arXiv subjects

Chris Jacobsen

Publications and source records attributed to Chris Jacobsen.

13 recordsLinked to original sources

arXiv2026

Realizing A Hard X-Ray Storage Ring Free Electron Laser Oscillator at the APS-U

We show that the APS-U could support a hard X-ray storage ring free electron laser oscillator, providing a promising avenue toward high repetition rate, narrow bandwidth coherent light sources. The results of our numerical simulations demonstrate that a transverse gradient undulator yields ~8% and ~6% single-pass gain at 8.05 keV and 10 keV respectively. We further identify a configuration at 5 keV that does not require a TGU but still exceeds a 5% gain threshold despite the relatively short 5-meter long insertion device. All cases presented retain spectral purity on the order of meV and reach a steady-state output whose equilibrium is consistent with the Renieri Saturation Limit. We have calculated the 5 keV case to have an average brightness of ~10^26 photons/(s * mm2 * mrad2 * 0.1% BW), representing an increase in more than four orders of magnitude from the standard APS-U undulator. These results indicate that a storage ring free electron laser oscillator at multi-keV photon energies is feasible with nominal APS-U parameters and standard x-ray cavity optics.

physics.acc-ph↗

arXiv2024

Generation of Spatially Coherent Light at Extreme Ultraviolet Wavelengths

We present spatial coherence measurements of extreme-ultraviolet light generated using the process of high-harmonic upconversion of a femtosecond laser. Using a phase-matched hollow-fiber geometry, the generated beam is found to exhibit essentially full spatial coherence. The coherence of this laser-like EUV source is demonstrated by recording Gabor holograms of small objects. This work demonstrates the capability to do EUV holography using a tabletop experimental setup. Such an EUV source, with low divergence and high spatial coherence, can be used for experiments such as high-precision metrology, inspection of optical components for EUV lithography (1), and for microscopy and holography (2) with nanometer resolution. Furthermore, the short time duration of the EUV radiation (a few femtoseconds) will enable EUV microscopy and holography to be performed with ultrahigh time resolution.

physics.optics↗

arXiv2023

Imaging extended single crystal lattice distortion fields with multi-peak Bragg ptychography

We describe a phase-retrieval-based imaging method to directly spatially resolve the vector lattice distortions in an extended crystalline sample by explicit coupling of independent Bragg ptychography data sets into the reconstruction process. Our method addresses this multi-peak Bragg ptychography (MPBP) inverse problem by explicit gradient descent optimization of an objective function based on modeling of the probe-lattice interaction, along with corrective steps to address spurious reconstruction artifacts. Robust convergence of the optimization process is ensured by computing exact gradients with the automatic differentiation capabilities of high-performance computing software packages. We demonstrate MPBP reconstruction with simulated ptychography data mimicking diffraction from a single crystal membrane containing heterogeneities that manifest as phase discontinuities in the diffracted wave. We show the superior ability of such an optimization-based approach in removing reconstruction artifacts compared to existing phase retrieval and lattice distortion reconstruction approaches.

cond-mat.mtrl-sci↗

arXiv2021

A matrix-free Levenberg-Marquardt algorithm for efficient ptychographic phase retrieval

The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these methods is tedious work, and formulating second order derivatives is even more laborious. Additionally, second order techniques often require the storage and inversion of large matrices of partial derivatives, with memory requirements that can be prohibitive for data-rich imaging modalities. We use a reverse-mode automatic differentiation (AD) framework to implement an efficient matrix-free version of the Levenberg-Marquardt (LM) algorithm, a longstanding method that finds popular use in nonlinear least-square minimization problems but which has seen little use in phase retrieval. Furthermore, we extend the basic LM algorithm so that it can be applied for general constrained optimization problems beyond just the least-square applications. Since we use AD, we only need to specify the physics-based forward model for a specific imaging application; the derivative terms are calculated automatically through matrix-vector products, without explicitly forming any large Jacobian or Gauss-Newton matrices. We demonstrate that this algorithm can be used to solve both the unconstrained ptychographic object retrieval problem and the constrained "blind" ptychographic object and probe retrieval problems, under both the Gaussian and Poisson noise models, and that this method outperforms best-in-class first-order ptychographic reconstruction methods: it provides excellent convergence guarantees with (in many cases) a superlinear rate of convergence, all with a computational cost comparable to, or lower than, the tested first-order algorithms.

eess.IV↗

arXiv2021

Using a modified double deep image prior for crosstalk mitigation in multislice ptychography

Multislice ptychography is a high-resolution microscopy technique used to image multiple separate axial planes using a single illumination direction. However, multislice ptychography reconstructions are often degraded by crosstalk, where some features on one plane erroneously contribute to the reconstructed image of another plane. Here, we demonstrate the use of a modified "double deep image prior" (DDIP) architecture in mitigating crosstalk artifacts in multislice ptychography. Utilizing the tendency of generative neural networks to produce natural images, a modified DDIP method yielded good results on experimental data. For one of the datasets, we show that using DDIP could remove the need of using additional experimental data, such as from x-ray fluorescence, to suppress the crosstalk. Our method may help x-ray multislice ptychography work for more general experimental scenarios.

