arXiv subjects

Zhaoke Huang

Publications and source records attributed to Zhaoke Huang.

4 recordsLinked to original sources

arXiv2026

Recover Cell Tensor: Diffusion-Equivalent Tensor Completion for Fluorescence Microscopy Imaging

Fluorescence microscopy (FM) imaging is a fundamental technique for observing live cell division, one of the most essential processes in the cycle of life and death. Observing 3D live cells requires scanning through the cell volume while minimizing lethal phototoxicity. That limits acquisition time and results in sparsely sampled volumes with anisotropic resolution and high noise. Existing image restoration methods, primarily based on inverse problem modeling, assume known and stable degradation processes and struggle under such conditions, especially in the absence of high-quality reference volumes. In this paper, from a new perspective, we propose a novel tensor completion framework tailored to the nature of FM imaging, which inherently involves nonlinear signal degradation and incomplete observations. Specifically, FM imaging with equidistant Z-axis sampling is essentially a tensor completion task under a uniformly random sampling condition. On one hand, we derive the theoretical lower bound for exact cell tensor completion, validating the feasibility of accurately recovering 3D cell tensor. On the other hand, we reformulate the tensor completion problem as a mathematically equivalent score-based generative model. By incorporating structural consistency priors, the generative trajectory is effectively guided toward denoised and geometrically coherent reconstructions. Our method demonstrates state-of-the-art performance on SR-CACO-2 and three real \textit{in vivo} cellular datasets, showing substantial improvements in both signal-to-noise ratio and structural fidelity.

eess.IV↗

arXiv2025

CTransformer: Deep-transformer-based 3D cell membrane tracking with subcellular-resolved molecular quantification

Deep learning segmentation and fluorescence imaging techniques allow the cellular morphology of living embryos to be constructed spatiotemporally. These development processes involve numerous molecules distributed at the subcellular scale, such as cell adhesion (E-cadherin), which accumulate at cell-cell interfaces to regulate intercellular connection. However, quantifying molecular distributions within specific subcellular regions across the entire embryo, where cell movement and molecular redistribution occur rapidly, is challenging due to the need for simultaneous cell morphology reconstruction and lineage tracing due to photobleaching and phototoxicity. We report a transformer-based pipeline, CTransformer, that establishes a 4D cellular morphology map before the 550-cell (late) stage. CTransformer constructed 4D cellular morphology atlases, reaching 80% accuracy at the 550-cell stage. Through this advanced architecture, we use only one channel to reconstruct cell morphology and achieve cell tracing. With each cell's morphology as a reference, the distribution of specific molecules throughout the cell body and at cell interfaces can be quantitatively measured in another fluorescence channel. We apply this methodology to track E-cadherin during embryonic development of the worm Caenorhabditis elegans, from fertilization to gastrulation. Our results reveal that E-cadherin is tightly regulated across individual embryos, both within single cells and at cell-cell interfaces, displaying an anterior-posterior gradient and cell- and lineage-specific patterns. Furthermore, its spatiotemporal heterogeneity influences cell mechanics and embryonic morphogenesis, helping explain how C. elegans achieves stereotypical developmental patterns at cellular resolution.

physics.bio-ph↗

arXiv2025

Scalable Co-Clustering for Large-Scale Data through Dynamic Partitioning and Hierarchical Merging

Co-clustering simultaneously clusters rows and columns, revealing more fine-grained groups. However, existing co-clustering methods suffer from poor scalability and cannot handle large-scale data. This paper presents a novel and scalable co-clustering method designed to uncover intricate patterns in high-dimensional, large-scale datasets. Specifically, we first propose a large matrix partitioning algorithm that partitions a large matrix into smaller submatrices, enabling parallel co-clustering. This method employs a probabilistic model to optimize the configuration of submatrices, balancing the computational efficiency and depth of analysis. Additionally, we propose a hierarchical co-cluster merging algorithm that efficiently identifies and merges co-clusters from these submatrices, enhancing the robustness and reliability of the process. Extensive evaluations validate the effectiveness and efficiency of our method. Experimental results demonstrate a significant reduction in computation time, with an approximate 83% decrease for dense matrices and up to 30% for sparse matrices.

cs.DC↗

arXiv2025

Volume Tells: Dual Cycle-Consistent Diffusion for 3D Fluorescence Microscopy De-noising and Super-Resolution

3D fluorescence microscopy is essential for understanding fundamental life processes through long-term live-cell imaging. However, due to inherent issues in imaging principles, it faces significant challenges including spatially varying noise and anisotropic resolution, where the axial resolution lags behind the lateral resolution up to 4.5 times. Meanwhile, laser power is kept low to maintain cell viability, leading to inaccessible low-noise and high-resolution paired ground truth (GT). To tackle these limitations, a dual Cycle-consistent Diffusion is proposed to effectively mine intra-volume imaging priors within 3D cell volumes in an unsupervised manner, i.e., Volume Tells (VTCD), achieving de-noising and super-resolution (SR) simultaneously. Specifically, a spatially iso-distributed denoiser is designed to exploit the noise distribution consistency between adjacent low-noise and high-noise regions within the 3D cell volume, suppressing the spatially varying noise. Then, in light of the structural consistency of the cell volume, a cross-plane global-propagation SR module propagates high-resolution details from the XY plane into adjacent regions in the XZ and YZ planes, progressively enhancing resolution across the entire 3D cell volume. Experimental results on 10 in vivo cellular dataset demonstrate high improvements in both denoising and super-resolution, with axial resolution enhanced from ~ 430 nm to ~ 90 nm.

eess.IV↗