Featured
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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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Research Highlight |
Next-generation expansion microscopy
A new twist on expansion microscopy called Magnify uses a mechanically sturdy gel to simultaneously anchor and expand diverse biological samples for super-resolution imaging.
- Rita Strack
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Article |
A framework for evaluating the performance of SMLM cluster analysis algorithms
This analysis compares the performance of seven algorithms for cluster analysis of single-molecule localization microscopy data. The results provide a framework for comparing these types of methods and point users to the best tools.
- Daniel J. Nieves
- , Jeremy A. Pike
- & Dylan M. Owen
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Article
| Open Access
ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study
The ELI-TriScope advances cryo-CLEM by focusing light, electron and ion beams on cryopreserved samples for markedly improved preparation of cryo-lamellae containing target structures.
- Shuoguo Li
- , Ziyan Wang
- & Fei Sun
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Method to Watch |
Fluorescence in structural biology
Advances in fluorescence microscopy and spectroscopy show their promise for applications that complement in situ structural biology methods like cryoelectron tomography.
- Rita Strack
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Research Briefing |
LocMoFit quantifies cellular structures in super-resolution data
Localization Model Fit (LocMoFit) is a tool that enables fitting of super-resolution microscopy data to an arbitrary geometric model. The fit extracts quantitative parameters of individual cellular structures, which can be used to investigate dynamic and heterogenous protein assemblies and to create average protein distribution maps.
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Matters Arising |
Reply to: Assessment of 3D MINFLUX data for quantitative structural biology in cells
- Klaus C. Gwosch
- , Francisco Balzarotti
- & Stefan W. Hell
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Article
| Open Access
Maximum-likelihood model fitting for quantitative analysis of SMLM data
Localization Model Fit (LocMoFit) is an open-source tool for extracting meaningful parameters from individual structures in localization microscopy data. The framework was used for quantitative analysis of diverse biological structures.
- Yu-Le Wu
- , Philipp Hoess
- & Jonas Ries
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Research Briefing |
Fast cryo-electron tomography data acquisition to determine molecular structures in situ
To accelerate data acquisition for in situ cryo-electron tomography, we created a method that takes into consideration sample geometry for the robust prediction of sample movement while the microscope stage is tilted. This approach enabled the parallel collection of tens to hundreds of tilt series.
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Article |
Parallel cryo electron tomography on in situ lamellae
The parallel cryo electron tomography (PACE-tomo) method increases the throughput on in situ samples by parallelizing acquisition. It maximizes the usable sample area on individual lamellae without compromising data quality.
- Fabian Eisenstein
- , Haruaki Yanagisawa
- & Radostin Danev
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Article
| Open Access
A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice
A lightweight three-photon miniature microscope allows imaging neuronal activity throughout the cortex in freely moving mice.
- Alexandr Klioutchnikov
- , Damian J. Wallace
- & Jason N. D. Kerr
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Article
| Open Access
Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging
Image-seq isolates cells from specific tissue locations under image guidance for analysis by single-cell RNA sequencing. The technique can be combined with in vivo imaging to document the temporal and dynamic history of the cells prior to sequencing.
- Christa Haase
- , Karin Gustafsson
- & Charles P. Lin
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Article |
Capturing the start point of the virus–cell interaction with high-speed 3D single-virus tracking
3D-TrIm combines real-time, high-speed, single-virion tracking with volumetric imaging of cellular microenvironments.
- Courtney Johnson
- , Jack Exell
- & Kevin D. Welsher
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Research Briefing |
Robust fluorescent proteins for high-resolution microscopy and biochemical techniques
Hyperfolder yellow fluorescent protein (hfYFP) and its variants are fluorescent proteins with high chemical and thermal stability. They resist aggregation, withstand diverse chemical challenges and show promise in expansion and electron microscopies. The chloride resistance and uncanny stability in guanidinium of hfYFP enable fluorescence-guided protein purification under denaturing conditions.
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Article
| Open Access
Chemically stable fluorescent proteins for advanced microscopy
The engineered hyperfolder YFP (hfYFP) and variants offer unprecedented chemical and thermal stability, making them versatile probes for microscopy as well as for challenging applications like correlative light and electron microscopy and expansion microscopy.
