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Petrus H. Zwart

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2 published item(s)

preprint2026arXiv

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.

preprint2022arXiv

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.