arXiv subjects

Petrus H. Zwart

Publications and source records attributed to Petrus H. Zwart.

9 recordsLinked to original sources

arXiv2026

From Reconstruction to Interpretation: Zero-Setup Multi-Phase Segmentation of X-ray Tomography Data

X-ray tomography enables nondestructive characterization of material microstructures, while advances in micro-CT imaging have accelerated volumetric data acquisition and reconstruction. However, rapid interpretation remains limited by image segmentation, which often requires manual thresholding, user prompting, or material-specific model training. We present a zero-setup framework for multi-phase segmentation of synchrotron X-ray tomography data that generates interpretable masks for previously unseen datasets without user input or retraining during deployment. The framework combines a material-agnostic mask preparation strategy with a pretrained semantic segmentation network. It represents commonly occurring structural regions as background, sample, bright, dark-gray, light-gray, and porosity masks. Unlike conventional deep learning pipelines that require dataset-specific annotations and retraining, the proposed framework can be applied directly to new scans and produce diagnostic-level segmentations within minutes of reconstruction. This enables rapid assessment of scan quality, sample morphology, porosity, and attenuation variations during ongoing beamline experiments. The generated masks can later be manually refined or used to fine-tune application-specific models when greater accuracy or material-specific labeling is required. Evaluation on held-out synchrotron micro-CT images and qualitative testing on additional datasets demonstrate consistent and physically meaningful segmentations across varying samples and imaging conditions. The framework also substantially outperforms conventional intensity-based thresholding. By connecting high-speed reconstruction with immediate interpretation, the approach supports near-real-time beamline feedback and scalable AI-assisted scientific imaging workflows.

cs.CV↗

arXiv2026

Unlocking Latent Dimensions: Exploring Representations of Large-Scale X-ray Scattering Data using Variational Autoencoders

Scientific user facilities generate X-ray scattering data faster than traditional workflows can process them. We address this challenge across two settings, offline dataset exploration and live on-the-fly analysis. We train a domain-specific attention-based Convolutional Variational Autoencoder (C-VAE) on 1.5 million X-ray scattering images to learn low-dimensional representations capturing structural variation across diverse experimental conditions. The learned latent space reveals well-organized clusters and smooth trajectories reflecting experimental progression. It further supports controlled synthetic scattering image generation across diverse structural states. When deployed without retraining, the model organizes time-resolved film formation experiments at two synchrotron facilities into interpretable latent structures. Benchmarking against DINOv3 (ViT-7B), a general-purpose vision foundation model, demonstrates that domain-specific training yields more interpretable latent organization for scattering data. Both workflows are integrated within Latent Space Explorer, a component of the MLExchange platform, supporting interactive structural exploration across archived datasets and live experiments.

cs.LG↗

arXiv2026

Machine Learning-Augmented Acceleration of Iterative Ptychographic Reconstruction

Iterative ptychographic reconstruction algorithms are widely used for coherent diffractive imaging but can exhibit slow convergence under realistic experimental conditions. We propose a machine learning-augmented approach that accelerates iterative ptychographic reconstruction by introducing a learned fast-forward operator applied during reconstruction. Following an initial warm-up using standard iterations, the fast-forward operator advances the reconstruction toward a more converged state, after which conventional iterative updates are resumed. This strategy preserves the physical consistency and flexibility of established ptychographic solvers while reducing the number of iterations required for convergence. The model is trained on diverse ptychographic datasets and evaluated on experimental data acquired in a different year, demonstrating robustness and temporal generalization. Compared with conventional iterative solvers, the machine learning-augmented method achieves comparable reconstruction quality while converging faster in terms of Poisson negative log-likelihood, yielding over a two-fold reduction in wall-clock time. The approach has been integrated into an existing reconstruction pipeline and deployed in production at a synchrotron beamline, demonstrating practicality for real-time experimental operation.

cs.LG↗

arXiv2026

Conformal Tradeoffs: Operational Profiles Beyond Coverage

Conformal prediction gives exact finite-sample coverage guarantees under exchangeability, but deployed systems are judged by more than coverage alone. For a fixed calibrated rule reused over a finite operational window, stakeholders also care about deployment-facing quantities such as commitment frequency, deferral, and decisive error exposure. These are not determined by coverage: calibration choices with similar coverage can still induce materially different operational profiles. We study this characterization gap in a scoped setting: binary split conformal prediction under exchangeability with a fixed deployed rule. We introduce the Small-Sample Beta Correction (SSBC) which gives finite-sample coverage semantics for the deployed rule: it inverts the Beta/Beta--Binomial law governing calibration-conditional coverage to map a user request $(α^\star,δ)$ to the least conservative calibration grid point with calibration-conditional PAC semantics for the realized deployed rule. Calibrate-and-Audit then fixes the rule by calibration and uses an independent audit split to estimate the induced region--class label table, a reusable summary from which deployment-facing Key Performance Indicators (KPIs) follow by projection. Under this design, fixed operational rates admit exact finite-sample Binomial inference, while Beta--Binomial envelopes serve as practical predictive summaries for future windows. The induced partition also exposes regime boundaries, Pareto-relevant tradeoffs, and inverse-pricing questions for fixed downstream conventions. Simulations validate the SSBC semantics and compare audit-based summaries with leave-one-out planning proxies; molecular toxicity data provide an audit-based empirical example, and a solubility case study illustrates scenario planning once coverage semantics are fixed.

