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Open Access
Featured
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Brief Communication
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SpatialData: an open and universal data framework for spatial omics
SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets.
- Luca Marconato
- , Giovanni Palla
- & Oliver Stegle
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Article |
Mapping enzyme activity in living systems by real-time mid-infrared photothermal imaging of nitrile chameleons
Real-time mid-infrared photothermal imaging of nitrile chameleons enables simultaneous, multiplexed measurement of enzymatic activity in living systems and is poised to reveal the spatiotemporal regulation of enzymes in health and disease.
- Hongjian He
- , Jiaze Yin
- & Ji-Xin Cheng
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Brief Communication
| Open Access
DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging
SABER-IMC combines DNA-based signal amplification by exchange reaction (SABER) with imaging mass cytometry (IMC) to enable simultaneous and highly multiplexed marker detection, even of low-abundance markers not detectable with IMC alone.
- Tsuyoshi Hosogane
- , Ruben Casanova
- & Bernd Bodenmiller
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Article
| Open Access
Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging
Multielement Z-tag X-ray fluorescence (MEZ-XRF) offers a new avenue for nondestructive and highly multiplexed tissue imaging and operates from the nanometer to whole-tissue scale, unlocking new biological observations.
- Merrick Strotton
- , Tsuyoshi Hosogane
- & Bernd Bodenmiller
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Research Highlight |
In situ sequencing of localized translation
Ribosome-bound mRNA mapping (RIBOmap) enables three-dimensional in situ detection of spatially resolved protein synthesis in single cells.
- Lei Tang
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Comment |
Making single-cell proteomics biologically relevant
Recent technological advances in mass spectrometry promise to add single-cell proteomics to the biologist’s toolbox. Here we discuss the current status and what is needed for this exciting technology to lead to biological insight — alone or as a complement to other omics technologies.
- Florian A. Rosenberger
- , Marvin Thielert
- & Matthias Mann
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Comment |
Mass spectrometry imaging: the rise of spatially resolved single-cell omics
Increasing evidence suggests that the spatial distribution of biomolecules within cells is a critical component in deciphering single-cell molecular heterogeneity. State-of-the-art single-cell MS imaging is uniquely capable of localizing biomolecules within cells, providing a dimension of information beyond what is currently available through in-depth omics investigations.
- Hua Zhang
- , Daniel G. Delafield
- & Lingjun Li
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Article
| Open Access
Convolutional networks for supervised mining of molecular patterns within cellular context
DeePiCt (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.
- Irene de Teresa-Trueba
- , Sara K. Goetz
- & Judith B. Zaugg
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Article
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles
Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.
- Barbora Špačková
- , Henrik Klein Moberg
- & Christoph Langhammer
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Article
| Open Access
Mass-sensitive particle tracking to elucidate the membrane-associated MinDE reaction cycle
An iSCAT image processing and analysis strategy enables mass-sensitive particle tracking (MSPT) of single unlabeled biomolecules on a supported lipid bilayer. MSPT was used to observe the (dis-)assembly of membrane complexes in real-time.
- Tamara Heermann
- , Frederik Steiert
- & Petra Schwille
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Review Article |
Spatial omics and multiplexed imaging to explore cancer biology
This Review describes spatial omics and multiplexed imaging technologies and their current and future impact in studying tumor heterogeneity and cancer biology.
- Sabrina M. Lewis
- , Marie-Liesse Asselin-Labat
- & Shalin H. Naik
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Comment |
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
- Ugis Sarkans
- , Wah Chiu
- & Alvis Brazma
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Article |
Genetically encoded tags for direct synthesis of EM-visible gold nanoparticles in cells
Genetically encoded cysteine-rich tags enable formation of gold nanoparticles in situ for single-molecule imaging of individual proteins in the context of cellular ultrastructure in bacterial, yeast and mammalian cells.
- Zhaodi Jiang
- , Xiumei Jin
- & Wanzhong He
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Research Highlight |
Super-resolution Raman imaging
Higher-order processes can be harnessed for super-resolution CARS vibrational microscopy.
- Nina Vogt
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Article |
Light-sheet microscopy in the near-infrared II window
Light-sheet microscopy in the NIR-II window enables rapid volumetric imaging of tissues at impressive depths in vivo without invasive preparations owing to the reduced light scattering and tissue autofluorescence at these wavelengths.
- Feifei Wang
- , Hao Wan
- & Hongjie Dai
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News & Views |
A detector for the sources
A new detector built for X-ray free-electron lasers provides unprecedented speed and accuracy for macromolecular crystallography at synchrotron radiation facilities—and finally allows crystallographers to harness the full capabilities of those sources.
- Henry N. Chapman
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Brief Communication |
Template-free 2D particle fusion in localization microscopy
An all-to-all registration approach allows for improved, high-resolution, template-free single-particle reconstruction from localization microscopy data under realistic experimental conditions such as low labeling density.
- Hamidreza Heydarian
- , Florian Schueder
- & Bernd Rieger
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Brief Communication |
Automated, parallel mass spectrometry imaging and structural identification of lipids
An automated method coupling tandem mass spectrometry with high-resolution mass spectrometry imaging simultaneously reveals both the molecular structure of lipids and their spatial locations in tissue.
