Interested in neuromodulators, especially #norepinephrine / #noradrenaline? Check out this #Naturemethods paper hot off the press from the Patriarchi lab on next-generation NE sensors. It was a pleasure to contribute to this team effort. A genuinely 💡enlightening 💡 advance for monitoring NE in vivo.

Next-generation multicolor indicators for in vivo imaging of norepinephrine - Nature Methods Improved red and green indicators for norepinephrine and their characterization are reported. These indicators allow detection of norepinephrine release in awake behaving mice in dual-color fiber phot...

The most sensitive green and red #norepinephrine #sensors engineered to date are out in #naturemethods! Deeply grateful to all our funders and contributors who made this work possible. A true team effort. @erc.europa.eu @snsf.ch doi.org/10.1038/s415...

Congratulations to first author Gangadhar Eluru, co-authors Steven De Gieter, Stephan Schenck, Annelore Stroobants, Binesh Shrestha, Paul Erbel and Ruslan Efremov.
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender

👏 Phys.org has featured the work of our colleagues at IOCB Prague.

The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0

#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods

AI connects mutations, protein modifications and disease The new AI tool, called DeepMVP, significantly outperforms previously published models and has implications for the development of novel therapeutics.

#DeepMVP improves the ability to predict gene #mutations that may lead to #disease. B. Zhang, C. Wang et al #naturemethods @bcmgenetics.bsky.social @bcmhouston.bsky.social #BCMCancerCenter blogs.bcm.edu/2025/09/09/f...

Help needed: submitted a manuscript to Nature Methods, and although I received a notification that it was rejected, I never received a formal decision letter. Has anyone experienced something similar? Any suggestions on how to phrase it? 🙏

#ManuscriptSubmission #NatureMethods

New mYongHong, a super stable monomeric red fluorescent protein, is here for high-res imaging! 🔬✨ Perfect for neuroscience and cell bio research. 🧠🔴 Check it out now! 👀👇
www.ebraincase.com/news/new-pro...

#FluorescentProtein
#BrainResearch
#BrainCase
#Neuroscience
#CellImaging
#NatureMethods

🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7

Two neurons in front of a Neuropixels probe. One neuron says to the other: "Don't look, but I think we're being followed!".

Our paper describing UnitMatch software "tracking neurons across days with high-density probes", appeared in this month's issue of #NatureMethods. Missed it? Read it here: www.nature.com/articles/s41...

Congratulations to @sergiomarcosalas.bsky.social, @nilssonlab.org, and their team on a new #NatureMethods publication featuring the Xenium platform! Read how Xenium spatial stacked up against 8 other systems & get independently validated best practices & recommendations: go.nature.com/3DZ0PpR

This is a flat grey image with cell structures in darker grey. Some of the cells are coloured and shown in green boxes. This image - Segmentation of electron microscopy images with μSAM - shows how the model can segment nuclei, with points and boxes from the user and the corresponding masks predicted by the model. Photo: The underlying image comes from data published in Cell (S0092-8674(21)00876-X). Image created by Anwai Archit using the μSAM tool.

This is a three dimensional representation with a cross-section showing dark patches in different colours and the outside of the structure with bright different colours (green, purple, blue, dark pink, yellow, orange). The image shows plant cells acquired with a fluorescence microscope that were segmented automatically with the model. The underlying data is three-dimensional and the image shows a rendering of the segmented cells, each represented by a different colour. Image from: Nature Methods: s41592-021-01249-6

Automatic cell analysis using #AI

Researchers retrained existing AI-based software on over 17,000 microscopy images with over 2 million structures to develop this new model - Segment Anything for Microscopy: www.uni-goettingen.de/en/3240.html...

#NatureMethods research: doi.org/10.1038/s415...

A comprehensive human embryo reference tool using single-cell RNA-sequencing data - Nature Methods This resource integrates different human embryo datasets to create a transcriptional reference map of human embryonic development from zygote to gastrula.

