Nature Methods
@natmethods.nature.com
A scientific journal publishing cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Posts by the editors.
Confocal Airy beam integrated with single-photon oblique light-sheet tomography is a high-throughput imaging approach for brain-wide mapping of neurons.
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Confocal Airy beam oblique light-sheet tomography for brain-wide cell type distribution and morphology - Nature Methods
Confocal Airy beam integrated with single-photon oblique light-sheet tomography (CAB-OLST) is a high-throughput imaging approach for brain-wide mapping of neurons, as demonstrated in cleared mouse bra...
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November 20, 2025 at 5:42 PM
Confocal Airy beam integrated with single-photon oblique light-sheet tomography is a high-throughput imaging approach for brain-wide mapping of neurons.
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Stimulus-modulated approach to steady state (SASS): an acquisition scheme for event-related fMRI that generates data interspaced with acquisition-free periods for stimulus presentation or response reporting.
@renilmathew.bsky.social @northernthrux.bsky.social
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@renilmathew.bsky.social @northernthrux.bsky.social
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Stimulus-modulated approach to steady state (SASS): a flexible paradigm for event-related fMRI - Nature Methods
Stimulus-modulated approach to steady state (SASS) is an acquisition scheme for event-related fMRI that generates data with high temporal signal-to-noise ratios interspaced with acquisition-free perio...
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November 20, 2025 at 5:27 PM
Stimulus-modulated approach to steady state (SASS): an acquisition scheme for event-related fMRI that generates data interspaced with acquisition-free periods for stimulus presentation or response reporting.
@renilmathew.bsky.social @northernthrux.bsky.social
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@renilmathew.bsky.social @northernthrux.bsky.social
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Jaxley: a platform for simulating biophysical models in neuroscience. @deismic.bsky.social @djdavid.bsky.social @unituebingen.bsky.social @ml4science.bsky.social science.bsky.social
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Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods
Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...
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November 20, 2025 at 5:01 PM
Jaxley: a platform for simulating biophysical models in neuroscience. @deismic.bsky.social @djdavid.bsky.social @unituebingen.bsky.social @ml4science.bsky.social science.bsky.social
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By developing a strategy of metagenomic coassembly and prioritizing divergent marker gene sequences, Bin Chicken efficiently recovers more than 77,000 microbial genomes with high novel diversity which expands the tree of life.
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Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes - Nature Methods
By developing a strategy of metagenomic coassembly and prioritizing divergent marker gene sequences, Bin Chicken efficiently recovers more than 77,000 microbial genomes with high novel diversity, ther...
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November 20, 2025 at 4:49 PM
By developing a strategy of metagenomic coassembly and prioritizing divergent marker gene sequences, Bin Chicken efficiently recovers more than 77,000 microbial genomes with high novel diversity which expands the tree of life.
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MISO: a micro isolation method for single-particle cryo-EM grid preparation for extremely small sample amounts.
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MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony - Nature Methods
The micro isolation (MISO) method combines microfluidics-based protein purification with cryo-EM grid preparation, enabling cryo-EM structure determination of soluble and membrane proteins starting fr...
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November 20, 2025 at 4:46 PM
MISO: a micro isolation method for single-particle cryo-EM grid preparation for extremely small sample amounts.
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Read this powerful piece from a computational neuroscientist who experienced a turning point in her research upon witnessing human brain surgery.
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What witnessing neurosurgery taught me about modeling the brain - Nature Methods
As a computational neuroscientist, I study the brain through models that reduce it to data points and 3D reconstructions, yet watching Dr. Obaid perform live neurosurgeries showed me what models alone...
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November 20, 2025 at 4:33 PM
Read this powerful piece from a computational neuroscientist who experienced a turning point in her research upon witnessing human brain surgery.
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Nature Methods is hiring! We are looking for candidates with expertise in genetics, genomics and/or molecular biology to join our editorial team in the US (NYC/Jersey City) or China (Shanghai/Beijing). Apply by December 12!
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ALT: a sign that says we 're hiring in orange on a white background
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November 18, 2025 at 6:30 PM
Nature Methods is hiring! We are looking for candidates with expertise in genetics, genomics and/or molecular biology to join our editorial team in the US (NYC/Jersey City) or China (Shanghai/Beijing). Apply by December 12!
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In our November issue we feature several papers on the theme of tools for cell segmentation and tracking. For a roadmap to the issue, read our Editorial.
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Following a cell’s every move - Nature Methods
Identifying individual cells and tracking their movements over time are two critically important tasks in bioimage analysis. We discuss a fresh wave of tools that push these techniques toward peak per...
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November 13, 2025 at 8:41 PM
In our November issue we feature several papers on the theme of tools for cell segmentation and tracking. For a roadmap to the issue, read our Editorial.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our November issue is now live! 🎉
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On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
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On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
November 13, 2025 at 8:38 PM
Our November issue is now live! 🎉
www.nature.com/nmeth/volume...
On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
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On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
u-Segment3D: a universal framework for 2D to 3D cell segmentation that generalizes across cell types and imaging modalities.
