Featured
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Brief Communication
| Open AccessOpen-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
Open-3DSIM is a versatile open-source software for high-fidelity reconstruction of three-dimensional structured illumination microscopy data (with polarization). It is available in three convenient forms for user-friendly and customizable applications.
- Ruijie Cao
- , Yaning Li
- & Peng Xi
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Article |
Sensitive multicolor indicators for monitoring norepinephrine in vivo
Red and green genetically encoded indicators for norepinephrine have been developed and employed to monitor norepinephrine during locomotion and reward behavior in mice. The strategy used for generating these indicators also produced indicators for other neuromodulators.
- Zacharoula Kagiampaki
- , Valentin Rohner
- & Tommaso Patriarchi
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Article
| Open AccessVoltage-Seq: all-optical postsynaptic connectome-guided single-cell transcriptomics
Voltage-Seq combines voltage imaging, optogenetics and single-cell RNA-seq for high-throughput analysis of functional and transcriptomic properties of neurons in situ.
- Veronika Csillag
- , Marianne Hiriart Bizzozzero
- & János Fuzik
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Brief Communication
| Open AccessOrgan 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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Editorial |
What’s next for bioimage analysis?
Advanced bioimage analysis tools are poised to disrupt the way in which microscopy images are acquired and analyzed. This Focus issue shares the hopes and opinions of experts on the near and distant future of image analysis.
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Comment |
The future of bioimage analysis: a dialog between mind and machine
The field of bioimage analysis is poised for a major transformation, owing to advancements in imaging technologies and artificial intelligence. The emergence of multimodal foundation models — which are akin to large language models (such as ChatGPT) but are capable of comprehending and processing biological images — holds great potential for ushering in a revolutionary era in bioimage analysis.
- Loïc A. Royer
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Comment |
Using AI in bioimage analysis to elevate the rate of scientific discovery as a community
The future of bioimage analysis is increasingly defined by the development and use of tools that rely on deep learning and artificial intelligence (AI). For this trend to continue in a way most useful for stimulating scientific progress, it will require our multidisciplinary community to work together, establish FAIR (findable, accessible, interoperable and reusable) data sharing and deliver usable and reproducible analytical tools.
- Damian Dalle Nogare
- , Matthew Hartley
- & Florian Jug
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Comment |
Scaling biological discovery at the interface of deep learning and cellular imaging
Concurrent advances in imaging technologies and deep learning have transformed the nature and scale of data that can now be collected with imaging. Here we discuss the progress that has been made and outline potential research directions at the intersection of deep learning and imaging-based measurements of living systems.
- Morgan Schwartz
- , Uriah Israel
- & David Van Valen
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Comment |
Towards effective adoption of novel image analysis methods
The bridging of domains such as deep learning-driven image analysis and biology brings exciting promises of previously impossible discoveries as well as perils of misinterpretation and misapplication. We encourage continual communication between method developers and application scientists that emphases likely pitfalls and provides validation tools in conjunction with new techniques.
- Talley Lambert
- & Jennifer Waters
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News & Views |
Lighting up action potentials with fast and bright voltage sensors
Three groundbreaking studies have created a new generation of genetically encoded voltage indicators, empowering us to tackle a host of questions on our path toward understanding the brain.
- Alessio Andreoni
- & Lin Tian
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Article |
A positively tuned voltage indicator for extended electrical recordings in the brain
The ASAP4 family of genetically encoded voltage indicators allows recording of action potentials and subthreshold activity with either one- or two-photon microscopy over extended periods of time.
- S. Wenceslao Evans
- , Dong-Qing Shi
- & Michael Z. Lin
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Research Highlight |
Capturing hyperspectral images
A single-shot hyperspectral phasor camera (SHy-Cam) enables fast, multiplexed volumetric imaging.
- Rita Strack
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Research Highlight |
Rethinking microscope objectives
A microscope objective inspired by the Schmidt telescope offers a large field of view, high numerical aperture, long working distance and compatibility with all homogeneous immersion media for versatile bioimaging.
- Rita Strack
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Article
| Open AccessCross-modality supervised image restoration enables nanoscale tracking of synaptic plasticity in living mice
XTC is a supervised deep-learning-based image-restoration approach that is trained with images from different modalities and applied to an in vivo modality with no ground truth. XTC’s capabilities are demonstrated in synapse tracking in the mouse brain.
- Yu Kang T. Xu
- , Austin R. Graves
- & Jeremias Sulam
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Article |
Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution
Photoselective sequencing combines targeted illumination and photocaged fragment libraries to enable the spatial analysis of genomic sequence and chromatin accessibility profiles with subcellular resolution in the context of complex tissues.
- Sarah M. Mangiameli
- , Haiqi Chen
- & Fei Chen
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Comment |
Volume EM: a quiet revolution takes shape
Volume electron microscopy (vEM) is a group of techniques that reveal the 3D ultrastructure of cells and tissues through continuous depths of at least 1 micrometer. A burgeoning grassroots community effort is fast building the profile and revealing the impact of vEM technology in the life sciences and clinical research.
- Lucy M. Collinson
- , Carles Bosch
- & Paul Verkade
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Research Briefing |
Photon-based communication between two neurons in Caenorhabditis elegans
Cells exchange information with one another using secreted chemicals as data carriers. We developed an all-optogenetic synaptic transmission system that replaced a chemical neurotransmitter with emitted photons. This system enabled synthetic signaling between unconnected neurons and the generation of prosthetic synaptic circuits.
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Article
| Open AccessVirtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging
Virtual-scanning light-field microscopy (VsLFM) uses a physics-based deep learning model to improve the quality and speed of LFM, reducing motion artifacts and enabling challenging demonstrations such as fast 3D voltage imaging in Drosophila.
