arXiv subjects

Luru Dai

Publications and source records attributed to Luru Dai.

5 recordsLinked to original sources

arXiv2026

A Zero-Shot Deep Image Prior Framework for Denoising and Deconvolution in Fluorescence Microscopy

Fluorescence microscopy images are degraded by noise and diffraction-induced blur, which compromise structural fidelity and limit quantitative analysis. Supervised deep learning methods achieve impressive restoration performance but require large-scale paired datasets that are difficult to obtain in practice. To address this issue, we propose SDIP, a zero-shot deep image prior (DIP) framework that sequentially performs denoising and deconvolution without external training data. An aSeqDIP-based module first suppresses noise while preserving fine structures through sequential autoencoding regularization. In the deconvolution stage, a wavelet-based background correction step is incorporated before the proposed RLG-DIP module performs artifact-reduced deconvolution. RLG-DIP uses the Richardson-Lucy deconvolution result as a physically consistent guidance prior, integrating the imaging model with the implicit prior of DIP to stabilize the ill-posed deconvolution process. Experiments on the BioSR dataset across multiple cellular structures demonstrate that SDIP improves both signal-to-noise ratio and resolution, achieving superior visual quality and improved quantitative performance on most evaluated structures. The proposed framework may also provide useful insights for designing physically guided DIP methods for other inverse problems.

eess.IV↗

arXiv2025

Computational TIRF enables optical sectioning beyond the evanescent field for widefield fluorescence microscopy

The resolving ability of widefield fluorescence microscopy is fundamentally limited by out-of-focus background owing to its low axial resolution, particularly for densely labeled biological samples. Although total internal reflection fluorescence (TIRF) microscopy provides strong near-surface sectioning, they are intrinsically restricted to shallow imaging depths. Here we present computational TIRF (cTIRF), a deep learning-based imaging modality that generates TIRF-like sectioned images directly from conventional widefield epifluorescence measurements without any optical modification. By integrating a physics-informed forward model into network training, cTIRF achieves effective background suppression and axial resolution enhancement while maintaining consistency with the measured widefield data. We demonstrate that cTIRF recovers near-surface structures with performance comparable to experimental TIRF, and further enables both single-frame and volumetric sectioned reconstruction in densely labeled samples where conventional TIRF fails. This work establishes cTIRF as a practical and deployable alternative to hardware-based optical sectioning in fluorescence microscopy, enabled by rapid adaptation to new imaging systems with minimal calibration data.

physics.optics↗

arXiv2002

A constant extension ensembles model of double-stranded chain molecules

Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $β$-sheets in proteins, with fixed extension constraint is built in this paper. Based on polymer-graph theory and the self-avoiding walks, sequence dependence and excluded-volume interactions are explicitly taken into account. Using the model, we investigate force-extension curves, contact distributions and force-temperature curves at given extensions. We find that, for the same homogeneous chains, the force-extension curves are almost consistent with the extension-force curves in the conjugated force ensembles. Especially, the consistence depends on chain lengths. But the curves of the two ensembles are completely different from each other if sequences are considered. In addition, contact distributions of homogeneous sequence show that the double-stranded regions in hairpin conformations tend to locate at two sides of the chain. We contribute the unexpected phenomena to the nonuniformity of excluded-volume interactions of the region and two tails with different lengths. This tendency will disappear if the interactions are canceled. Finally, in constant extension ensemble, the force-flipping transitions conjugated with re-entering phenomena in constant force ensemble are observed in hairpin conformations, while they do not present in secondary structure conformations.

cond-mat.soft↗

arXiv2002

A model for the force stretching double-stranded chain molecules

We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $β-$sheets in protein, by including the constant force stretching at one end of molecules as in a typical single-molecule experiment. The conformations of double-stranded regions of the chain are calculated based on polymer graph-theoretic approach [S-J. Chen and K. A. Dill, J. Chem. Phys. {\bf109}, 4602(1998)], while the unpaired single-stranded regions are treated as self-avoiding walks. Sequence dependence and excluded volume interaction are taken into account explicitly. Two classes of conformations, hairpin and RNA secondary structure are explored. For the hairpin conformations, all possible end-to-end distances corresponding to the different types of double-stranded regions are enumerated exactly. For the RNA secondary structure conformations, a new recursive formula incorporating the secondary structure and end-to-end distribution has been derived. Using the model, we investigate the extension-force curves, contact and population distributions and re-entering phenomena, respectively. we find that the force stretching homogeneous chains of hairpin and secondary structure conformations are very different: the unfolding of hairpins is two-state, while unfolding the latter is one-state. In addition, re-entering transitions only present in hairpin conformations, but are not observed in secondary structure conformations.

cond-mat.soft↗

arXiv2002

Maximum-entropy calculation of end-to-end distance distribution of force stretching chains

Using the maximum-entropy method, we calculate the end-to-end distance distribution of the force stretched chain from the moments of the distribution, which can be obtained from the extension-force curves recorded in single-molecule experiments. If one knows force expansion of the extension through the $(n-1)$th power of force, it is enough information to calculate the $n$ moments of the distribution. We examine the method with three force stretching chain models, Gaussian chain, free-joined chain and excluded-volume chain on two-dimension lattice. The method reconstructs all distributions precisely. We also apply the method to force stretching complex chain molecules: the hairpin and secondary structure conformations. We find that the distributions of homogeneous chains of two conformations are very different: there are two independent peaks in hairpin distribution; while only one peak is observed in the distribution of secondary structure conformations. Our discussion also shows that the end-to-end distance distribution may discover more critical physical information than the simpler extension-force curves can give.

cond-mat.soft↗