arXiv subjects

Mengrui Wang

Publications and source records attributed to Mengrui Wang.

4 recordsLinked to original sources

arXiv2026

A unified reconstruction algorithm for reduced-frame structured illumination microscopy

Reduced-frame structured illumination microscopy (SIM) is attractive for live-cell imaging because it can improve temporal throughput and reduce photobleaching, but incomplete phase sampling makes reconstruction unstable and computationally demanding. Here we present URA-SIM, a unified reduced-acquisition framework that turns fixed reduced-frame measurements into pipeline- compatible raw stacks through model-consistent phase-domain completion. Instead of solving a large object-level inverse problem or replacing established SIM reconstruction, URA-SIM estimates the missing phase content on the low-dimensional phase-harmonic manifold required by the target modality and then delegates order separation and image formation to classical reconstruction pipeline. This design combines three practical advantages: fidelity from the SIM forward structure, lightweight online computation, and direct compatibility with existing reconstruction workflows. For 2D-SIM, URA-SIM uses the first-harmonic phase structure of three-phase SIM to estimate a shared zero-order field and complete missing phase samples by direction-wise harmonic fitting. On calibration and biological 2D-SIM data, reduced-frame reconstructions preserve resolvable structures and remain competitive on COS7 mitochondria comparison data. In live-cell COS7 mitochondria imaging, URA-SIM reconstructs each time point from five acquired raw frames and resolves mitochondrial cristae across different temporal sampling regimes. Experiments on 3D-SIM and nonlinear SIM further show that the same design principle can be transferred when the phase model and reconstruction-pipeline interface are adapted to the target modality. These results support URA-SIM as a transparent, model-consistent and computationally lightweight route from fixed reduced-frame acquisition to classical SIM reconstruction workflows.

physics.optics↗

arXiv2026

Source localization realizes single frame super-resolution for fluorescence imaging

Existing super-resolution microscopy is often constrained by inherent trade-offs between resolution, acquisition speed, phototoxicity, and hardware complexity. Computational post-processing approaches offer a promising alternative, but they typically suffer from linearity distortion, high computational cost, reliance on pre-training data, or reconstruction artifacts. Here, we present Source Localization (SoLo), a novel single-frame super-resolution algorithm for fluorescence imaging without these limitations. Built on the principle of inferring fluorescent source positions via sampling-detection strategy, SoLo achieves non-iterative, parallelizable computation, enabling real-time live-cell imaging with high spatiotemporal resolution. The intensity linearity preservation of SoLo makes it compatible with quantitative analysis such as calcium imaging and fluorescence resonance energy transfer. We further extended this framework to 3D-SoLo for volumetric imaging and nonlinear SoLo (NL-SoLo) for high-density fluorescence fluctuation imaging. With its ease of parameter tuning and compatibility with existing imaging systems, SoLo offers an accessible solution for ordinary labs, enabling diverse biomedical imaging applications.

physics.optics↗

arXiv2025

ProtoBERT-LoRA: Parameter-Efficient Prototypical Finetuning for Immunotherapy Study Identification

Identifying immune checkpoint inhibitor (ICI) studies in genomic repositories like Gene Expression Omnibus (GEO) is vital for cancer research yet remains challenging due to semantic ambiguity, extreme class imbalance, and limited labeled data in low-resource settings. We present ProtoBERT-LoRA, a hybrid framework that combines PubMedBERT with prototypical networks and Low-Rank Adaptation (LoRA) for efficient fine-tuning. The model enforces class-separable embeddings via episodic prototype training while preserving biomedical domain knowledge. Our dataset was divided as: Training (20 positive, 20 negative), Prototype Set (10 positive, 10 negative), Validation (20 positive, 200 negative), and Test (71 positive, 765 negative). Evaluated on test dataset, ProtoBERT-LoRA achieved F1-score of 0.624 (precision: 0.481, recall: 0.887), outperforming the rule-based system, machine learning baselines and finetuned PubMedBERT. Application to 44,287 unlabeled studies reduced manual review efforts by 82%. Ablation studies confirmed that combining prototypes with LoRA improved performance by 29% over stand-alone LoRA.

cs.CL↗

arXiv2024

High SNR 3D Imaging from Millimeter-scale Thick Tissues to Cellular Dynamics via Structured Illumination Microscopy

Three-dimensional (3D) fluorescence imaging provides a vital approach for study of biological tissues with intricate structures, and optical sectioning structured illumination microscopy (OS-SIM) stands out for its high imaging speed, low phototoxicity and high spatial resolution. However, OS-SIM faces the problem of low signal-to-noise ratio (SNR) when using traditional decoding algorithms, especially in thick tissues. Here we propose a Hilbert-transform decoding and space domain based high-low (HT-SHiLo) algorithm for noise suppression in OS-SIM. We demonstrate HT-SHiLo algorithm can significantly improve the SNR of optical sectioning images at rapid processing speed, and double the imaging depth in thick tissues. With our OS-SIM system, we achieve high quality 3D images of various biological samples including mouse brains, Drosophila clock neurons, organoids, and live cells. We anticipate that this approach will render OS-SIM a powerful technique for research of cellular organelles or thick tissues in 3D morphology.

physics.optics↗