Featured
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News & Views |
Breaking up the StayGold dimer yields three photostable monomers
The exceptionally photostable green fluorescent protein StayGold has been monomerized in different laboratories, which has generated three unique monomeric variants that will enable new imaging applications.
- Joachim Goedhart
- & Theodorus W. J. Gadella Jr
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Article |
Smart lattice light-sheet microscopy for imaging rare and complex cellular events
smartLLSM uses artificial intelligence-based instrument control to switch between epiflouorescence and lattice light-sheet microscopy to monitor cells at the population level while also capturing multicolor three-dimensional datasets of rare events of interest.
- Yu Shi
- , Jimmy S. Tabet
- & Wesley R. Legant
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Article
| Open Access
StayGold variants for molecular fusion and membrane-targeting applications
Monomeric and tandem dimer derivatives of the bright and photostable green fluorescent protein StayGold offer versatile tools for tagging target proteins and membranes in extended live-cell imaging.
- Ryoko Ando
- , Satoshi Shimozono
- & Atsushi Miyawaki
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Article
| Open Access
Bio-friendly long-term subcellular dynamic recording by self-supervised image enhancement microscopy
DeepSeMi is a self-supervised denoising framework that can enhance SNR over 12 dB across diverse samples and imaging modalities. DeepSeMi enables extended longitudinal imaging of subcellular dynamics with high spatiotemporal resolution.
- Guoxun Zhang
- , Xiaopeng Li
- & Qionghai Dai
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This Month |
When you lose a mentor or a colleague
The heartbreak of losing a mentor or a colleague to illness can be part of a researcher’s life.
- Vivien Marx
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Brief Communication |
Molecular mechanocytometry using tension-activated cell tagging
Tension-activated cell tagging (TaCT) is a new method that uses flow cytometry to sort mechanically active cells based on the forces generated by their surface adhesion receptors.
- Rong Ma
- , Sk Aysha Rashid
- & Khalid Salaita
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Article
| Open Access
Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome
Single-cell Deep Visual Proteomics integrates imaging, cell segmentation, laser microdissection and multiplexed mass spectrometry for spatial single-cell proteomics measurements in complex tissues.
- Florian A. Rosenberger
- , Marvin Thielert
- & Matthias Mann
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Research Briefing |
Mapping deformations and increasing quantitative accuracy in expansion microscopy
We introduce GelMap, a flexible workflow for reporting deformations and anisotropy in expansion microscopy. By intrinsically calibrating the expansion hydrogel using a fluorescent grid that scales with expansion and deforms with anisotropy, GelMap enables the reliable quantification of expansion factors and correction of deformations.
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Brief Communication
| Open Access
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging
Organ Mapping Antibody Panels are a community-led initiative to create standardized antibody panels for multiplexed spatial imaging.
- Ellen M. Quardokus
- , Diane C. Saunders
- & Andrea J. Radtke
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Comment |
When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis
A key step toward biologically interpretable analysis of microscopy image-based assays is rigorous quantitative validation with metrics appropriate for the particular application in use. Here we describe this challenge for both classical and modern deep learning-based image analysis approaches and discuss possible solutions for automating and streamlining the validation process in the next five to ten years.
- Jianxu Chen
- , Matheus P. Viana
- & Susanne M. Rafelski
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Article |
SCS: cell segmentation for high-resolution spatial transcriptomics
Subcellular spatial transcriptomics cell segmentation (SCS) combines information from stained images and sequencing data to improve cell segmentation in high-resolution spatial transcriptomics data.
- Hao Chen
- , Dongshunyi Li
- & Ziv Bar-Joseph
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This Month |
Languages in the lab
Members of a lab often have a varied language background. This rich language diversity leads to lab dynamics that take mindful handling.
- Vivien Marx
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Article |
ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology
ERnet is a deep learning-based software tool for automatic segmentation and classification of structures in the endoplasmic reticulum. ERnet is compatible with many fluorescence imaging modalities and can uncover subtle phenotypic changes.
- Meng Lu
- , Charles N. Christensen
- & Clemens F. Kaminski
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Article |
Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging
FD-DeepLoc uses field-dependent deep learning for precise localization of spatially variant point emitters over the full chip of a modern sCMOS camera, enabling fast and high-throughput volumetric localization microscopy.
