arXiv subjects

Tong-Tian Weng

Publications and source records attributed to Tong-Tian Weng.

4 recordsLinked to original sources

arXiv2026

Learning Transferable Self-Supervised Priors for Super-Resolution Reconstruction in Structured Illumination Microscopy

Structured illumination microscopy (SIM) extends the optical passband, and reconstruction of detail beyond it depends on prior knowledge. Hand-designed regularizers depend on how well their structural assumptions match the specimen; learned priors can be sensitive to changes in imaging conditions and specimen structure. We introduce SIMAdapter, which pretrains a network that predicts the emitter and the point-spread function (PSF) by self-supervision on 23,237 raw SIM stacks from BioSR, BioTISR, and simulations spanning different PSFs and specimen structures, then adapts it to a single unlabeled target stack. Adaptation refines the network against a differentiable image-formation model, with the light pattern calibrated from that stack. Both stages take their supervision from the raw measurements and need no paired high-resolution reference. On two held-out synthetic domains, SIMAdapter reaches a mean emitter normalized root-mean-square error of 0.156, compared with 0.403 for Sparse-SIM. The same adaptation started from a network pretrained on BioSR alone is less accurate in both domains. In three experimental case studies, adaptation reduces flanking artifacts and yields more distinct profiles across filament pairs, mitochondrial boundaries, and calibration lines. A single pretrained network can thus be reused across SIM measurements, with each reconstruction refined against its own raw data.

physics.optics↗

arXiv2025

Self-supervised prior learning improves structured illumination microscopy resolution

Structured illumination microscopy (SIM) is a wide-field super-resolution technique normally limited to roughly twice the diffraction-limited resolution ($\approx 100$--$200$~nm). Surpassing this bound is a classic ill-posed inverse problem: recovering high-frequency structure from band-limited raw data. We introduce SIMFormer, a fully blind SIM reconstruction framework that learns a powerful, data-driven prior directly from raw images via self-supervision. This learned prior regularizes the solution and enables reliable extrapolation beyond the optical transfer function cutoff, yielding an effective resolution of approximately 45~nm. We validate SIMFormer on synthetic data and the BioSR dataset, where it resolves features such as flattened endoplasmic reticulum lipid bilayers previously reported to require STORM-level resolution. A self-distilled variant, SIMFormer+, further improves noise robustness while preserving high resolution at extremely low photon counts. These results show that learned priors can substantially extend SIM resolution and robustness, enabling rapid, large-scale imaging with STORM-level detail.

physics.optics↗

arXiv2025

Enhancing Deep Learning Based Structured Illumination Microscopy Reconstruction with Light Field Awareness

Structured illumination microscopy (SIM) is a pivotal technique for dynamic subcellular imaging in live cells. Conventional SIM reconstruction algorithms depend on accurately estimating the illumination pattern and can introduce artefacts when this estimation is imprecise. Although recent deep learning-based SIM reconstruction methods have improved speed, accuracy, and robustness, they often struggle with out-of-distribution data. To address this limitation, we propose an Awareness-of-Light-field SIM (AL-SIM) reconstruction approach that directly estimates the actual light field to correct for errors arising from data distribution shifts. Through comprehensive experiments on both simulated filament structures and live BSC1 cells, our method demonstrates a 7% reduction in the normalized root mean square error (NRMSE) and substantially lowers reconstruction artefacts. By minimizing these artefacts and improving overall accuracy, AL-SIM broadens the applicability of SIM for complex biological systems.

physics.optics↗

arXiv2023

Learning imaging mechanism directly from optical microscopy observations

Optical microscopy image plays an important role in scientific research through the direct visualization of the nanoworld, where the imaging mechanism is described as the convolution of the point spread function (PSF) and emitters. Based on a priori knowledge of the PSF or equivalent PSF, it is possible to achieve more precise exploration of the nanoworld. However, it is an outstanding challenge to directly extract the PSF from microscopy images. Here, with the help of self-supervised learning, we propose a physics-informed masked autoencoder (PiMAE) that enables a learnable estimation of the PSF and emitters directly from the raw microscopy images. We demonstrate our method in synthetic data and real-world experiments with significant accuracy and noise robustness. PiMAE outperforms DeepSTORM and the Richardson-Lucy algorithm in synthetic data tasks with an average improvement of 19.6\% and 50.7\% (35 tasks), respectively, as measured by the normalized root mean square error (NRMSE) metric. This is achieved without prior knowledge of the PSF, in contrast to the supervised approach used by DeepSTORM and the known PSF assumption in the Richardson-Lucy algorithm. Our method, PiMAE, provides a feasible scheme for achieving the hidden imaging mechanism in optical microscopy and has the potential to learn hidden mechanisms in many more systems.

physics.optics↗