Nature Methods

MicroSplit: a computational unmixing method for multiplexed fluorescence imaging of up to 4 structures per imaging channel. @ashesh0 @florianjug nature.com/articles/s4159…

UDMT: a multi-animal tracker for behavioral research including on mice, rats, flies, worm and betta fish. nature.com/articles/s4159…

A study investigates sources of noise in Xenium spatial transcriptomics data and introduces a method to resolve mixed signals and enhance cell type specificity. nature.com/articles/s4159…

eSIG-Net: an interaction language model that predicts the effects on mutations on protein interactions. nature.com/articles/s4159…

For a quick summary, read the Research Briefing here: nature.com/articles/s4159…

A self-localized ultrafast pencil beam can be applied for near-diffraction-limited, high-throughput volumetric imaging in intact tissues and in vitro models. nature.com/articles/s4159…

Single-molecule localization and diffusivity microscopy (SMLDM) provides insights into dynamic biological processes in living cells. @orchid_5 nature.com/articles/s4159…

Spatial 5mC-seq offers nonbiased spatiotemporal analysis of the genome-wide methylome at single cell resolution. nature.com/articles/s4159…

sm-PORE-cupine combines SHAPE chemical probing with RNA nanopore sequencing to identify RNA structural ensembles. nature.com/articles/s4159…

PinkyCaMP: a red genetically encoded calcium indicator with improved brightness and stability. @LabMasseck nature.com/articles/s4159…

Multi-Embed is an interpretable framework that enables integrated analyses of histological images and multilayer molecular profiles. nature.com/articles/s4159…

Antigen-stabilizable fluorescent nanobodies that become fluorescent upon binding intracellular targets enable background-free multicolor imaging and biosensing in living systems. @EinsteinMed @salkinstitute @animmerj nature.com/articles/s4159…

NirFAP680 is a near-IR fluorogen-activating protein with an order of magnitude greater cellular brightness and photostability than currently available NIR FAPs. nature.com/articles/s4159…

And read the associated News & Views here: nature.com/articles/s4159…

Orthus: an RNA foundation model pretrained via contrastive learning based on splicing isoforms and orthologous transcripts. @phil_fradkin @ianshi3 @Taykhoom_Dalal @BoWang87 @quaidmorris @UofT @VectorInst @MSKCancerCenter nature.com/articles/s4159…

Predictive virtual embryo models integrate single-cell and spatial data with AI, offering a tool for modeling mammalian embryogenesis across scales, as discussed in this Comment. nature.com/articles/s4159…

Spontaneous blinking dyes in the far-red range facility single-molecule localization microscopy. nature.com/articles/s4159…

New voltage indicators JEDI3sub and JEDI3hyp allow monitoring subthreshold neuronal activity in awake mice. @stpierrelab nature.com/articles/s4159…

In this month's Editorial, we demystify the appeals process at Nature Methods. nature.com/articles/s4159…

Planetary biology has made its stage entrances across cell and molecular biology, biochemistry and biophysics. A nascent group of researchers sees planetary health as an urgent reason to bridge the molecular and planetary scales. @metricausa investigates. nature.com/articles/s4159…