eess.IV↗

arXiv2020

Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation

We describe and demonstrate an optimization-based x-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to and fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement.

eess.IV↗

arXiv2020

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials (revised)

Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 micron (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified. The as-published article [Ultramicroscopy 184, 293--309 (2018); doi:10.1016/j.ultramic.2017.10.003] had some minor mistakes that we correct here, with all changes from the as-published article shown in blue.

physics.app-ph↗

arXiv2020

Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic coherent imaging

Different studies in x-ray microscopy have arrived at conflicting conclusions about the dose efficiency of imaging modes involving the recording of intensity distributions in the near (Fresnel regime) or far (Fraunhofer regime) field downstream of a specimen. We present here a numerical study on the dose efficiency of near-field holography (NFH), near-field ptychography (NFP), and far-field ptychography (FFP), where ptychography involves multiple overlapping finite-sized illumination positions. Unlike what has been reported for coherent diffraction imaging (CDI), which involves recording a single far-field diffraction pattern, we find that all three methods offer similar image quality when using the same fluence on the specimen, with far-field ptychography offering slightly better spatial resolution and lower mean error. These results support the concept that (if the experiment and image reconstruction are done properly) the sample can be near, or far; wherever you are, photon fluence on the specimen sets one limit to spatial resolution.

eess.IV↗

arXiv2019

Three dimensions, two microscopes, one code: automatic differentiation for x-ray nanotomography beyond the depth of focus limit

Conventional tomographic reconstruction algorithms assume that one has obtained pure projection images, involving no within-specimen diffraction effects nor multiple scattering. Advances in x-ray nanotomography are leading towards the violation of these assumptions, by combining the high penetration power of x-rays which enables thick specimens to be imaged, with improved spatial resolution which decreases the depth of focus of the imaging system. We describe a reconstruction method where multiple scattering and diffraction effects in thick samples are modeled by multislice propagation, and the 3D object function is retrieved through iterative optimization. We show that the same proposed method works for both full-field microscopy, and for coherent scanning techniques like ptychography. Our implementation utilizes the optimization toolbox and the automatic differentiation capability of the open-source deep learning package TensorFlow, which demonstrates a much straightforward way to solve optimization problems in computational imaging, and endows our program great flexibility and portability.

eess.IV↗

arXiv2019

Using Automatic Differentiation as a General Framework for Ptychographic Reconstruction

Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical calculation of the derivatives of the error metric, which is not always straightforward. This limits our ability to explore variations of basic imaging approaches. In this paper, we propose to substitute analytical derivative expressions with the automatic differentiation method, whereby we can achieve object reconstruction by specifying only the physics-based experimental forward model. We demonstrate the generality of the proposed method through straightforward object reconstruction for a variety of complex ptychographic experimental models.

eess.IV↗

arXiv2018

X-ray tomography of extended objects: a comparison of data acquisition approaches

The penetration power of x-rays allows one to image large objects. For example, centimeter-sized specimens can be imaged with micron-level resolution using synchrotron sources. In this case, however, the limited beam diameter and detector size preclude the acquisition of the full sample in a single take, necessitating strategies for combining data from multiple regions. Object stitching involves the combination of local tomography data from overlapping regions, while projection stitching involves the collection of projections at multiple offset positions from the rotation axis followed by data merging and reconstruction. We compare these two approaches in terms of radiation dose applied to the specimen, and reconstructed image quality. Object stitching involves an easier data alignment problem, and immediate viewing of subregions before the entire dataset has been acquired. Projection stitching is more dose-efficient, and avoids certain artifacts of local tomography; however, it also involves a more difficult data assembly and alignment procedure, in that it is more sensitive to accumulative registration error.

eess.IV↗

arXiv2016

Quantifying mesoscale neuroanatomy using X-ray microtomography

Methods for resolving the 3D microstructure of the brain typically start by thinly slicing and staining the brain, and then imaging each individual section with visible light photons or electrons. In contrast, X-rays can be used to image thick samples, providing a rapid approach for producing large 3D brain maps without sectioning. Here we demonstrate the use of synchrotron X-ray microtomography ($μ$CT) for producing mesoscale $(1~μm^3)$ resolution brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for $μ$CT-based brain mapping that combines methods for sample preparation, imaging, automated segmentation of image volumes into cells and blood vessels, and statistical analysis of the resulting brain structures. Our results demonstrate that X-ray tomography promises rapid quantification of large brain volumes, complementing other brain mapping and connectomics efforts.

q-bio.QM↗

arXiv2016

Processing of X-ray Microcalorimeter Data with Pulse Shape Variation using Principal Component Analysis

We present a method using principal component analysis (PCA) to process x-ray pulses with severe shape variation where traditional optimal filter methods fail. We demonstrate that PCA is able to noise-filter and extract energy information from x-ray pulses despite their different shapes. We apply this method to a dataset from an x-ray thermal kinetic inductance detector which has severe pulse shape variation arising from position-dependent absorption.

physics.ins-det↗