- Shuang Fu
- , Wei Shi
- & Yiming Li
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Brief Communication |
An improved imaging system that corrects MS2-induced RNA destabilization
An improved version of the MS2-MCP system for imaging RNA dynamics involves tethering translation termination factors to tagged mRNAs to bypass destabilization caused by NMD machinery.
- Weihan Li
- , Anna Maekiniemi
- & Robert H. Singer
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News & Views |
Fluorophores’ talk turns them dark
Dipole–dipole crosstalk between fluorophores separated by a distance of less than 10 nm induces changes in their photophysics, which adds a challenge to localization microscopy in the sub-10-nm regime.
- Karim Almahayni
- , Malte Spiekermann
- & Leonhard Möckl
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Technology Feature |
The making of microscope camera standards
Cameras are a crucial part of microscopes and are also built into many kinds of instruments. To make their output comparable takes standards.
- Vivien Marx
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Technology Feature |
Imaging standards to ease reproducibility and the everyday
Imaging and microscopy technology advances in leaps and bounds. To address accumulated pain points, academics and companies are making headway on standards.
- Vivien Marx
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Article |
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification
A method for high-content 3D imaging of organoids.
- Anne Beghin
- , Gianluca Grenci
- & Virgile Viasnoff
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Article |
Isotropic super-resolution light-sheet microscopy of dynamic intracellular structures at subsecond timescales
Combining a double-ring modulated SPIM with reduced side lobes and a sectionalized deep-learning based super-resolution algorithm enables fast, high-resolution, volumetric imaging of organelle interactions and dynamics in live cells.
- Yuxuan Zhao
- , Meng Zhang
- & Yu-Hui Zhang
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Article
| Open Access
Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM)
Cryo-ExM combines the expansion microscopy for super-resolution imaging with cryofixation for ultrastructure preservation. Cryo-ExM outperforms established fixation methods on a range of sensitive subcellular structures.
- Marine H. Laporte
- , Nikolai Klena
- & Paul Guichard
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Method to Watch |
Deconstructing subcellular composition
High-throughput and ultrasensitive mass spectrometry–based approaches are gaining ground in subcellular compositional analysis.
- Arunima Singh
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Editorial |
Minding microscopy metadata
Guidelines for improving reporting and reproduciblity in microscopy take center stage in this month’s Focus issue.
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Research Highlight |
Dissecting subcellular architecture of whole cells
Technological advances in volume electron microscopy allow imaging and analysis of whole cells at record resolution.
- Arunima Singh
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Review Article |
The power of imaging to understand extracellular vesicle biology in vivo
This Review describes the state of the art in imaging extracellular vesicles in animals to study their release, biodistribution and uptake, and covers labeling strategies, microscopy methods and discoveries made in model organisms.
- Frederik J. Verweij
- , Leonora Balaj
- & Guillaume van Niel
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Article |
Automated segmentation and tracking of mitochondria in live-cell time-lapse images
Mitometer enables efficient, rapid, and accurate automated segmentation and tracking of mitochondria from time-lapse images. Mitometer performs well on diverse input images and can be used to monitor dynamic fission and fusion events.
- Austin E. Y. T. Lefebvre
- , Dennis Ma
- & Michelle A. Digman
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This Month |
Reto Fiolka
A flight path into biology and fast 3D projection of sample dynamics.
- Vivien Marx
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Article |
Real-time multi-angle projection imaging of biological dynamics
Multiangle projection imaging accelerates volumetric imaging by up to two orders of magnitude and is readily implemented on diverse microscopes, including spinning disk confocal and light-sheet microscopes.
- Bo-Jui Chang
- , James D. Manton
- & Reto Fiolka
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Article |
Three-dimensional adaptive optical nanoscopy for thick specimen imaging at sub-50-nm resolution
The combination of adaptive optics with an improved isoSTED nanoscope allows imaging of cells and tissues with sub-50-nm isotropic resolution.
- Xiang Hao
- , Edward S. Allgeyer
- & Joerg Bewersdorf
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Article |
Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging
Phasor S-FLIM combines novel electronics for multichannel fluorescence lifetime acquisition and a phasor-based unmixing algorithm for real-time analysis of reliable spectral lifetime imaging data, enabling new biological observations.
- Lorenzo Scipioni
- , Alessandro Rossetta
- & Enrico Gratton
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Article |
Evaluation and development of deep neural networks for image super-resolution in optical microscopy
This study explores the performance of deep-learning models for super-resolution imaging and introduces models that utilize frequency content information in the Fourier domain to improve SIM reconstruction under low-SNR conditions.
