Method to Watch |
Featured
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Research Highlight |
Flexibility in mesoscopic imaging
Two microscopy approaches bring flexibility to mesoscopic imaging in the brain, allowing independent imaging in multiple regions simultaneously.
- Nina Vogt
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Article |
Fast optical recording of neuronal activity by three-dimensional custom-access serial holography
3D-CASH is a random-access microscopy approach that avoids in vivo motion artifacts by sampling each targeted neuron with a holographically shaped grid of illumination spots. The technology allows recording neuronal activity in the mouse cortex at a throughput of 20,000 neurons per second.
- Walther Akemann
- , Sébastien Wolf
- & Laurent Bourdieu
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Article |
FlyWire: online community for whole-brain connectomics
FlyWire is an online community and a platform for proofreading electron microscopy-based connectome data of the Drosophila brain.
- Sven Dorkenwald
- , Claire E. McKellar
- & H. Sebastian Seung
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Article
| Open AccessEngineered HaloTag variants for fluorescence lifetime multiplexing
HaloTag variants offer distinct brightness and fluorescence lifetimes compared with HaloTag7 when labeled with rhodamines. These variants were used for multiplexed imaging with a single fluorophore and to create lifetime-based cell cycle indicators.
- Michelle S. Frei
- , Miroslaw Tarnawski
- & Kai Johnsson
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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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This Month |
Caterina Strambio-De-Castillia
Sharing, teaching and singing to bring people together on microscopy standards.
- Vivien Marx
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Brief Communication
| Open AccessMicro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
Micro-Meta App is an intuitive, highly interoperable, open-source software tool designed to facilitate the extraction and collection of relevant microscopy metadata as specified by recent community guidelines.
- Alessandro Rigano
- , Shannon Ehmsen
- & Caterina Strambio-De-Castillia
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Editorial |
The art of microscopy
This month, we celebrate the value and beauty of images of biological processes captured by microscopes.
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Technology Feature |
Microscopy made to order
The proliferation of versatile open software and hardware for microscopy is helping to democratize biological imaging for both current and aspiring scientists.
- Michael Eisenstein
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Article |
Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms
DeepFinder is a deep learning-based tool for identifying macromolecules in cellular cryo-electron tomograms. DeepFinder performs with an accuracy comparable to expert-supervised ground truth annotations on multiple experimental datasets.
- Emmanuel Moebel
- , Antonio Martinez-Sanchez
- & Charles Kervrann
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Correspondence |
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
- Joel Ryan
- , Thomas Pengo
- & Claire M. Brown
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Article |
Removing independent noise in systems neuroscience data using DeepInterpolation
DeepInterpolation is a self-supervised deep learning-based denoising approach for calcium imaging, electrophysiology and fMRI data. The approach increases the signal-to-noise ratio and allows extraction of more information from the processed data than from the raw data.
- Jérôme Lecoq
- , Michael Oliver
- & Christof Koch
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Research Highlight |
A multimodal whole-body atlas
Researchers have registered a gene expression atlas to a whole-body EM volume of a marine bristle worm.
- Rita Strack
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Article |
An adaptive optics module for deep tissue multiphoton imaging in vivo
A compact adaptive optics module corrects aberrations in two-photon and three-photon microscopy, enabling structural and functional imaging deep in the mouse brain, the mouse spinal cord and the zebrafish larva.
- Cristina Rodríguez
- , Anderson Chen
- & Na Ji
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Article
| Open AccessMass-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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Article
| Open AccessHigh-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy
Three-photon microscopy in combination with adaptive optics-based aberration correction and ECG-triggered gating allows high-resolution imaging of neurons and astrocytes up to a depth of 1.4 mm in the mouse brain.
- Lina Streich
- , Juan Carlos Boffi
- & Robert Prevedel
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Research Highlight |
Thermodynamic profiling of single molecules
A single-molecule calorimeter measures the thermodynamic properties of individual proteins.
- Rita Strack
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Research Highlight |
Measuring condensation forces
Researchers use an in vitro assay in combination with a polymer model to study protein–DNA condensation and how condensates bring distant DNA elements into close proximity.
- Lei Tang
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Article |
Deep learning enables fast and dense single-molecule localization with high accuracy
DECODE uses deep learning for localizing single emitters in high-density two-dimensional and three-dimensional single-molecule localization microscopy data. DECODE outperforms available methods and enables fast live-cell SMLM of dynamic processes.
- Artur Speiser
- , Lucas-Raphael Müller
- & Srinivas C. Turaga
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Article |
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy
Light beads microscopy is a two-photon microscopy approach that allows high-speed volumetric imaging of neuronal activity at the mesoscale.
- Jeffrey Demas
- , Jason Manley
- & Alipasha Vaziri
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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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Research Highlight |
Atomic force microscopy in super-resolution
Applying principles from super-resolution fluorescence microscopy increases the resolution of atomic force microscopy.
- Nina Vogt
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Article |
Clear optically matched panoramic access channel technique (COMPACT) for large-volume deep brain imaging
COMPACT allows imaging of large volumes in the brain through a periscope-like probe inside a glass capillary.
