Phase retrieval in inline holography is a fundamental yet ill-posed inverse problem due to the nonlinear coupling between amplitude and phase in coherent imaging. We present a novel off-the-shelf solution that leverages a diffusion model trained solely on object amplitude to recover both amplitude and phase from diffraction intensities. Using a predictor-corrector sampling framework with separate likelihood gradients for amplitude and phase, our method enables complex field reconstruction without requiring ground-truth phase data for training. We validate the proposed approach through extensive simulations and experiments, demonstrating robust generalization across diverse object shapes, imaging system configurations, and modalities, including lensless setups. Notably, a diffusion prior trained on simple amplitude data (e.g., polystyrene beads) successfully reconstructs complex biological tissue structures, highlighting the method's adaptability. This framework provides a cost-effective, generalizable solution for nonlinear inverse problems in computational imaging, and establishes a foundation for broader coherent imaging applications beyond holography.

Fourier ptychography (FP) is a powerful light-based synthetic aperture imaging technique that allows one to reconstruct a high-resolution, wide field-of-view image by computationally integrating a diverse collection of low-resolution, far-field measurements. Typically, FP measurement diversity is introduced by changing the angle of the illumination or the position of the camera; either approach results in sampling different portions of the target's spatial frequency content, but both approaches introduce substantial costs and complexity to the acquisition process. In this work, we introduce Inverse Synthetic Aperture Fourier Ptychography, a novel approach to FP that foregoes changing the illumination angle or camera position and instead generates measurement diversity through target motion. Critically, we also introduce a novel learning-based method for estimating k-space coordinates from dual plane intensity measurements, thereby enabling synthetic aperture imaging without knowing the rotation of the target. We experimentally validate our method in simulation and on a tabletop optical system.

Phase retrieval (PR), a long-established challenge for recovering a complex-valued signal from its Fourier intensity-only measurements, has attracted considerable attention due to its widespread applications in digital imaging. Recently, deep learning-based approaches were developed that achieved some success in single-shot PR. These approaches require a single Fourier intensity measurement without the need to impose any additional constraints on the measured data. Nevertheless, vanilla deep neural networks (DNN) do not give good performance due to the substantial disparity between the input and output domains of the PR problems. Physics-informed approaches try to incorporate the Fourier intensity measurements into an iterative approach to increase the reconstruction accuracy. It, however, requires a lengthy computation process, and the accuracy still cannot be guaranteed. Besides, many of these approaches work on simulation data that ignore some common problems such as saturation and quantization errors in practical optical PR systems. In this paper, a novel physics-driven multi-scale DNN structure dubbed PPRNet is proposed. Similar to other deep learning-based PR methods, PPRNet requires only a single Fourier intensity measurement. It is physics-driven that the network is guided to follow the Fourier intensity measurement at different scales to enhance the reconstruction accuracy. PPRNet has a feedforward structure and can be end-to-end trained. Thus, it is much faster and more accurate than the traditional physics-driven PR approaches. Extensive simulations and experiments on a practical optical platform were conducted. The results demonstrate the superiority and practicality of the proposed PPRNet over the traditional learning-based PR methods.

With the success of deep learning methods in many image processing tasks, deep learning approaches have also been introduced to the phase retrieval problem recently. These approaches are different from the traditional iterative optimization methods in that they usually require only one intensity measurement and can reconstruct phase images in real-time. However, because of tremendous domain discrepancy, the quality of the reconstructed images given by these approaches still has much room to improve to meet the general application requirements. In this paper, we design a novel deep neural network structure named SiSPRNet for phase retrieval based on a single Fourier intensity measurement. To effectively utilize the spectral information of the measurements, we propose a new feature extraction unit using the Multi-Layer Perceptron (MLP) as the front end. It allows all pixels of the input intensity image to be considered together for exploring their global representation. The size of the MLP is carefully designed to facilitate the extraction of the representative features while reducing noises and outliers. A dropout layer is also equipped to mitigate the possible overfitting problem in training the MLP. To promote the global correlation in the reconstructed images, a self-attention mechanism is introduced to the Up-sampling and Reconstruction (UR) blocks of the proposed SiSPRNet. These UR blocks are inserted into a residual learning structure to prevent the weak information flow and vanishing gradient problems due to their complex layer structure. Extensive evaluations of the proposed model are performed using different testing datasets of phase-only images and images with linearly related magnitude and phase. Experiments were conducted on an optical experimentation platform to understand the performance of different deep learning methods when working in a practical environment.

We demonstrate that it is possible to use deep neural networks to produce tomographic reconstructions of dense layered objects with small illumination angle as low as 10 . It is also shown that a DNN trained on synthetic data can generalize well to and produce reconstructions from experimental measurements. This work has application in the field of X-ray tomography for the inspection of integrated circuits and other materials studies. We present a machine learning-based method for tomographic reconstruction of dense layered objects, with range of projection angles limited to 10 . Whereas previous approaches to phase tomography generally require 2 steps, first to retrieve phase projections from intensity projections and then to perform tomographic reconstruction on the retrieved phase projections, in our work a physics-informed preprocessor followed by a deep neural network (DNN) conduct the 3-dimensional reconstruction directly from the intensity projections. We demonstrate this single-step method experimentally in the visible optical domain on a scaled-up integrated circuit phantom. We show that even under conditions of highly attenuated photon fluxes a DNN trained only on synthetic data can be used to successfully reconstruct physical samples disjoint from the synthetic training set. Thus, the need for producing a large number of physical examples for training is ameliorated. The method is generally applicable to tomography with electromagnetic or other types of radiation at all bands. Tomography is the quintessential inverse problem.

We address the challenge of assessing conservation of gene expression in complex, non-homogeneous datasets. Recent studies have demonstrated the success of probabilistic models in studying the evolution of gene expression in simple eukaryotic organisms such as yeast, for which measurements are typically scalar and independent. Models capable of studying expression evolution in much more complex organisms such as vertebrates are particularly important given the medical and scientific interest in species such as human and mouse. We present a statistical model that makes a number of significant extensions to previous models to enable characterization of changes in expression among highly complex organisms. We demonstrate the efficacy of our method on a microarray dataset containing diverse tissues from multiple vertebrate species. We anticipate that the model will be invaluable in the study of gene expression patterns in other diverse organisms as well, such as worms and insects.