Neural networks, while effective for tackling many challengi ng scientific tasks, are not known to perform well out-of-distribution (OOD), i.e., within domains which d iffer from their training data. Understanding neural network OOD generalization is paramount to their suc cessful deployment in experimental workflows, especially when ground-truth knowledge about the experime nt is hard to establish or experimental conditions significantly vary. With inherent access to ground-truth in formation and fine-grained control of underlying distributions, simulation-based data curation facilitate s precise investigation of OOD generalization behavior. Here, we probe generalization with respect to imaging condi tions of neural network segmentation models for high-resolution transmission electron microscopy (HRTEM) imaging of nanoparticles, training and measuring the OOD generalization of over 12,000 neural networks using synthetic data generated via random structure sampling and multislice simulation. Using the HRTEM contra st transfer function, we further develop a framework to compare information content of HRTEM datasets an d quantify OOD domain shifts. We demonstrate that neural network segmentation models enjoy significant performance stability, but will smoothly and predictably worsen as imaging conditions shift from the training distribution. Lastly, we consider limitations of our approach in explaining other OOD shifts, s uch as of the atomic structures, and discuss complementary techniques for understanding generalizatio n in such settings.

High harmonic generation (HHG) is a nonlinear process that enables table-top generation of tunable, high-energy, coherent, ultrashort radiation pulses in the extreme ultraviolet (EUV) to soft X-ray range. These pulses find applications in photoemission spectroscopy in condensed matter physics, pump-probe spectroscopy for high-energy-density plasmas, and attosecond science. However, optical aberrations in the high-power laser systems required for HHG degrade beam quality and reduce efficiency. W e present a machine learning approach to optimize aberration correction using a spatial light modulator . W e implemented and compared Bayesian optimization and convolutional neural network (CNN) methods to predict optimal Zernike polynomial coefficients for wavefront correction. Our CNN achieved promising results with 80.39% accuracy on test data, demonstrating the potential for automated aberration correction in HHG systems.

Emerging deep-learning-based lens library pre-training (LensLib-PT) pipeline offers a new avenue for blind lens aberration correction by training a universal neural network, demonstrating strong capability in handling diverse unknown optical degradations. This work proposes the OmniLens++ framework, which resolves two challenges that hinder the generalization ability of existing pipelines: the difficulty of scaling data and the absence of prior guidance characterizing optical degradation. To improve data scalability, we expand the design specifications to increase the degradation diversity of the lens source, and we sample a more uniform distribution by quantifying the spatial-variation patterns and severity of optical degradation. In terms of model design, to leverage the Point Spread Functions (PSFs), which intuitively describe optical degradation, as guidance in a blind paradigm, we propose the Latent PSF Representation (LPR). The VQVAE framework is introduced to learn latent features of LensLib's PSFs, which is assisted by modeling the optical degradation process to constrain the learning of degradation priors. Experiments on diverse aberrations of real-world lenses and synthetic LensLib show that OmniLens++ exhibits state-of-the-art generalization capacity in blind aberration correction. Beyond performance, the AODLibpro is verified as a scalable foundation for more effective training across diverse aberrations, and LPR can further tap the potential of large-scale LensLib. The source code and datasets will be made publicly available at https://github.com/zju-jiangqi/OmniLens2.

Abstract--We present a new computational near-eye display method that addresses the vergence-accommodation conflict problem in stereoscopic displays through accommodation-invariance. We employ end-to-end learning to jointly optimize the wavefront-coding optics and the image pre-processing module. T o implement this approach, we develop a differentiable retinal image formation model that accounts for limiting aperture and chromatic aberrations introduced by the eye optics. We further integrate the neural transfer function and the contrast sensitivity function into the loss model to account for related perceptual effects. T o tackle off-axis distortions, we incorporate position dependency into the pre-processing module. In addition to conducting rigorous analysis based on simulations, we also fabricate the designed diffractive optical element and build a benchtop setup, demonstrating accommodation-invariance for depth ranges of up to four diopters. HE simplicity of stereoscopic near-eye display (NED) design has made these systems particularly attractive for virtual reality (VR) and augmented reality (AR) applications. However, a major drawback hindering their widespread adoption is the vergence-accommodation conflict (V AC), which is caused by the mismatch between the two visual cues. In natural viewing conditions, vergence and accommodation work in synchrony, but the link between them gets broken in stereoscopic NEDs, resulting in severe visual discomfort [1], [2], [3]. Two groups of methods have addressed the V AC. Accommodation-enabling (AE) displays have aimed at delivering close-to-natural viewing experience by recreating near-correct retinal blur to drive the accommodation to the vergence distance of the object. We discuss AE display approaches in more details in Sec. Instead of recreating focus cues, accommodation-invariant (AI) displays have aimed at coupling vergence with accommodation by removing the retinal defocus blur completely.

