Light-activated tetanus neurotoxin for conditional proteolysis and inducible synaptic inhibition in vivo - Nature Methods

LATeNT is a light-activatable form of tetanus neurotoxin that can be used for spatiotemporally precise inhibition of exocytosis in neurons and other cells. It can inhibit synaptic transmission in vivo...

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Inference of secreted protein signaling activities in intercellular communication - Nature Methods

SecAct is a framework that leverages transcriptomic data to infer secreted protein signaling activities.

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Spike inference from calcium imaging data acquired with GCaMP8 indicators - Nature Methods

In this Analysis, Rupprecht et al. investigate the behavior of GCaMP8 variants in spike inference using several different algorithms. They highlight the role of the indicators’ linearity in the infere...

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Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data - Nature Methods

Spatialproteomics is a Python-based toolbox that supports end-to-end analysis of highly multiplexed imaging data.

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Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain - Nature Methods

Fullscope-seq combines a spatial transcriptomics approach (Stereo-seq) with long-read sequencing. The approach provides isoform information at single-cell resolution across a large field of view, as d...

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A versatile platform for two-photon neuronal population voltage imaging across cortical depths - Nature Methods

FlatMux is an optimized microscope system for multiplexed two-photon imaging of neuronal activity with genetically encoded voltage sensors. The flexible system is demonstrated in a variety of scenario...

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Design and optimization of a kinase-controlled allosteric switch - Nature Methods

This Article introduces a phospho-switch for allosterically regulating target proteins in response to ERK kinase activity.

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Siibra: a software tool suite for realizing a Multilevel Human Brain Atlas from complex data resources - Nature Methods

Siibra is a software suite for working with diverse human brain atlases. It links data acquired with different modalities and at different resolution, thereby creating a Multilevel Human Brain Atlas.

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Simultaneous single-cell calcium imaging of neuronal population activity and brain-wide BOLD fMRI - Nature Methods

Imaging of brain-wide vascular activity with BOLD fMRI in combination with calcium imaging at single-cell resolution using MRI-compatible components provides detailed insights into neurovascular coupl...

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NicheTrans: spatial-aware cross-omics translation - Nature Methods

NicheTrans is a multimodal framework that enables translation of spatial data across modalities.

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Towards a standardized file format and open-source analysis framework for Brillouin microscopy data - Nature Methods

Nature Methods - Towards a standardized file format and open-source analysis framework for Brillouin microscopy data

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A comprehensive benchmark of sequence-based subcellular localization predictors for human proteins - Nature Methods

This Registered Report presents the results of a study to evaluate the performance of sequence-based protein localization predictors on a curated test dataset of 3,814 human proteins.

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Efficient evidence-based genome annotation with EviAnn - Nature Methods

EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

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ClairS: a deep-learning method for long-read tumor–normal pair somatic small variant calling - Nature Methods

ClairS accurately detects somatic small variants using long-read sequencing data from tumor–normal pair samples.

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RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation - Nature Methods

RNAbpFlow generates all-atom RNA conformational ensembles for single-chain RNA monomers without the explicit or implicit use of evolutionary information or homologous structural templates.

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Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution - Nature Methods

Spatio-DARLIN combines the DARLIN mouse model with sequencing-based spatial transcriptomics to enable high-resolution spatial lineage tracing in mice.

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EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control - Nature Methods

EasyGrid is a fully automated and modular platform for high-throughput sample vitrification for cryo-EM and cryo-ET. It integrates in-line plasma treatment of the sample support, microfluidic dispensi...

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A cloud-based miniscope for neurosurveillance of brain health and disease in freely behaving animals - Nature Methods

A miniscope with cloud-based operation and multicontrast capabilities enables continuous recording of neuronal activity, hemodynamics or cellular dynamics over multiple days. This allows monitoring br...

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Derivation of elephant induced pluripotent stem cells - Nature Methods

This study reports the first successful derivation of elephant induced pluripotent stem cells.

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3D pathology-guided microdissection - Nature Methods

This method combines open-top light-sheet microscopy with computer numerical controlled milling for high-precision 3D microdissection of tissues.

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SmartTrap: automated precision experiments with optical tweezers - Nature Methods

SmartTrap is a smart optical tweezers platform that integrates real-time three-dimensional particle tracking, electronics and microfluidics to perform single-molecule biophysics and cell mechanics exp...

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A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species - Nature Methods

HiCFoundation is a foundation model pretrained on a large corpus of Hi-C data for comprehensive 3D genome and epigenomics analysis.

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Search, organize, aggregate and share image data with BioFile Finder (BFF) - Nature Methods

Nature Methods - Search, organize, aggregate and share image data with BioFile Finder (BFF)

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A human induced pluripotent stem cell model for the holistic study of epithelial-to-mesenchymal transitions - Nature Methods

This study presents an human induced pluripotent stem-cell-based culture model for studying cell state transitions during epithelial-to-mesenchymal transition.

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Evaluating the role of pretraining dataset size and diversity on single-cell foundation model performance - Nature Methods

The performance of single-cell foundation models is dependent on many factors. This study assesses the effect of the pretraining dataset’s size and diversity, revealing potential challenges in pursuin...

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Simultaneous two- and three-photon multiplane imaging across cortical layers in freely moving mice - Nature Methods

A lightweight head-mounted multiplane microscope allows simultaneous imaging from >1,800 neurons spread across the cortical layers in freely moving mice performing complex behavioral tasks, sampled...

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Spatially resolved m6A profiling using m6A-ARTR-DBiT - Nature Methods

m6A-ARTR-DBiT offers a spatial assay to profile the distribution of N6-methyladenosine (m6A) across the transcriptome in intact tissue sections.

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