- Benjamin C. Campbell
- , Maria G. Paez-Segala
- & Ce Feng Liu
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Editorial |
The beauty of imaging
This month we continue our yearly celebration of the beauty of imaging.
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Research Briefing |
Doubling the resolution of light-sheet fluorescence microscopy
A combination of light-sheet fluorescence microscopy (LSFM) with structured illumination doubles resolving power over LSFM alone. We show a practical implementation using a single objective for illumination and fluorescence detection and demonstrate its use for rapid volumetric imaging.
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News & Views |
Mapping of the zebrafish brain takes shape
The generation of a whole larval zebrafish brain electron microscopy volume in tandem with automated tools lays the groundwork for producing the first vertebrate brain connectome.
- Paul Brooks
- , Andrew Champion
- & Marta Costa
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Article |
Resolution doubling in light-sheet microscopy via oblique plane structured illumination
The longstanding goal of combining the optical sectioning of light-sheet illumination and the resolving power of multidirectional structured illumination microscopy is realized using an oblique plane microscope for improved fast 3D subcellular imaging.
- Bingying Chen
- , Bo-Jui Chang
- & Reto P. Fiolka
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Resource
| Open Access
Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain
This Resource presents a serial block-face EM dataset of the whole larval zebrafish brain, including automated segmentation of neurons, detection of synapses and reconstruction of circuitry for visual motion processing.
- Fabian Svara
- , Dominique Förster
- & Herwig Baier
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Brief Communication
| Open Access
SyConn2: dense synaptic connectivity inference for volume electron microscopy
SyConn2 is a machine learning-based framework for inferring and analyzing the connectomes contained in a volume electron microscopy dataset of brain tissue, for example from the zebra finch.
- Philipp J. Schubert
- , Sven Dorkenwald
- & Joergen Kornfeld
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Perspective |
Practical considerations for quantitative light sheet fluorescence microscopy
This Perspective describes common pitfalls that can occur when using light sheet microscopy and offers guidance for improved quantitative imaging with these instruments.
- Chad M. Hobson
- , Min Guo
- & Teng-Leong Chew
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Research Briefing |
Light-Seq: from microscopy to transcriptomics and back
Light-Seq combines high resolution imaging with next generation sequencing of selected cell populations in fixed biological samples. Specifically, microscopically analyzed cells can be subjected to RNA expression profiling while keeping the sample intact for further assays, enabling cellular phenotypes and states to be assessed in the context of the original tissue.
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Article |
Cell region fingerprints enable highly precise single-cell tracking and lineage reconstruction
TracX improves the accuracy of single-cell tracking by using a fingerprinting approach to measure the similarity between cells in two consecutive images. The approach is applicable across modalities and enables biological discovery.
- Andreas P. Cuny
- , Aaron Ponti
- & Jörg Stelling
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News & Views |
Microscopes are coming for your job
Advances in microscopy, computer vision and open source software are converging to usher in a new era of microscopes that control themselves.
- Henry Pinkard
- & Laura Waller
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Article
| Open Access
Event-triggered STED imaging
Event-triggered STED is an automated approach that can initiate 2D or 3D STED imaging of specific regions in biological samples after detection of an event of interest. This approach can help maximize observations in live cell imaging and enable discovery.
- Jonatan Alvelid
- , Martina Damenti
- & Ilaria Testa
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This Month |
Hi, new PI
Your name is on the door to your new lab. Life is getting exciting and turbulent.
- Vivien Marx
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Brief Communication
| Open Access
DNA-PAINT MINFLUX nanoscopy
A systematic exploration of MINFLUX nanoscopy with DNA-PAINT labeling leads to improved nanoscopy in fixed cells and MINFLUX imaging with increased multiplexing, as exemplified by three-color imaging of mitochondria in mammalian cells.
- Lynn M. Ostersehlt
- , Daniel C. Jans
- & Stefan Jakobs
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Article
| Open Access
Antibody stabilization for thermally accelerated deep immunostaining
Thermostable antibodies called SPEARs enable rapid immunostaining with improved tissue penetration.
- Hei Ming Lai
- , Yumi Tang
- & Ho Ko
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This Month |
When labs welcome under-represented groups
To diversify science, some labs open summer doors wide to reach out to under-represented groups.
- Vivien Marx
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Research Highlight |
Spatial proteomics with subcellular resolution
Deep Visual Proteomics combines the power of deep-learning-based image analysis with microdissection and ultrasensitive mass spectrometry to provide insights into the spatial proteome.
