Zichao Wendy Di

Anthony P. Austin, Zichao Wendy Di, Sven Leyffer et al.

Tomography can be used to reveal internal properties of a 3D object using any penetrating wave. Advanced tomographic imaging techniques, however, are vulnerable to both systematic and random errors associated with the experimental conditions, which are often beyond the capabilities of the state-of-the-art reconstruction techniques such as regularizations. Because they can lead to reduced spatial resolution and even misinterpretation of the underlying sample structures, these errors present a fundamental obstacle to full realization of the capabilities of next-generation physical imaging. In this work, we develop efficient and explicit recovery schemes of the most common experimental error: movement of the center of rotation during the experiment. We formulate new physical models to capture the experimental setup, and we devise new mathematical optimization formulations for reliable inversion of complex samples. We demonstrate and validate the efficacy of our approach on synthetic data under known perturbations of the center of rotation.

Borong Zhang, Qin Li, Zichao Wendy Di

We introduce MAGPIE (Multilevel-Adaptive-Guided Ptychographic Iterative Engine), a stochastic multigrid solver for the ptychographic phase-retrieval problem. The ptychographic phase-retrieval problem is inherently nonconvex and ill-posed. To address these challenges, we reformulate the original nonlinear and nonconvex inverse problem as the iterative minimization of a quadratic surrogate model that majorizes the original objective. This surrogate not only ensures favorable convergence properties but also generalizes the Ptychographic Iterative Engine (PIE) family of algorithms. By solving the surrogate model using a multigrid method, MAGPIE achieves substantial gains in convergence speed and reconstruction quality over traditional approaches.

Chengru Eric Zou, Elle Buser, Zichao Wendy Di et al.

Recovering high-resolution structural and compositional information from coherent X-ray measurements involves solving coupled, nonlinear, and ill-posed inverse problems. Ptychography reconstructs a complex transmission function from overlapping diffraction patterns, while X-ray fluorescence provides quantitative, element-specific contrast at lower spatial resolution. We formulate a joint variational framework that integrates these two modalities into a single nonlinear least-squares problem with shared spatial variables. This formulation enforces cross-modal consistency between structural and compositional estimates, improving conditioning and promoting stable convergence. The resulting optimization couples complementary contrast mechanisms (i.e., phase and absorption from ptychography, elemental composition from fluorescence) within a unified inverse model. Numerical experiments on simulated data demonstrate that the joint reconstruction achieves faster convergence, sharper and more quantitative reconstructions, and lower relative error compared with separate inversions. The proposed approach illustrates how multimodal variational formulations can enhance stability, resolution, and interpretability in computational X-ray imaging.

Canberk Ekmekci, Tekin Bicer, Zichao Wendy Di et al.

Ptychography is a scanning coherent diffractive imaging technique that enables imaging nanometer-scale features in extended samples. One main challenge is that widely used iterative image reconstruction methods often require significant amount of overlap between adjacent scan locations, leading to large data volumes and prolonged acquisition times. To address this key limitation, this paper proposes a Bayesian inversion method for ptychography that performs effectively even with less overlap between neighboring scan locations. Furthermore, the proposed method can quantify the inherent uncertainty on the ptychographic object, which is created by the ill-posed nature of the ptychographic inverse problem. At a high level, the proposed method first utilizes a deep generative model to learn the prior distribution of the object and then generates samples from the posterior distribution of the object by using a Markov Chain Monte Carlo algorithm. Our results from simulated ptychography experiments show that the proposed framework can consistently outperform a widely used iterative reconstruction algorithm in cases of reduced overlap. Moreover, the proposed framework can provide uncertainty estimates that closely correlate with the true error, which is not available in practice. The project website is available here.

Agnimitra Dasgupta, Zichao Wendy Di

Ptychography, as an essential tool for high-resolution and nondestructive material characterization, presents a challenging large-scale nonlinear and non-convex inverse problem; however, its intrinsic photon statistics create clear opportunities for statistical-based deep learning approaches to tackle these challenges, which has been underexplored. In this work, we explore normalizing flows to obtain a surrogate for the high-dimensional posterior, which also enables the characterization of the uncertainty associated with the reconstruction: an extremely desirable capability when judging the reconstruction quality in the absence of ground truth, spotting spurious artifacts and guiding future experiments using the returned uncertainty patterns. We demonstrate the performance of the proposed method on a synthetic sample with added noise and in various physical experimental settings.

Agnimitra Dasgupta, Carlo Graziani, Zichao Wendy Di

Tomographic reconstruction, despite its revolutionary impact on a wide range of applications, suffers from its ill-posed nature in that there is no unique solution because of limited and noisy measurements. Therefore, in the absence of ground truth, quantifying the solution quality is highly desirable but under-explored. In this work, we address this challenge through Gaussian process modeling to flexibly and explicitly incorporate prior knowledge of sample features and experimental noises through the choices of the kernels and noise models. Our proposed method yields not only comparable reconstruction to existing practical reconstruction methods (e.g., regularized iterative solver for inverse problem) but also an efficient way of quantifying solution uncertainties. We demonstrate the capabilities of the proposed approach on various images and show its unique capability of uncertainty quantification in the presence of various noises.