- Zhi Lu
- , Yu Liu
- & Qionghai Dai
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Article
| Open AccessRapid detection of neurons in widefield calcium imaging datasets after training with synthetic data
DeepWonder removes background signals from widefield calcium recordings and enables accurate and efficient neuronal segmentation with high throughput.
- Yuanlong Zhang
- , Guoxun Zhang
- & Qionghai Dai
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News & Views |
Line-scanning speeds up Brillouin microscopy
Two new Brillouin microscopes leverage line-scanning to overcome previous limitations of the technique, enabling fast imaging, with low phototoxicity, of mechanical properties in living embryos of model organisms and tumor spheroids.
- Nargess Khalilgharibi
- , Giulia Paci
- & Yanlan Mao
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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
| Open AccessHigh-resolution line-scan Brillouin microscopy for live imaging of mechanical properties during embryo development
Line-scan Brillouin microscopy enables fast 3D imaging of mechanical properties with low phototoxicity, as shown for Drosophila and mouse embryos, as well as ascidians.
- Carlo Bevilacqua
- , Juan Manuel Gomez
- & Robert Prevedel
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Brief Communication |
An optical design enabling lightweight and large field-of-view head-mounted microscopes
Two miniature microscopes with innovative light paths are described and applied to imaging of juvenile zebra finches and mice.
- Joseph R. Scherrer
- , Galen F. Lynch
- & Michale S. Fee
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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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Brief Communication |
Rapid biomechanical imaging at low irradiation level via dual line-scanning Brillouin microscopy
A dual line-scanning approach increases imaging speed and reduces illumination levels in Brillouin microscopy, which is demonstrated on spheroids.
- Jitao Zhang
- , Milos Nikolic
- & Giuliano Scarcelli
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News & Views |
Deep brain imaging on the move
New three-photon miniature microscopes open the study of neuronal networks to those deep in the brains of behaving animals.
- Jérôme A. Lecoq
- , Roman Boehringer
- & Benjamin F. Grewe
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Article |
Miniature three-photon microscopy maximized for scattered fluorescence collection
A three-photon miniature microscope with optimized light-collection efficiency facilitates imaging of neuronal activity throughout the cortex, as well as in the hippocampus, in freely moving mice.
- Chunzhu Zhao
- , Shiyuan Chen
- & Heping Cheng
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Article |
Mesoscale volumetric light-field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz
Light-field microscopy is extended to mesoscale fields of view, allowing calcium imaging of thousands of neurons at a high frame rate and high spatial resolution.
- Tobias Nöbauer
- , Yuanlong Zhang
- & Alipasha Vaziri
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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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Brief Communication |
LILAC: enhanced actin imaging with an optogenetic Lifeact
LILAC is a photoactivatable version of Lifeact, a tool for labeling F-actin. LILAC can help avoid cytotoxicity, which is sometimes associated with the use of Lifeact.
- Kourtney L. Kroll
- , Alexander R. French
- & Ronald S. Rock
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Article
| Open AccessConvolutional 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
| Open AccessHyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence
Hybrid Unmixing offers enhanced imaging of multiplexed fluorescence labels, enabling longitudinal imaging of multiple fluorescent signals with reduced illumination intensities.
- Hsiao Ju Chiang
- , Daniel E. S. Koo
- & Francesco Cutrale
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Article
| Open AccessIntegrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation
Cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) integrates three-dimensional confocal microscopy with focused ion beam–scanning electron microscopy for efficient preparation of lamellae containing target structures for in situ structural biology with cryo-electron tomography.
- Weixing Li
- , Jing Lu
- & Wei Ji
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Method to Watch |
Reproducibility in MRI
Strategies to overcome poor reproducibility in MRI studies are needed.
- Nina Vogt
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Method to Watch |
A light switch for targeted genomics
The combination of microscopy, targeted illumination and single-cell sequencing is driving applications from direct evolution to spatial omics.
- Rita Strack
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Research Briefing |
Digital brain atlases reveal postnatal development to 2 years of age in human infants
During the first two years of postnatal development, the human brain undergoes rapid, pronounced changes in size, shape and content. Using high-resolution MRI, we constructed month-to-month atlases of infants 2 weeks to 2 years old, capturing key spatiotemporal traits of early brain development in terms of cortical geometries and tissue properties.
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Resource
| Open AccessMultifaceted atlases of the human brain in its infancy
This Resource presents surface and volume atlases of human brain development during early infancy, at monthly intervals.
- Sahar Ahmad
- , Ye Wu
- & Pew-Thian Yap
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Article
| Open AccessOptimizing multiplexed imaging experimental design through tissue spatial segregation estimation
A statistical approach for optimal design of multiplexed imaging studies has been developed. It determines experimental parameters that facilitate cell phenotype identification.
- Pierre Bost
- , Daniel Schulz
- & Bernd Bodenmiller
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Matters Arising |
Assessment of 3D MINFLUX data for quantitative structural biology in cells
- Kirti Prakash
- & Alistair P. Curd
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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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Brief Communication |
Deep-tissue SWIR imaging using rationally designed small red-shifted near-infrared fluorescent protein
miRFP718nano is a rationally designed small near-infrared fluorescent protein with an emission tail that extends into the short-wave infrared range for improved multiplexed and deep-tissue imaging applications.
- Olena S. Oliinyk
- , Chenshuo Ma
- & Vladislav V. Verkhusha
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Article
| Open AccessA 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 AccessImage-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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Technology Feature |
Eavesdropping on extracellular vesicles
A rapidly evolving toolbox is helping researchers to get a handle on the biological and functional diversity of these ubiquitous — but still somewhat enigmatic — cell-secreted nanoparticles
- Michael Eisenstein
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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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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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- Time-lapse imaging
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