stat.ME↗

arXiv2025

Probabilistic Conformal Coverage Guarantees in Small-Data Settings

Conformal prediction provides distribution-free prediction sets with guaranteed marginal coverage. However, in split conformal prediction this guarantee is training-conditional only in expectation: across many calibration draws, the average coverage equals the nominal level, but the realized coverage for a single calibration set may vary substantially. This variance undermines effective risk control in practical applications. Here we introduce the Small Sample Beta Correction (SSBC), a plug-and-play adjustment to the conformal significance level that leverages the exact finite-sample distribution of conformal coverage to provide probabilistic guarantees, ensuring that with user-defined probability over the calibration draw, the deployed predictor achieves at least the desired coverage.

cs.LG↗

arXiv2025

Behind the Noise: Conformal Quantile Regression Reveals Emergent Representations

Scientific imaging often involves long acquisition times to obtain high-quality data, especially when probing complex, heterogeneous systems. However, reducing acquisition time to increase throughput inevitably introduces significant noise into the measurements. We present a machine learning approach that not only denoises low-quality measurements with calibrated uncertainty bounds, but also reveals emergent structure in the latent space. By using ensembles of lightweight, randomly structured neural networks trained via conformal quantile regression, our method performs reliable denoising while uncovering interpretable spatial and chemical features -- without requiring labels or segmentation. Unlike conventional approaches focused solely on image restoration, our framework leverages the denoising process itself to drive the emergence of meaningful representations. We validate the approach on real-world geobiochemical imaging data, showing how it supports confident interpretation and guides experimental design under resource constraints.

cs.AI↗

arXiv2023

DLSIA: Deep Learning for Scientific Image Analysis

We introduce DLSIA (Deep Learning for Scientific Image Analysis), a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing, or for experiment-in-the-loop computing scenarios. DLSIA features easy-to-use architectures such as autoencoders, tunable U-Nets, and parameter-lean mixed-scale dense networks (MSDNets). Additionally, we introduce sparse mixed-scale networks (SMSNets), generated using random graphs and sparse connections. As experimental data continues to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration, and advance research in scientific image analysis.

cs.CV↗

arXiv2023

MLExchange: A web-based platform enabling exchangeable machine learning workflows for scientific studies

Machine learning (ML) algorithms are showing a growing trend in helping the scientific communities across different disciplines and institutions to address large and diverse data problems. However, many available ML tools are programmatically demanding and computationally costly. The MLExchange project aims to build a collaborative platform equipped with enabling tools that allow scientists and facility users who do not have a profound ML background to use ML and computational resources in scientific discovery. At the high level, we are targeting a full user experience where managing and exchanging ML algorithms, workflows, and data are readily available through web applications. Since each component is an independent container, the whole platform or its individual service(s) can be easily deployed at servers of different scales, ranging from a personal device (laptop, smart phone, etc.) to high performance clusters (HPC) accessed (simultaneously) by many users. Thus, MLExchange renders flexible using scenarios -- users could either access the services and resources from a remote server or run the whole platform or its individual service(s) within their local network.

cs.LG↗

arXiv2022

Deep learning-based identification of sub-nuclear structures in FIB-SEM images

Three-dimensional volumetric imaging of cells allows for in situ visualization, thus preserving contextual insights into cellular processes. Despite recent advances in machine learning methods, morphological analysis of sub-nuclear structures have proven challenging due to both the shallow contrast profile and the technical limitation in feature detection. Here, we present a convolutional neural network, supervised deep learning-based approach which can identify sub-nuclear structures with 90% accuracy. We develop and apply this model to C. elegans gonads imaged using focused ion beam milling combined with scanning electron microscopy resulting in the accurate identification and segmentation of all sub-nuclear structures including entire chromosomes. We discuss in depth the architecture, parameterization, and optimization of the deep learning model, as well as provide evaluation metrics to assess the quality of the network prediction. Lastly, we highlight specific aspects of the model that can be optimized for its broad application to other volumetric imaging data as well as in situ cryo-electron tomography.

q-bio.QM↗