Wang et al. introduce DVR-NeMF, a neural magnetic field framework that reconstructs dynamic 4D MRI in real-time level with high fidelity. By leveraging spatiotemporal priors, the method enables reliable heart-function assessment, offering a step toward broader clinical use of MRI for dynamic imaging.

Lou et al. present stLVG, a lightweight vector-guided graph model for spatial multi-slice and multi-omics data integration. stLVG incorporates distance- and angle-based weights to capture spatial geometry, enabling robust alignment, cross-omics label transfer, and identification of tumor boundary regions across diverse spatial transcriptomics datasets.

Rice et al. report Fuzzion2, a high-performance program for targeted gene fusion detection in unmapped read pairs. Sensitivity meets or exceeds that of de novo callers, making Fuzzion2 well suited for clinical testing and large-scale research investigations such as the mapping of distinct fusion landscapes between pediatric and adult cancers.

Cramer et al. present TRACE-QC, a method for quality control of time-course imaging in 3D cell cultures. Using iterative Procrustes analysis, it reorders and aligns spheroid positions, corrects mislabeled images, and improves data integrity. TRACE-QC enhances assay reliability and interpretability without experimental modifications or parameter tuning.

Krieg et al. develop melanoma brain metastasis models based on cortical brain organoids. They demonstrate the potential for therapeutic applications, screening a library of anti-cancer compounds and identifying the XPO1 inhibitor selinexor as a promising candidate that demonstrates effectiveness against cancer cells while maintaining low toxicity.

Williamson et al. present FlickerPrint, an open-source computational analysis tool for measuring the interfacial tension and bending rigidity of soft bodies from their shape fluctuations in time-series confocal microscopy videos. The package allows for thousands of biomolecular condensates, vesicles, and other soft bodies to be analyzed.

Shevade et al. present CAT-ATAC (CRISPR and transcriptomics-assay for transposase-accessible chromatin), a single-cell sequencing assay that profiles gene expression, chromatin accessibility, and CRISPR perturbation from the same cells by modifying the commercially available 10× Multiome assay, and demonstrate its utility in multiple biological and therapeutically relevant applications.

Zhang et al. develop two types of multiplexed miniaturized two-photon microscopes (M-MINI2Ps) that increase imaging speed via beam multiplexing while preserving spatial resolution and demonstrate their utility in large-scale calcium imaging and voltage imaging of brain activity in freely moving mice.

Forbes et al. benchmark human read removal methods for viral and microbial metagenomics. Using synthetic and microbiome datasets, along with a set of benchmark methods, they demonstrate that a custom Bowtie2 configuration (“very-sensitive-local” mode with single end) with the T2T-CHM13 reference best balances host read removal and microbial integrity.

Teles-Reis et al. present EyaHOST, a modular Drosophila system that enables clone generation in the eye disc with independent genetic manipulation of other tissues. EyaHOST uses an Eya-KD “kick-out” system for clonal QF2-driven tumor initiation and GAL4 for organ-specific host perturbation, providing a scalable platform for dissecting tumor-host interactions.

Rybczynski et al. introduce a method to measure DNA repair timing at specific genomic loci using very fast CRISPR and labeling of locally denatured genomic DNA and associated repair proteins. This approach enables detailed analysis of diverse repair processes, advancing our understanding of genomic instability and its role in disease.

Noh et al. present DynamicNeuronTracker, which segments single neurons despite positional jitter from tissue deformation in 3D calcium imaging. Analyzing the imaging of pheromone-sensing neurons under controlled stimulation, they identify 15 neuronal subpopulations with distinct responses to eight bile acids and steroids, revealing a pronounced bias toward estrogen and pregnanolone.

Kunigo et al. introduce t-nanoEM, a practical method that enables high-depth, target-specific long-read methylation analysis with as little as 8 ng of DNA. They develop a pipeline for haplotype-resolved and mutated allele-specific methylation analysis and demonstrate its utility by successfully applying it to clinical breast and lung cancer samples.

Bhattacharyya et al. present DiffHiChIP, a statistical framework for detecting differential chromatin loops from HiChIP data. By modeling distance decay of contacts and integrating multiple statistical models and dispersion estimation strategies, DiffHiChIP improves detection of long-range differential interactions and provides a robust tool for studying condition-specific chromatin regulation.

To establish a standardized and reproducible method for TBI research in human organoids, Sirtori et al. develop a cost-effective and easy-to-use tabletop device that generates tunable pressure waves. These blast waves lead to acute neurodegeneration and the onset of chronic neuronal dysfunction, mimicking in vivo pathologies.

Xin et al. present MetaLigand, a computational tool that infers cellular communication involving non-peptide molecules in health and disease. We apply this tool to analyze complex cellular interactions and identify molecular changes relevant to age-related macular degeneration.

Cysteine oxidation controls diverse signaling pathways but remains difficult to study at scale. Lilla et al. present SICyLIA-cTMT, a quantitative mass spectrometry workflow that simultaneously measures cysteine redox dynamics and protein abundance with high accuracy from minimal input. The method enhances coverage, reduces instrument time, and enables comprehensive analysis of oxidative signaling in cells and tissues.

Kiessling et al. introduce a TEM platform and analysis workflow that consistently images the nuclear center and perinuclear mitochondria in adult cardiomyocytes, enabling automated quantification and discovery of spatially resolved remodeling. Using Drp1-deficient mice, they demonstrate the ability to detect stress-induced anomalies in nanoscale organellar architecture.

Niu et al. present scPairing, a deep learning tool facilitating the integration and generation of single-cell multiomics data through cell pairing. Pairing produces realistic multiomics data that can be used in downstream analyses to uncover relationships between cellular modalities. scPairing also extends to trimodal data generation.

(Cell Reports Methods 5, 101203; October 20, 2025)

Zhao et al. present an optimized 3D click chemistry method (C4-3D) that enables visualization of EdU-labeled proliferating cells in tissue-cleared whole mouse brains. The method is compatible with major tissue-clearing protocols and fluorescent reporters and allows precise mapping of proliferating cells to the Allen Brain Atlas enabling spatiotemporal identification of neurogenesis in development, injury, aging, and disease models.

Zhou et al. develop the optical looping interactive viewing engine (OLIVE), a web-based application for browsing and exploring user-generated and publicly available chromatin tracing datasets.

Yassine et al. adapt an APEX2-based RNA proximity labeling approach that labels RNAs in both gram-negative and gram-positive bacteria. This method involves fusing an RNA-binding protein to APEX2, which rapidly labels localized RNAs on a faster timescale than the short lifetimes of RNAs in bacteria.

Zähringer et al. introduce AIstain, a U-Net-based deep learning approach for label-free microglial detection in live cell image cytometry. Their method outperforms fluorescence staining and common segmentation tools, enabling accurate, high-throughput phagocytosis analysis while avoiding cytotoxic dyes.

Zhou et al. present stTransfer, a transfer-learning framework that unites scRNA-seq and spatial transcriptomics to achieve single-cell-resolution annotation. Benchmarked on diverse datasets, it surpasses current tools and uncovers cell types in the optic tectum in zebra finch.