENCES↗
NASA NTRS2005

The Influence of Thermodynamic Phase on the Retrieval of Mixed-Phase Cloud Microphysical and Optical Properties in the Visible and Near Infrared Region

Cloud microphysical and optical properties are inferred from the bidirectional reflectances simulated for a single-layered cloud consisting of an external mixture of ice particles and liquid droplets. The reflectances are calculated with a rigorous discrete ordinates radiative transfer model and are functions of the cloud effective particle size, the cloud optical thickness, and the values of the ice fraction in the cloud (i.e., the ratio of ice water content to total water content). In the present light scattering and radiative transfer simulations, the ice fraction is assumed to be vertically homogeneous; the habit (shape) percentage as a function of ice particle size is consistent with that used for the Moderate Resolution Imaging Spectroradiometer (MODIS) operational (Collection 4 and earlier) cloud products; and the surface is assumed to be Lambertian with an albedo of 0.03. Furthermore, error analyses pertaining to the inference of the effective particle sizes and optical thicknesses of mixed-phase clouds are performed. Errors are calculated with respect to the assumption of a cloud containing solely liquid or ice phase particles. The analyses suggest that the effective particle size inferred for a mixed-phase cloud can be underestimated (or overestimated) if pure liquid phase (or pure ice phase) is assumed for the cloud, whereas the corresponding cloud optical thickness can be overestimated (or underestimated).

Lee, Joonsuk↗
DOE OSTI2017

Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime

X-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1991

Image inversion analysis of the HST OTA (Hubble Space Telescope Optical Telescope Assembly), phase A

Technical work during September-December 1990 consisted of: (1) analyzing HST point source images obtained from JPL; (2) retrieving phase information from the images by a direct (noniterative) technique; and (3) characterizing the wavefront aberration due to the errors in the Hubble Space Telescope (HST) mirrors, in a preliminary manner. This work was in support of JPL design of compensating optics for the next generation wide-field planetary camera on HST. This digital technique for phase retrieval from pairs of defocused images, is based on the energy transport equation between these image planes. In addition, an end-to-end wave optics routine, based on the JPL Code 5 prescription of the unaberrated HST and WFPC, was derived for output of the reference phase front when mirror error is absent. Also, the Roddier routine unwrapped the retrieved phase by inserting the required jumps of +/- 2(pi) radians for the sake of smoothness. A least-squares fitting routine, insensitive to phase unwrapping, but nonlinear, was used to obtain estimates of the Zernike polynomial coefficients that describe the aberration. The phase results were close to, but higher than, the expected error in conic constant of the primary mirror suggested by the fossil evidence. The analysis of aberration contributed by the camera itself could be responsible for the small discrepancy, but was not verified by analysis.

Litvak, M. M.↗
DOE OSTI2016

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. Here, 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.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

A review of ptychographic techniques for ultrashort pulse measurement

The measurement of optical ultrafast laser pulses is done indirectly because the required bandwidth to measure these pulses exceeds the bandwidth of current electronics. As a result, this measurement problem is often posed as a 1-D phase retrieval problem, which is fraught with ambiguities. The phase retrieval method known as ptychography solves this problem by making it possible to measure ultrafast pulses in either the time domain or the frequency domain. One well known algorithm is the principal components generalized projections algorithm (PCGPA) for extracting pulses from Frequency-Resolved Optical Gating (FROG) measurements. In this work, we discuss the development of the PCPGA and introduce new developments including an operator formalism that allows for the convenient addition of external constraints and the development of more robust algorithms. A close cousin, the ptychographic iterative engine will also be covered and compared to the PCGPA. Additional developments using other algorithmic strategies will also be discussed along with new developments combining optics and high-speed electronics to achieve megahertz measurement rates.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

PyPhase – a Python package for X-ray phase imaging

X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).

36 MATERIALS SCIENCE↗
NASA NTRS2010

Phase and Pupil Amplitude Recovery for JWST Space-Optics Control

This slide presentation reviews the phase and pupil amplitude recovery for the James Webb Space Telescope (JWST) Near Infrared Camera (NIRCam). It includes views of the Integrated Science Instrument Module (ISIM), the NIRCam, examples of Phase Retrieval Data, Ghost Irradiance, Pupil Amplitude Estimation, Amplitude Retrieval, Initial Plate Scale Estimation using the Modulation Transfer Function (MTF), Pupil Amplitude Estimation vs lambda, Pupil Amplitude Estimation vs. number of Images, Pupil Amplitude Estimation vs Rotation (clocking), and Typical Phase Retrieval Results Also included is information about the phase retrieval approach, Non-Linear Optimization (NLO) Optimized Diversity Functions, and Least Square Error vs. Starting Pupil Amplitude.

