FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer

๐Ÿ“… 2023-04-04
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๐Ÿ“ˆ Citations: 2
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๐Ÿค– AI Summary
Cryo-electron tomography (cryo-ET) suffers from a critical scarcity of realistic, annotated training data: deep learning methods require large-scale ground-truth annotations, while physics-based simulation is computationally expensive and struggles to model complex, biologically realistic degradations. To address this, we propose the first neural style transfer framework tailored for cryo-ET simulationโ€”a fully end-to-end 3D style transfer method that transforms synthetic or low-fidelity volume data into high-fidelity, biophysically consistent tomograms without paired supervision. Our approach integrates Adaptive Instance Normalization (AdaIN) with a 3D U-Net architecture, augmented by frequency-domain constraints, structural similarity (SSIM) loss, and a biologically inspired contrast prior. It further enables controllable artifact injection and multi-scale structural preservation. On multiple benchmarks, our simulated tomograms achieve an 18.7% SSIM improvement and yield a 12.3% Dice score gain in downstream segmentation, significantly enhancing pretraining efficacy and robustness evaluation of cryo-ET analysis models.
Problem

Research questions and friction points this paper is trying to address.

Simulates cryo-electron tomograms efficiently
Reduces training data generation time
Enhances particle localization and classification accuracy
Innovation

Methods, ideas, or system contributions that make the work stand out.

Neural Style Transfer for simulation
Boosts data generation speed
Leverages GPU acceleration
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Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Linz, Austria
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Mathematical Data Science (MDS), Faculty of Mathematics, University of Vienna, Vienna, Austria; Research Network Data Science, University of Vienna, Vienna, Austria
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Haselbach Lab, Research Institute of Molecular Pathology (IMP), Vienna, Austria