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Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
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November 12, 2025 at 2:58 PM
u-Segment3D: a universal framework for 2D to 3D cell segmentation that generalizes across cell types and imaging modalities.
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November 11, 2025 at 5:49 PM
nELISA: a miniaturized sandwich immunoassay that serves as a massively scalable platform for quantitative proteomics.
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nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome - Nature Methods
nELISA miniaturizes the sandwich immunoassay and transforms it into a massively scalable platform for quantitative proteomics.
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November 11, 2025 at 5:42 PM
nELISA: a miniaturized sandwich immunoassay that serves as a massively scalable platform for quantitative proteomics.
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Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social
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Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data - Nature Methods
Monod fits biophysically motivated models to single-cell transcriptomics data, empowering multifaceted and integrative insights of gene expression dynamics, stochasticity and regulation.
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November 11, 2025 at 5:35 PM
Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social
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CABLE: a method that uses information about cell or nuclear shape to infer fiber tracts in the brain.
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Whole-brain reconstruction of fiber tracts based on cytoarchitectonic organization - Nature Methods
CABLE harnesses cytoarchitectural information such as cell or nuclear shape to infer fiber tracts in the brain of, for example, marmosets, macaques or humans.
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November 7, 2025 at 3:00 PM
CABLE: a method that uses information about cell or nuclear shape to infer fiber tracts in the brain.
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Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
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Squidiff: predicting cellular development and responses to perturbations using a diffusion model - Nature Methods
Squidiff is a diffusion-based model to predict transcriptomic changes in response to perturbations.
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November 7, 2025 at 2:41 PM
Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
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ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
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ESPRESSO: spatiotemporal omics based on organelle phenotyping - Nature Methods
ESPRESSO leverages functional information obtained from organelles for deep spatiotemporal phenotyping of single cells.
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November 6, 2025 at 5:40 PM
ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
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Cyclone, an acyclovir-controlled poison exon cassette, enables regulation of transgene and endogenous gene expression with minimal background.
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A portable poison exon for small-molecule control of mammalian gene expression - Nature Methods
This work introduces Cyclone, an acyclovir-controlled cassette that enables regulation of both transgene and endogenous gene expression with minimal background activity.
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November 6, 2025 at 4:29 PM
Cyclone, an acyclovir-controlled poison exon cassette, enables regulation of transgene and endogenous gene expression with minimal background.
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By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data. @gabrielpeyre.bsky.social @cantinilab.bsky.social
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STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
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November 6, 2025 at 4:07 PM
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data. @gabrielpeyre.bsky.social @cantinilab.bsky.social
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By pretraining on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances building foundation models for spatial single-cell analysis.
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Nicheformer: a foundation model for single-cell and spatial omics - Nature Methods
Pretrained on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances toward building foun...
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November 6, 2025 at 4:02 PM
By pretraining on SpatialCorpus-110M, a curated resource of vast and diverse transcriptomes of dissociated and spatially resolved cells from both human and mouse, Nicheformer advances building foundation models for spatial single-cell analysis.
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High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
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October 30, 2025 at 3:41 PM
High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
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SegmentNT: a general segmentation model for genome annotation that can process DNA sequences up to 50-kb long and shows strong generalization across unseen species.
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Annotating the genome at single-nucleotide resolution with DNA foundation models - Nature Methods
By leveraging the power of pretrained DNA foundation models, SegmentNT achieves performant genome annotation through segmenting different genic and regulatory elements.
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October 29, 2025 at 3:41 PM
SegmentNT: a general segmentation model for genome annotation that can process DNA sequences up to 50-kb long and shows strong generalization across unseen species.
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CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
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Improved reconstruction of single-cell developmental potential with CytoTRACE 2 - Nature Methods
CytoTRACE 2 is an interpretable deep learning framework that leverages single-cell RNA sequencing data to predict absolute developmental potential across datasets.
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October 29, 2025 at 3:14 PM
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets.
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PHLOWER infers complex cell differentiation trajectories from single-cell multimodal data.
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PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories - Nature Methods
PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories.
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October 23, 2025 at 3:16 PM
PHLOWER infers complex cell differentiation trajectories from single-cell multimodal data.
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scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @johahi.bsky.social @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
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scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution - Nature Methods
scooby achieves DNA sequence-based single-cell level modeling of RNA-sequencing coverage and ATAC-sequencing insertion profiles by adapting a deep learning model that predicts bulk RNA-sequencing cove...
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October 22, 2025 at 4:48 PM
scooby achieves DNA sequence-based single-cell level modeling of RNA-seq coverage and ATAC-seq insertion profiles by adapting a deep learning model that predicts bulk RNA-seq coverage. @johahi.bsky.social @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de
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CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
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CELLECT: contrastive embedding learning for large-scale efficient cell tracking - Nature Methods
CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
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October 22, 2025 at 4:31 PM
CELLECT learns contrastive embeddings to enable high-fidelity cell tracking.
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