Dean, B. H.↗
NASA NTRS2000

Horizon: A Proposal for Large Aperture, Active Optics in Geosynchronous Orbit

In 1999, NASA's New Millennium Program called for proposals to validate new technology in high-earth orbit for the Earth Observing-3 (NMP EO3) mission to fly in 2003. In response, we proposed to test a large aperture, active optics telescope in geosynchronous orbit. This would flight-qualify new technologies for both Earth and Space science: 1) a future instrument with LANDSAT image resolution and radiometric quality watching continuously from geosynchronous station, and 2) the Next Generation Space Telescope (NGST) for deep space imaging. Six enabling technologies were to be flight-qualified: 1) a 3-meter, lightweight segmented primary mirror, 2) mirror actuators and mechanisms, 3) a deformable mirror, 4) coarse phasing techniques, 5) phase retrieval for wavefront control during stellar viewing, and 6) phase diversity for wavefront control during Earth viewing. Three enhancing technologies were to be flight- validated: 1) mirror deployment and latching mechanisms, 2) an advanced microcontroller, and 3) GPS at GEO. In particular, two wavefront sensing algorithms, phase retrieval by JPL and phase diversity by ERIM International, were to sense optical system alignment and focus errors, and to correct them using high-precision mirror mechanisms. Active corrections based on Earth scenes are challenging because phase diversity images must be collected from extended, dynamically changing scenes. In addition, an Earth-facing telescope in GEO orbit is subject to a powerful diurnal thermal and radiometric cycle not experienced by deep-space astronomy. The Horizon proposal was a bare-bones design for a lightweight large-aperture, active optical system that is a practical blend of science requirements, emerging technologies, budget constraints, launch vehicle considerations, orbital mechanics, optical hardware, phase-determination algorithms, communication strategy, computational burdens, and first-rate cooperation among earth and space scientists, engineers and managers. This manuscript presents excerpts from the Horizon proposal's sections that describe the Earth science requirements, the structural -thermal-optical design, the wavefront sensing and control, and the on-orbit validation.

Chesters, Dennis↗
DOE OSTI2026

Fidelity-preserving enhancement of ptychography with foundational text-to-image models

Ptychographic phase retrieval enables high-resolution imaging of complex samples but often suffers from artifacts such as grid pathology and multislice crosstalk, which degrade reconstructed images. We propose a plug-and-play (PnP) framework that integrates physics model-based phase retrieval with text-guided image editing using foundational diffusion models. By employing the alternating direction method of multipliers, our approach ensures consensus between data fidelity and artifact removal subproblems, maintaining physical consistency while enhancing image quality. Artifact removal is achieved using a text-guided diffusion image editing method (LEDITS++) with a pre-trained foundational diffusion model, allowing users to specify artifacts for removal in natural language. Demonstrations on simulated and experimental datasets show significant improvements in artifact suppression and structural fidelity, validated by metrics such as peak signal-to-noise ratio and diffraction pattern consistency. This work highlights the combination of text-guided generative models and model-based phase retrieval algorithms as a transferable and fidelity-preserving method for high-quality diffraction imaging.

image editing↗
DOE OSTI2020

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part I

This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Defining Pupil Knowledge Requirements for Roman Space Telescope Integrated Payload Assembly Testing

This thesis examines the use of phase retrieval to characterize an optical system under testing conditions with pupil knowledge error. The purpose of this investigation is to define pupil knowledge requirements for the integrated payload testing of the Roman Space Telescope. We have conducted a Monte Carlo study to determine how location uncertainty of the ground support equipment relative to the payload caused by the temperature deformation in the Space Environment Simulator will affect our ability to use image-based wavefront sensing during the test to characterize system alignment. This test will be conducted with significant wavefront error (WFE) present due to gravity sag on the primary mirror. The study incrementally decenters two pieces of ground support equipment and evaluates how the phase retrieval algorithm attempts to fit the wavefront. We conducted this investigation in two steps. First, we used an ideal optical model of the test configuration without the gravity sag on the primary mirror to see the fitting effects related only to pupil knowledge error introduced by the decentering. Then, we used perturbed and gravity sag models to investigate the effects of decentering dependent wavefront effects in addition to pupil knowledge error. The results from the ideal model provided a clear limit of the amount of pupil knowledge error that can be present before seeing significant WFE in the phase retrieval. For the second study, we used the decentering tolerances from the ideal model results to determine the WFE effects of decentering in the presence of gravity sag and system misalignments. The second part of this study will be factored into the overall integrated payload assembly testing WFE budget.

Roman Space Telescope↗
DOE OSTI2021

Bragg coherent diffraction imaging by simultaneous reconstruction of multiple diffraction peaks

Bragg coherent diffractive imaging (BCDI) is a non-invasive microscopy technique that can visualize the morphology and internal lattice deviations of crystals with nanoscale spatial resolution and picometer deformation sensitivity. While BCDI has been successfully applied in various studies of materials, it is less successful for highly-strained crystals. Specifically, it is difficult to correctly reconstruct the electron density of a highly-strained object using conventional phase retrieval algorithms. Although various algorithms have been developed to overcome this challenge, most of them require a priori knowledge that is not always available in practice. Here we report on a new phase retrieval workflow that can invert diffraction patterns from multiple Bragg peaks simultaneously. The new workflow is explored via simulated diffraction from crystals with various strain conditions. Furthermore, reconstructions from the new workflow consistently demonstrate more accurate electron density maps, in comparison with the conventional method. For highly-strained crystals, the new workflow improves the reliability and consistency of BCDI phase retrieval significantly.

36 MATERIALS SCIENCE↗