It's that time of year!! 🎉We are so excited to announce our 2023 pick for Nature Methods' Method of the Year: methods for modeling development. Read the Editorial to find out why we chose this as our pick.
#moty2023
Are you curious about using organic dyes in your microscopy experiments but not sure where to start? This Perspective from
@rhodamine110
and
@jonathangrimm
introduces readers to the world of dyes and their pros and cons for biological applications.
It's finally here!! Our Method of the Year 2022 is....long-read sequencing! 🎉
Read our (free!) Editorial to learn why we felt the time was right to select this class of powerful technologies as the Method of the Year.
20 years after the announcement of the "working draft" of the human genome, we have the first complete assembly of a human chromosome. It's hard work to chase down every last base!
For this Focus issue, we asked experts in bioimaging from around the world to tell us what excited them about the future of bioimage analysis for the next 5-20 years. (1/n)
All Focus content can also be found here:
Out today: SCENIC+ is a comprehensive toolbox for inferring and analyzing enhancer-driven gene regulatory networks (eGRN) using single-cell multiomic data.
@steinaerts
@seppe_winter
@Bravo_Potato
By using a new deep learning architecture, Enformer leverages long-range information to improve prediction of gene expression based on DNA sequence.
@deepmind
@calico
Open access paper:
From the Mougous and Wiggins labs comes Omnipose! A versatile tool for segmenting diverse and arbitrarily shaped cells in microscopy images, with an emphasis on challenging bacterial shapes.
Out today! DeepImageJ offers a user-friendly solution in ImageJ to run trained deep learning models for biomedical image analysis. It includes guiding tools for reliable analyses, contributing to the democratization of deep learning in microscopy.
Method to Watch by Nina Vogt: Assembloids are emerging models for studying human brain development, complex neural circuits or interactions between different tissues.
Introducing Mitometer, an algorithm for automated segmentation and tracking of mitochondria in live-cell 2D and 3D time-lapse images.
@michelledigman
@Austin_Lefebvre
Excited to announce the Spatial Omics DataBase (SODB), a web-based platform for sharing and analyzing >25 types of spatial omics data. SODB promotes data reuse, offers novel viz tools and can streamline development of omics analysis tools.
Single-cell methods are becoming the norm, but what about proteins? Chirlmin Joo and colleagues provide a detailed survey of the emerging landscape of single-molecule protein sequencing technologies in a Review out today!
mStayGold, a monomeric derivative of the extremely photostable GFP StayGold, offers improved protein tagging while maintaining desirable photophysical properties. mStayGold extends the possibilities of what can be achieved with fluorescent protein labels.
The estimation of effect sizes and their uncertainty allows researchers to move from the question ‘Does it?’ to ‘How much?’ DABEST ()
is a tool to generate such estimation graphics.
Tangram is a versatile tool for aligning single-cell and single-nucleus RNA-seq data to spatially-resolved transcriptomics data using deep learning.
@broadinstitute
@tbyanc
@gabo_scalia
OA paper:
Love napari but missing some ImageJ functions? Look no further than napari-imagej, which provides an accessible and comprehensive solution to ImageJ ecosystem access from napari.
The Yin group from Wuhan University leverages a pair of pegRNAs to efficiently insert DNA fragments up to 250bp without the need of donor DNA, named GRAND editing.
Out today from the Stegle, Theis, and Moore labs! SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets.
Out today! Best practices and tools for reporting reproducible fluorescence microscopy methods!! These are the among the most comprehensive guidelines we've seen, and we hope they become second nature to microscopists and improve rigor and reproducibility.
Henikoff,
@NadiyaKhyzha
and
@KamiAhmad3
introduce RT&Tag that enables mapping RNA molecules in proximity to a protein of interest in intact nuclei.
OA paper:
Bioinformatics advancements unleash the full potential of long-read sequencing in various areas of genomics. A Comment from Michael Schatz (
@mike_schatz
) and colleagues highlights this thriving domain of active methods development.
@JohnsHopkins
It's finally here! The May issue of
@NatureSMB
is LIVE and we are excited to share these gorgeous covers with you! 🎉
We split this painting depicting the transport and release of antibody-filled vesicles (from a B-cell) by
@dsgoodsell
to create these matching covers for
#PDB50
!
scRNA-seq offers a snapshot of transcriptomes but not RNA dynamics. scNT-seq from the Wu lab
@hao_wu_7
integrates metabolic labeling and droplet sequencing to perform parallel analysis of newly-transcribed and pre-existing mRNAs.
Out today, a fantastic Review on spatial omics and multiplexed imaging methods for exploring cancer biology from Shalin Naik and Kelly Rogers
@shalinhnaik
@KRogers1001
This Review from
@OliverStegle
and
@BrittaVelten
discusses statistical and computational strategies for analyzing various spatial and temporal omics data types, with an emphasis on the common modeling principles.