A comprehensive human embryo reference tool using single-cell RNA-sequencing data. #SingleCell #scRNAseq #HumanEmbryo #ReferenceDataSet #NatureMethods #BioSky #SciSky 🧪
www.nature.com/articles/s41...

Genes2Genes

Comparing/Aligning scRNAseq pseudotime trajectories at gene-/cell-level to capture mismatched genes b/w two conditions

#DynamicProgramming
Gotoh’s algorithm (affine Gap/Indel scoring) + #DynamicTimeWarping

vs CellAlign Tragedy

#NatureMethods 2024
www.nature.com/articles/s41...

Build your own online integrated platform for single-cell & spatial transcriptomic data using WebAtlas pipeline

Cell2location
StabMap
Unify image & gene expression files into Zarr format
Compatible with SpatialData
Based on Vitessce framework

#Naturemethods 2024
www.nature.com/articles/s41...

Systematic comparison of 11 sequencing-based #SpatialTranscriptomics methods 🤠
Visium
DynaSpatial
HDST
BMKMANU S1000
Slide-seq V2
Curio Seeker
Slide-tag
Stereo-seq
PIXEL-seq
Salus
DBiT-seq
Guess which behaves best for🧠microvasculature?😁

#naturemethods 2024
www.nature.com/articles/s41...

#TidyOmics

Harmonizing different omics packages with a common R syntax/grammar

tidySpatialExperiment "provides specialized operations such as gating based on geometric & hand-drawn shapes"😍

#NatureMethods 2024
www.nature.com/articles/s41...

The tidyomics ecosystem: enhancing omic data analyses - Nature Methods tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.

#tidyomics made it to #NatureMethods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽 Will, Timothy, and Team!

32 researchers | 26 institutes | 10 countries | 4 continents

A #crowd/#community-research success

nature.com/articles/s41...

#CZI, Thanks @mikelove.bsky.social !

Am I outperforming GPT-4 in cell type annotation based on scRNAseq marker genes?

Unlikely, except for SMC subpopulations😌

So I will use
1⃣R::GPTCelltype
winnie09.github.io/Wenpin_Hou/p...
2⃣Cell Type Annotations GTP
chatgpt.com/g/g-F8xUJrnK...

#Naturemethods 2024
www.nature.com/articles/s41...

SpatialData
spatialdata.scverse.org/en/latest/

Establish a global common coordinate framework->
Multi-modal #SpatialOmics integration
Align multislice for 3D #SpatialOmics

Work with
(RNA) Visium Xenium CosMx MEFISH
(protein) CycIF MIBI-TOF IMC

#Naturemethods 2024
www.nature.com/articles/s41...

Effortless Landmark Detection

Unsupervised spatial landmark detection-registration
Align HE Histology with #SpatialOmics
#Visium #SpatialTranscriptomics
#MassSpectrometryImaging

Also working on reconstructing 3D histology from serial slices
#NatureMethods 2024
www.nature.com/articles/s41...

#SCENIC+

Single-cell/-nucleus transcriptome + chromatin accessibility▶️
eRegulon/enhancer-driven regulon
>30k #Transcriptionfactor motifs from 29 databases

GRN velocity for differentiation trajectories
#EvoDevo at TF level

@steinaerts.bsky.social #NatureMethods 2023
www.nature.com/articles/s41...

#spacexr (advanced ver #RTCD)

Cell type-specific inference of differential expression/C-SIDE
github.com/dmcable/spac...

Requiring annotated single-cell reference

Work with #Visium #Slideseq #MERFISH

#NatureMethods 2022
www.nature.com/articles/s41...

Subcellular #SpatialTranscriptomics Cell Segmentation
#TransformerNeuralNetwork
based on Image AND Transcriptome

For Single-Cell/Subcellular ST
Stereo-seq; Seq-scope

vs other #DeepLearning methods #StarDist #CellPose #DeepCell

#NatureMethods 2023
www.nature.com/articles/s41...