- Shane R. Ellis
- , Martin R. L. Paine
- & Ron M. A. Heeren
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Brief Communication |
Autofocusing MALDI mass spectrometry imaging of tissue sections and 3D chemical topography of nonflat surfaces
A mass spectrometry imaging system combined with a laser triangulation system provides simultaneous topographic and molecular information for 3D biological samples and eliminates height-related artifacts in imperfect tissue sections.
- Mario Kompauer
- , Sven Heiles
- & Bernhard Spengler
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Methods in Brief |
Track first and identify later
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Review Article |
In vivo imaging of neural activity
Yang and Yuste review currently available technologies for optical imaging of neural circuits, comparing them to help researchers choose optimal ones for their applications.
- Weijian Yang
- & Rafael Yuste
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Editorial |
Imaging beyond the coverslip
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Article |
Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution
An instrumental setup for atmospheric pressure MALDI-based mass spectrometry imaging with improved lateral resolution enables subcellular-level details to be resolved.
- Mario Kompauer
- , Sven Heiles
- & Bernhard Spengler
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Brief Communication |
FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry
The authors present a computational framework for false-discovery-rate-controlled metabolite annotation from high-resolution imaging mass spectrometry data.
- Andrew Palmer
- , Prasad Phapale
- & Theodore Alexandrov
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This Month |
Daniel J. Müller
A new way to quantify ligand-binding interactions of individual membrane proteins.
- Vivien Marx
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Article |
Imaging G protein–coupled receptors while quantifying their ligand-binding free-energy landscape
A force-distance curve–based atomic force microscopy method is developed and applied to both image and quantify the ligand-binding free-energy landscape of single protease-activated receptor-1 (PAR1) molecules under physiologically relevant conditions.
- David Alsteens
- , Moritz Pfreundschuh
- & Daniel J Müller
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Brief Communication |
Structural analysis of multicellular organisms with cryo-electron tomography
Tissues from multicellular organisms can be imaged by cryo-electron tomography using an optimized combination of vitrification, milling and application of fiducial markers.
- Jan Harapin
- , Mandy Börmel
- & Ohad Medalia
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Methods in Brief |
Mass spectrometry imaging with MALDI-2
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Methods in Brief |
Closing in on video-rate STED nanoscopy
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Article |
Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping
An approach to fuse images from imaging mass spectrometry and microscopy provides biological insights into molecular tissue distributions beyond what can be obtained from either modality individually.
- Raf Van de Plas
- , Junhai Yang
- & Richard M Caprioli
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Tools in Brief |
Finding new RNA mimics of GFP
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Methods in Brief |
Imaging nascent proteins in living cells
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Review Article |
Multiparametric imaging of biological systems by force-distance curve–based AFM
This Review of force-distance curve-based atomic force microscopy highlights the unique capabilities of the technique to simultaneously image the architecture of complex biological systems and map their physical, chemical and biological properties at nanometer resolution.
- Yves F Dufrêne
- , David Martínez-Martín
- & Daniel J Müller
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Research Highlights |
A brief history of nuclear organization
By marking protein-DNA interactions in real time, scientists track chromosomal rearrangements in the nuclei of living cells.
- Michael Eisenstein
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Research Highlights |
How vesicles put on their coat
Single-molecule imaging helps researchers to begin a biography for clathrin-coated vesicles.
- Michael Eisenstein
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Article |
Single-cell systems biology by super-resolution imaging and combinatorial labeling
Super-resolution microscopy of fluorescently labeled oligonucleotides bound to individual mRNA transcripts is used for highly multiplexed imaging and quantification of transcripts in single cells. The method is used to profile transcripts from 32 stress-response genes in single yeast cells in response to extracellular stress.
- Eric Lubeck
- & Long Cai
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Article |
FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography–X-ray computed tomography
A hybrid fluorescence molecular tomography–X ray computed tomography system is applied for in vivo imaging of multiple mouse models, and its performance is validated on post-mortem cryosection data.
- Angelique Ale
- , Vladimir Ermolayev
- & Vasilis Ntziachristos
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Brief Communication |
Direct visualization of specifically modified extracellular glycans in living animals
Transgenic expression of secreted antibodies specific for modified heparan sulfates fused to GFP allow the visualization of these modifications in vivo.
- Matthew Attreed
- , Muriel Desbois
- & Hannes E Bülow
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Methods in Brief |
Quantifying RNA localization
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Research Highlights |
Mapping molecules on the move
Using a sheet of light to perform fluorescence-correlation analysis, scientists can track protein dynamics in entire cellular 'neighborhoods'.
- Michael Eisenstein
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Research Highlights |
A GFP for RNA
Researchers describe a GFP mimic for fluorescently labeling RNA molecules.
- Allison Doerr
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Article |
Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis
Implementation of pair correlation analysis for photoactivated localization microscopy allows quantitative analysis of protein clustering in the plasma membrane, revealing the degree to which different perturbations alter protein arrangements.
- Prabuddha Sengupta
- , Tijana Jovanovic-Talisman
- & Jennifer Lippincott-Schwartz
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Research Highlights |
Turning the lights on a few molecules at a time
Researchers adapt split-GFP complementation to single-molecule imaging.
- Tal Nawy
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Research Highlights |
Programming molecular instruments
Small conditional RNAs prove their mettle in multiplexed mRNA imaging and show promise as potential cancer therapeutics.
- Nicole Rusk
Molecular pixelation: spatial proteomics of single cells by sequencing