The Meltome Atlas compiles the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans, providing a resource for analyzing protein stability in the context of function and interactions.
@kusterlab
@savitski_lab
In their Comment, AlphaFold developers John Jumper and
@demishassabis
of
@DeepMind
describe the design of AlphaFold’s neural network and give their views on how it will transform the field of structural biology.
Researchers present a comprehensive benchmarking analysis of computational methods that integrate spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.
Out yesterday from
@adam_k_glaser
and
@jonliu123
, a versatile hybrid open top light sheet microscope for imaging of large cleared samples. Check out their images! 🤩
Long-read sequencing tools can capture the full picture of genomes and transcriptomes. An Analysis assesses the performance of long-read RNA sequencing analysis tools including isoform detection and differential expression analysis workflows.
Is cell segmentation a solved problem? Maybe not yet, but the results of this multimodality cell segmentation challenge get us closer! (Spoiler, the winner is a generalist Transformer-based model).
@BoWang87
A clever strategy for multiplexed immunolabeling out today from Peng Yin's lab. "Thermal-plex" uses DNA probes that fluoresce sequentially when, and only when, activated with transient exposure to heating spikes at designated temperatures.
Out today! Hierarchical phase-contrast tomography (HiP-CT) enables multiscale imaging of any region within an intact human organ down to cellular resolution.
Come see CellPose from the Pachitariu lab for your image segmentation needs! Cellpose is a generalist, deep learning-based approach for segmenting structures in a wide range of image types.
@marius10p
Using a sequence-based deep neural network, scBasset facilitates various tasks of single-cell ATAC-seq analysis in a unified framework.
@HY3952
@drklly
@calico
In a new Analysis paper, researchers compare the performance of 9 computational methods to identify and rank reprogramming transcription factors for 8 target cell types.
Our March issue is live! 🎉
On the cover, multiplexed tissue imaging evokes a stained glass window. This gorgeous image was created by Stefan Uderhardt
@red_ven
and Andrea Radtke.
Nanopore sequencing allows profiling long-range patterns on single molecules. nanoNOMe uses nanopore sequencing to profile CpG methylation and chromatin accessibility in human cells.
@timp0
So excited to be sharing this Perspective online today from Hamprecht and Kreshuk on Ilastik! Ilastik is a powerful tool for bringing sophisticated image analysis to biologists. Read it here or for free here
An iterative approach for improving
#AlphaFold
protein model quality using experimental density maps, where rebuilt models are used as templates in new AlphaFold predictions, from
@TerwillTom
and colleagues.
OA paper:
Out today! Radial Symmetry-FISH (RS-FISH) -- an accurate, fast, and user-friendly software for spot detection in 2D and 3D images. Bring on your smFISH, spatial transcriptomics, or spatial genomics applications!
@kisharrington
@successprocess
@preibischs
Out today! nnU-Net is a deep learning-based image segmentation method that automatically configures itself for diverse biological and medical image segmentation tasks. And its performance is impressive!
A cool chemical biology paper from the Loh lab! Adaptable, turn-on maturation (ATOM) biosensors use mono/nanobody targeting to control fluorescent protein maturation, enabling bright and specific cellular biosensing.
CODA is a method for 3D reconstruction of large tissues at subcellular resolution from serially sectioned H&E images, from Pei-Hsun Wu,
@deniswirtz
and colleagues.
@johnshopkins
@ashleykiemen
Microbial eukaryotes are important, but often overlooked, organisms in the global ecosystem. A Resource, supported by a community effort, describes valuable transformation tools for marine protists that have been challenging to genetically manipulate.
Out today from the Johnsson lab: HaloTag variants that change the brightness and fluorescence lifetimes of rhodamines compared to HaloTag7. Lots of potential for multiplexed FLIM, including new lifetime-based cell cycle reporters. Open access!
Excited to share my work w/
@CarolynBertozzi
describing the discovery of glycoRNA today
@CellCellPress
. Since our
@biorxivpreprint
we uncovered an unexpected twist: glycoRNAs are on the surface of cells+some Siglec receptors have RNA-dependent cell binding
The Trump administration in the US has interfered with scientific research and ignored scientific knowledge. Read our take here, and most importantly, VOTE!!!
Out today from
@bewersdorflab
! Two-color fluorogenic DNA-PAINT introduces self-quenching, kinetics-optimized probe designs. This approach improves imaging speed 26-fold and eliminates the need for optical sectioning.