- Bowen Wei
- , Chenmao Wang
- & Meng Cui
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Article |
Universal autofocus for quantitative volumetric microscopy of whole mouse brains
RAPID (rapid autofocusing via pupil-split image phase detection) is a sample-agnostic real-time autofocus method for widefield microscopy. RAPID removes most image degradation in large, cleared samples for enhanced quantitative analyses.
- L. Silvestri
- , M. C. Müllenbroich
- & F. S. Pavone
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Research Highlight |
Breaking barriers for intravital imaging
Advances in adaptive optics combined with a twist on light field microscopy enable high-quality imaging.
- Rita Strack
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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 |
Structured illumination microscopy with noise-controlled image reconstructions
Super-resolution structured illumination microscopy reconstruction algorithms are described that can handle structured noise artifacts in two and three dimensions. The algorithms lack adjustable parameters and enhance objective representation of imaged objects.
- Carlas S. Smith
- , Johan A. Slotman
- & Sjoerd Stallinga
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Perspective |
Best practices and tools for reporting reproducible fluorescence microscopy methods
Comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities are reported with the goal of improving microscopy reporting, rigor and reproducibility.
- Paula Montero Llopis
- , Rebecca A. Senft
- & Michelle S. Itano
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This Month |
Jie Xiao
Reaching ground truth in super-res microscopy, powered by a love of cooking and food.
- Vivien Marx
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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 |
A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM
Distance distribution correction (DDC) eliminates repeat localizations caused by fluorophore blinking without the need for calibrations. Use of DDC yields accurate and quantifiable single-molecule localization microscopy data.
- Christopher H. Bohrer
- , Xinxing Yang
- & Jie Xiao
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Comment |
QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy
The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.
- Ulrike Boehm
- , Glyn Nelson
- & Roland Nitschke
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Correspondence |
PYMEVisualize: an open-source tool for exploring 3D super-resolution data
- Zach Marin
- , Michael Graff
- & David Baddeley
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Research Highlight |
iSCAT gets a signal boost
Photonic resonator interferometric scattering microscopy offers label-free imaging of biomolecules in vitro with improved signal-to-noise ratio.
- Rita Strack
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Review Article |
Understanding the invisible hands of sample preparation for cryo-EM
The quality of structural data obtained in cryo-EM is affected by multiple factors pertaining to sample preparation. This Review discusses available techniques and current challenges.
- Giulia Weissenberger
- , Rene J. M. Henderikx
- & Peter J. Peters
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Article |
Deep learning-enhanced light-field imaging with continuous validation
A deep learning–based algorithm enables efficient reconstruction of light-field microscopy data at video rate. In addition, concurrently acquired light-sheet microscopy data provide ground truth data for training, validation and refinement of the algorithm.
- Nils Wagner
- , Fynn Beuttenmueller
- & Anna Kreshuk
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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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Research Highlight |
Expanding views of the transcriptome
In situ long-read sequencing combined with expansion microscopy enables precise views of transcriptomes in intact biological systems.
- Rita Strack
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Brief Communication |
Molecular-scale axial localization by repetitive optical selective exposure
ROSE-Z achieves axial interference through an asymmetrical optical scheme, yielding 2 nm axial localization precision with ~3,000 photons and a single objective, which offers improved multicolor three-dimensional localization microscopy for cellular structures.
- Lusheng Gu
- , Yuanyuan Li
- & Wei Ji
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Article |
Deep learning-based point-scanning super-resolution imaging
Point-scanning super-resolution imaging uses deep learning to supersample undersampled images and enable time-lapse imaging of subcellular events. An accompanying ‘crappifier’ rapidly generates quality training data for robust performance.
- Linjing Fang
- , Fred Monroe
- & Uri Manor
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Research Highlight |
Super-resolution 3D live cell imaging
3D pRESOLFT enables volumetric live cell imaging with high spatial and temporal resolution.
- Nina Vogt
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Correspondence |
Pycro-Manager: open-source software for customized and reproducible microscope control
- Henry Pinkard
- , Nico Stuurman
- & Laura Waller
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Article |
High-definition imaging using line-illumination modulation microscopy
HD-fMOST is a microscopy technique for imaging large samples at high throughput and with high definition, which is achieved with a line-illumination modulation approach. The technology is illustrated by imaging fluorescently labeled neurons in whole mouse brains.
- Qiuyuan Zhong
- , Anan Li
- & Qingming Luo
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Article |
Real-time volumetric reconstruction of biological dynamics with light-field microscopy and deep learning
Reconstruction of light-field microscopy data with a deep-learning network achieves high reconstruction speed and reduces artifacts, as illustrated for moving C. elegans and beating zebrafish hearts.
- Zhaoqiang Wang
- , Lanxin Zhu
- & Peng Fei
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Research Highlight |
DNA-PAINT takes a left turn
DNA-PAINT with left-handed DNA oligomers enables imaging of nuclear structures with reduced background.
- Rita Strack
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News & Views |
The promise and peril of deep learning in microscopy
- David P. Hoffman
- , Isaac Slavitt
- & Casey A. Fitzpatrick
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Method to Watch |
Single-objective light sheet microscopy
Single-objective light sheet fluorescence microscopes are driving innovation in volumetric imaging.
- Rita Strack
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- Atomic force microscopy
- Ca2+ imaging
- Confocal microscopy
- Cryoelectron microscopy
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- 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