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Nature Methods is a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry relevant to the life sciences.

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Author Correction: Deep-tissue SWIR imaging using rationally designed small red-shifted near-infrared fluorescent protein

Nature Methods, Published online: 02 February 2023; doi:10.1038/s41592-023-01798-yAuthor Correction: Deep-tissue SWIR imaging using rationally designed small red-shifted near-infrared fluorescent protein

LILAC: enhanced actin imaging with an optogenetic Lifeact

Nature Methods, Published online: 30 January 2023; doi:10.1038/s41592-022-01761-3LILAC is a photoactivatable version of Lifeact, a tool for labeling F-actin. LILAC can help avoid cytotoxicity, which is sometimes associated with the use of Lifeact.

A mathematical method and software for spatially mapping intercellular communication

Nature Methods, Published online: 24 January 2023; doi:10.1038/s41592-022-01729-3Communication between cells is crucial for coordinated cellular functions in multicellular organisms. We present an optimal transport theory-based tool to infer cell–cell communication networks, spatial signaling directions and downstream targets in multicellular systems...

Seeing the wood for the trees

Nature Methods, Published online: 23 January 2023; doi:10.1038/s41592-022-01741-7A deep learning approach called DeepPiCt facilitates segmentation and macromolecular identification in the cellular jungle of electron cryotomography data.

Convolutional networks for supervised mining of molecular patterns within cellular context

Nature Methods, Published online: 23 January 2023; doi:10.1038/s41592-022-01746-2DeePiCt (deep picker in context) is a versatile, open-source deep-learning framework for supervised segmentation and localization of subcellular organelles and biomolecular complexes in cryo-electron tomography.

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Nature Methods, Published online: 23 January 2023; doi:10.1038/s41592-022-01728-4This work presents a computational framework, COMMOT, to spatially infer cell–cell communication from transcriptomics data based on a variant of optimal transport (OT).

Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

Nature Methods, Published online: 23 January 2023; doi:10.1038/s41592-023-01768-4Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping

Publisher Correction: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density

Nature Methods, Published online: 19 January 2023; doi:10.1038/s41592-023-01765-7Publisher Correction: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density

Jasmine and Iris: population-scale structural variant comparison and analysis

Nature Methods, Published online: 19 January 2023; doi:10.1038/s41592-022-01753-3An optimized pipeline for improved inference and analysis of structural variants (SVs) has been developed, which uses Iris for refining breakpoints and sequences, and Jasmine for comparing SV calls at population scale.

HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence

Nature Methods, Published online: 19 January 2023; doi:10.1038/s41592-022-01751-5Hybrid Unmixing offers enhanced imaging of multiplexed fluorescence labels, enabling longitudinal imaging of multiple fluorescent signals with reduced illumination intensities.

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