- Chang Qiao
- , Di Li
- & Dong Li
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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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Article |
Homogeneous multifocal excitation for high-throughput super-resolution imaging
Multifocal flat illumination for field-independent imaging (mfFIFI) enables patterned illumination over an extended field of view. Integration with instant structured illumination microscope allowed for high-speed, multicolor, volumetric super-resolution imaging over 100 × 100 µm2.
- Dora Mahecic
- , Davide Gambarotto
- & Suliana Manley
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Article |
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors
CRISPR-based microraft followed by guide RNA identification (CRaft-ID) combines microraft arrays, microscopy and CRISPR–Cas9 technology for high-content image-based phenotyping. CRaft-ID was used to identify proteins involved in stress granule formation.
- Emily C. Wheeler
- , Anthony Q. Vu
- & Gene W. Yeo
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Perspective |
Visualizing the genome in high resolution challenges our textbook understanding
This Perspective highlights how high-resolution imaging has informed our view and helped overturn the textbook understanding of 4D genome organization.
- Melike Lakadamyali
- & Maria Pia Cosma
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Article |
Nanoscale subcellular architecture revealed by multicolor three-dimensional salvaged fluorescence imaging
4Pi single-molecule switching microscopy combined with ‘salvaged fluorescence’ enables improved ratiometric imaging that bypasses chromatic aberrations and allows for multicolor whole-cell imaging with sub-10-nm localization precision.
- Yongdeng Zhang
- , Lena K. Schroeder
- & Joerg Bewersdorf
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Article |
In situ structure determination at nanometer resolution using TYGRESS
The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.
- Kangkang Song
- , Zhiguo Shang
- & Daniela Nicastro
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Research Highlight |
Lipid biology in super-resolution
BODIPY dimerization is exploited for super-resolution imaging and single-particle tracking of lipids in living cells.
- Rita Strack
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News & Views |
Resolution upgrades for light-sheet microscopy
Single objective light-sheet fluorescence microscopes combine the convenience of conventional sample mounting with sensitive subcellular and super-resolution imaging of cells and tissues.
- Reto Fiolka
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Brief Communication |
Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM
The red form of the photoconvertible fluorescent protein mEos4b has a long-lived dark state with specific chromophore conformation. Weak 488-nm light depopulates this state, improving track lengths in single-particle tracking experiments.
- Elke De Zitter
- , Daniel Thédié
- & Dominique Bourgeois
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News & Views |
Peering into cells at high resolution just got easier
Light-sheet fluorescence microscopes are making it possible to follow subcellular dynamics with unprecedented detail, but they are complex to build and maintain. A new method that can generate arbitrary light sheets provides much-needed simplicity and additional versatility.
- Manu Forero-Shelton
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Brief Communication |
Imaging cellular ultrastructures using expansion microscopy (U-ExM)
U-ExM enables near-native expansion microscopy of samples in vitro and in cells. The combination of U-ExM with confocal microscopy and HyVolution revealed details of centriole chirality that were previously accessible only by electron microscopy.
- Davide Gambarotto
- , Fabian U. Zwettler
- & Paul Guichard
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This Month |
Yamuna Krishnan
A probe for a journey into bubbles and why it’s good to be both inventor and discoverer.
- Vivien Marx
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Article |
A pH-correctable, DNA-based fluorescent reporter for organellar calcium
The DNA-based, ratiometric fluorescent reporter CalipHluor enables quantitative imaging of pH and calcium in acidic organelles with single-organelle resolution. The probe was used to identify a lysosome-specific Ca2+ importer in animals.
- Nagarjun Narayanaswamy
- , Kasturi Chakraborty
- & Yamuna Krishnan
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Brief Communication |
FLIRT: fast local infrared thermogenetics for subcellular control of protein function
FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light targeted to the region(s) of interest.
- Sophia M. Hirsch
- , Sriramkumar Sundaramoorthy
- & Julie C. Canman
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Research Highlight |
A tissue-to-organelle view of cellular proteins
By coupling multiplex iterative indirect immunofluorescence imaging with computer vision methods, researchers can detect at least 40 different proteins with subcellular resolution.
- Vesna Todorovic
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Correspondence |
Assessing photodamage in live-cell STED microscopy
- Nicole Kilian
- , Alexander Goryaynov
- & Joerg Bewersdorf
Studying cell membrane tension and mechanosensation during mechanical stimulation
Structures in situ