What's new in spatial 'omics? Light-seq from the
@SinemKSaka1
, Kishi, Cepko, and Yin labs! Light-Seq uses light-directed DNA barcoding in fixed cells and tissues for multiplexed spatial indexing and subsequent next gen sequencing of even rare cell types.
Introducing STELLAR: a geometric deep learning method for cell type discovery and identification in spatially resolved single-cell datasets.
@jure
@GarryPNolan
@SnyderShot
Ever wonder why nm localization precisions often don't translate to similar resolution below 10 nm? A paper from
@LabSauer
points to RET between fluorophores as a major factor. and see the accompanying N&V from
@LMoeckl
Our February issue is live! 🎉
On the cover, a beautiful example of cryo-expansion microscopy (Cryo-ExM) used to observe a human cell in mitosis, from
@MarineLaporte8
of
@CentrioleLab
. OA paper here:
As part of our commitment to increasing transparency in our editorial and peer review processes, we are very pleased to announce that we are now publishing peer review reports (including editorial decisions letters and author rebuttals) for original research papers.
Our May issue is now live! 🎉
On the cover, a beautiful optically cleared mouse brain imaged with a hybrid open-top light-sheet microscope, from
@adam_k_glaser
(paper here: ).
The Signac framework enables end-to-end analysis of single-cell chromatin data and offers interoperability with the Seurat package for multimodal analysis.
@timoast
@satijalab
@nygenome
Extra-long tandem repeats (ETRs) such as centromeres and immunoglobulin loci are difficult to align. UniAligner is a computational method for efficiently and accurately aligning ETRs, facilitating analysis of their variation and evolution.
@AndreyBzikadze
Really pleased to publish this timely set of checklists to help improve the presentation and reproducibility of microscopy data. Wonderful community effort led by
@ChriSchmied
@helenajambor
@tischitischer
Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices.
@RonZeira
@benjraphael
A Review provides an overview of computational methods recently developed for detecting and analyzing structural variants using long-read sequencing data.
Research Highlight by
@DrArunimaSingh
:
@cees_dekker
and colleagues
@tudelft
have expanded nanopore-based single-molecule sequencing technology to post-translational modifications. They demonstrate the detection of phosphorylation along single peptides.
CoTECH uses split-pool barcoding strategy to jointly profile histone modifications and transcriptome in single cells, which offers a multiomics tool to study epigenetic regulations during development.
@AibinHe
@PKU1898
Out today from the
@davidvanvalen
lab! DeepCell Kiosk: cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets.
We are so pleased to announce that this month, we are officially launching a new article format for comparative analyses of established, related tools or methods, called Registered Reports. Read all about it in this month's Editorial:
Out today! Trying to improve your spatial resolution for sequencing-based spatial transcriptomics? Look no further than Expansion Spatial Transcriptomics from the Lundeberg and Wang labs.
The Tyson lab presents CheckM2, which leverages machine learning for improved estimation of completeness and contamination of metagenome-assembled genomes (MAGs) generated using metagenomics data.
@CMR_QUT
@AChklovski
Interested in near-infrared fluorescent proteins but don't know where to start? Our very first Registered Report can help! In it Piatkevich and colleagues perform a quantitative comparison of NIR FPs (and some far-red) in vitro, in cells, and in vivo.
Out today! Enhanced super-resolution radial fluctuations (eSRRF) for improved volumetric live-cell super-resolution imaging at high speeds.
@HenriquesLab
@christlet
@Bassam_A_HAJJ
Genetic modifications to the bioluminescence pathway in the fungus Neonothopanus nambi enhance bioluminescence by 1-2 orders of magnitude in plants and other eukaryotes.
New from the
@SandoghdarLab
! μkiss is a micropipette-based approach for delivering very small amounts of nanoparticles and small molecules to the cell surface with exquisite spatiotemporal control, enabling a wide range of biological investigations.
The LIVECell dataset comprises annotated phase-contrast images of over 1.6 million cells from different cell lines during growth from sparse seeding to confluence for improved training of deep learning-based models of image segmentation.
The Tang group presents scNanoHi-C: a single cell Hi-C method based on nanopore long-read sequencing. scNanoHi-C allows researchers to capture high-order chromatin structures and detect genomic variations such as CNVs and SVs.
So happy we've published TrackMate 7!
@guijacquemet
@jytinevez
TrackMate 7 combines the benefits of deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.
Cell interaction by multiplet sequencing (CIM-seq) by Martin Enge and colleagues is a RNA-seq-based method to analyze physical cell-cell interactions in complex tissues.
Our latest Tech Feature 'Microscopy made to order' by
@eisensteinium
covers 'do-it-yourself' microscopy, and how open software and hardware tools are advancing science. (This gorgeous image brought to you by the mesoSPIM)