- Rita Strack
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Research Highlight |
A fluorescent protein with staying power
A newly described fluorescent protein, StayGold, is bright and extremely photostable, enabling extended time-lapse imaging.
- Rita Strack
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This Month |
Everyday ups and downs for LGBT+ scientists
How to gauge academic culture and celebrate being an LGBT+ scientist.
- Vivien Marx
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Technology Feature |
Modeling the early embryo
Widespread adoption of new embryo models hinges on how faithfully they mirror real embryos.
- Vivien Marx
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Article
| Open Access
Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models
A dynamic model of the 4Pi point spread function enables localization microscopy with exceptional three-dimensional resolution and a simpler optical design. 4Pi-STORM images of neurons and mitochondria reveal new details of nanoscale protein and nucleic acid organization.
- Mark Bates
- , Jan Keller-Findeisen
- & Stefan W. Hell
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News & Views |
Imaging cleared tissues made easy
A flexible open-top light-sheet microscope has been developed that can perform deep three-dimensional imaging on all clearing protocols with low and high optical resolution.
- Shigeaki Kanatani
- & Per Uhlén
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Research Highlight |
Two-photon imaging in freely behaving mice
The MINI2P is a two-photon miniscope that enables robust calcium imaging during mouse behavior.
- Nina Vogt
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Article |
Correction of multiple-blinking artifacts in photoactivated localization microscopy
A model-based correction (MBC) algorithm offers fast and accurate correction of multiple-blinking artifacts in PALM data. MBC outperforms other algorithms in both speed and accuracy and improves quantitative downstream image analysis.
- Louis G. Jensen
- , Tjun Yee Hoh
- & Dylan M. Owen
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Article |
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues
A ‘hybrid’ open-top light-sheet microscope is described, which can be used for broad multi-scale volumetric imaging of one or more large tissues, cleared with diverse protocols, and conveniently mounted on an array of sample holders.
- Adam K. Glaser
- , Kevin W. Bishop
- & Jonathan T. C. Liu
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This Month |
Vahid Sandoghdar
From a physicist who explores biology’s unknowns, greater precision by linking two methods.
- Vivien Marx
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Article
| Open Access
Precision size and refractive index analysis of weakly scattering nanoparticles in polydispersions
iNTA combines interferometric detection of scattering with nanoparticle tracking analysis for determining the size and refractive index distributions of nanoparticles in suspension with high sensitivity and precision.
- Anna D. Kashkanova
- , Martin Blessing
- & Vahid Sandoghdar
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Research Highlight |
Image in vivo, skip the lenses
A lensless microscope captures 3D fluorescence images of complex biological tissues.
- Rita Strack
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Research Briefing |
DaXi: pushing the limits of single-objective light-sheet microscopy
A new single-objective light-sheet microscope has been developed that uses novel optics and imaging protocols to increase resolution without compromising imaging speed and volume.
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Article
| Open Access
DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy
The DaXi single-objective light-sheet microscope achieves fast, high-quality imaging of large volumes. DaXi’s design allows increased scanning range without sacrificing imaging speed or quality, multiview imaging and versatile sample mounting.
- Bin Yang
- , Merlin Lange
- & Loic A. Royer
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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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Research Highlight |
Three views are better than one
Researchers push the limits of confocal microscopy by combining multiple views, super-resolution and deep learning.
- Rita Strack
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News & Views |
Expansion microscopy opens the door to exploring more challenges
Cryofixation-based ultrastructure-expansion microscopy (cryo-ExM) bypasses artifacts caused by chemical fixation and establishes more-native preservation of biological samples.
- Mengfei Gao
Miniature three-photon microscopy maximized for scattered fluorescence collection
A diamond microscopeBrowse broader subjects
Browse narrower subjects
- Atomic force microscopy
- Ca2+ imaging
- Confocal microscopy
- Cryoelectron microscopy
- Interference microscopy
- Light-sheet microscopy
- Multiphoton microscopy
- Phase-contrast microscopy
- Polarization microscopy
- Scanning electron microscopy
- Scanning probe microscopy
- Super-resolution microscopy
- Total internal reflection microscopy
- Transmission electron microscopy
- Transmission light microscopy
- Wide-field fluorescence microscopy