Sample-induced aberrations and optical imperfections limit the resolution of fluorescence microscopy. Phase diversity is a powerful technique that leverages complementary phase information in sequentially acquired images with deliberately introduced aberrations--the phase diversities--to enable phase and object reconstruction and restore diffraction-limited resolution. These phase diversities are typically introduced into the optical path via a deformable mirror. Existing phase-diversity-based methods are limited to Zernike modes, require large numbers of diversity images, or depend on accurate mirror calibration--which are all suboptimal. We present DeepPD, a deep learning-based framework that combines neural representations of the object and wavefront with a learned model of the deformable mirror to jointly estimate both object and phase from only five images. DeepPD improves robustness and reconstruction quality over previous approaches, even under severe aberrations. We demonstrate its performance on calibration targets and biological samples, including immunolabeled myosin in fixed PtK2 cells. Keywords: phase diversity, deformable mirror, adaptive optics, fluorescence microscopy, neural networks, supervised learning, neural representations, deep learning 1 Introduction The potential of light microscopy is often unrealized due to aberrations introduced either by imperfections in the optical system or by the sample itself, yielding blurry and distorted images that fail to achieve diffraction-limited resolution. The goal of adaptive optics is to estimate the aberrations present in an image and counter them during acquisition via a deformable mirror (DM) or spatial light modulator [1], or, in computational settings, to estimate and correct them post-acquisition. Aberrations are caused by variations in the phase of the optical field. Yet the phase cannot be measured directly, as conventional imaging systems only capture light intensity. Estimating the phase is a challenging problem, and various wavefront estimation 1 arXiv:2504.14157v1 These methods can be broadly classified into two categories: guidestar-based and guidestar-free methods [1]. Guidestar-based methods rely on the presence of a point source in the sample, and the phase aberration can be retrieved, for example, by a Shack-Hartmann (SH) wavefront sensor [1] that measures the phase aberration based on displacements of the point source's images on a microlens array.

Accurate camera calibration is a fundamental task for 3D perception, especially when dealing with real-world, in-the-wild environments where complex optical distortions are common. Existing methods often rely on pre-rectified images or calibration patterns, which limits their applicability and flexibility. In this work, we introduce a novel framework that addresses these challenges by jointly modeling camera intrinsic and extrinsic parameters using a generic ray camera model. Unlike previous approaches, AlignDiff shifts focus from semantic to geometric features, enabling more accurate modeling of local distortions. We propose AlignDiff, a diffusion model conditioned on geometric priors, enabling the simultaneous estimation of camera distortions and scene geometry. To enhance distortion prediction, we incorporate edge-aware attention, focusing the model on geometric features around image edges, rather than semantic content. Furthermore, to enhance generalizability to real-world captures, we incorporate a large database of ray-traced lenses containing over three thousand samples. This database characterizes the distortion inherent in a diverse variety of lens forms. Our experiments demonstrate that the proposed method significantly reduces the angular error of estimated ray bundles by ~8.2 degrees and overall calibration accuracy, outperforming existing approaches on challenging, real-world datasets.

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. While wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement, and slow when serially mapping spatially varying aberrations across large fields of view. Here, we introduce AOViFT (Adaptive Optical Vision Fourier Transformer) -- a machine learning-based aberration sensing framework built around a 3D multistage Vision Transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time, and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or post-acquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Abstract: The design and performance analysis of relay lenses that provide high-performance image transmission for target acquisition and tracking in military optical systems. Relay lenses are critical components for clear and lossless image transmission over long distances. In this study, the optical performance of a relay lens system designed and optimized using ZEMAX software is investigated in detail. The analysis focuses on important optical properties such as modulation transfer function (MTF), spot diagrams, Seidel diagram, field curvature and distortion. The results show that the lens has significant potential in military applications for target detection and tracking with high resolution and low aberration. Accepted: 1. Introduction Military optical systems provide high-performance and reliable monitoring for target identification and tracking in critical missions. These systems have become indispensable in modern warfare, where the ability to process and analyze real-time visual data can determine the success or failure of operations. By combining advanced optical technologies with robust design methodologies, military systems aim to deliver precise and effective solutions for a variety of applications. In this context, optical components must ensure exceptional image clarity, resolution, and durability to withstand challenging operational environments.

Optical imaging quality can be severely degraded by system and sample induced aberrations. Existing adaptive optics systems typically rely on iterative search algorithm to correct for aberrations and improve images. This study demonstrates the application of convolutional neural networks to characterise the optical aberration by directly predicting the Zernike coefficients from two to three phase-diverse optical images. We evaluated our network on 600,000 simulated Point Spread Function (PSF) datasets randomly generated within the range of -1 to 1 radians using the first 25 Zernike coefficients. The results show that using only three phase-diverse images captured above, below and at the focal plane with an amplitude of 1 achieves a low RMSE of 0.10 radians on the simulated Point Spread Function (PSF) dataset. Furthermore, this approach directly predicts Zernike modes simulated extended 2D samples, while maintaining a comparable RMSE of 0.15 radians. We demonstrate that this approach is effective using only a single prediction step, or can be iterated a small number of times. This simple and straightforward technique provides rapid and accurate method for predicting the aberration correction using three or less phase-diverse images, paving the way for evaluation on real-world dataset.

Cancer has complex patterns of progression that include converging as well as diverging progressional pathways. Vogelstein's path model of colon cancer was a pioneering contribution to cancer research. Since then, several attempts have been made at obtaining mathematical models of cancer progression, devising learning algorithms, and applying these to cross-sectional data. Beerenwinkel et al. provided, what they coined, EM-like algorithms for Oncogenetic Trees (OTs) and mixtures of such. Given the small size of current and future data sets, it is important to minimize the number of parameters of a model. For this reason, we too focus on tree-based models and introduce Hidden-variable Oncogenetic Trees (HOTs). In contrast to OTs, HOTs allow for errors in the data and thereby provide more realistic modeling.