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Open Access
Featured
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Research Highlight |
Sequencing RNA isoforms in brain tissue
Single-nuclei isoform RNA sequencing enables cell-type specific isoform analysis in frozen brain samples.
- Lei Tang
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Article
| Open AccessSLEAP: A deep learning system for multi-animal pose tracking
SLEAP is a versatile deep learning-based multi-animal pose-tracking tool designed to work on videos of diverse animals, including during social behavior.
- Talmo D. Pereira
- , Nathaniel Tabris
- & Mala Murthy
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Research Briefing |
HYBRiD: a simple method for clearing and visualizing mammalian bodies
A simple and affordable technique passively clears and images whole mammalian bodies or large tissues. This technique is compatible with the use of endogeneous fluoresent proteins, without the loss of signal associated with other existing methods for whole-animal clearing.
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Article |
HYBRiD: hydrogel-reinforced DISCO for clearing mammalian bodies
HYBRiD is a tissue-clearing approach that combines elements of solvent-based and aqueous, hydrogel-based methods, thereby achieving high transparency while maintaining fluorescence.
- Victoria Nudell
- , Yu Wang
- & Li Ye
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Article |
Detecting and correcting false transients in calcium imaging
SEUDO is a tool for detecting and correcting errors introduced by automated processing of calcium imaging data.
- Jeffrey L. Gauthier
- , Sue Ann Koay
- & Adam S. Charles
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Research Highlight |
Potent optogenetics
Two groups report improved variants of the channelrhodopsins ChRmine and ChroME, respectively.
- Nina Vogt
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Research Highlight |
Jellyfish enter neuroscience research
Jellyfish are established as a model system for neuroscience.
- Nina Vogt
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Article |
A genetically encoded sensor for in vivo imaging of orexin neuropeptides
OxLight1 is a genetically encoded sensor for the orexin neuropeptides. It has been applied in fiber photometry recordings and two-photon imaging in mice during a variety of behaviors.
- Loïc Duffet
- , Seher Kosar
- & Tommaso Patriarchi
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Method to Watch |
Neuroscience goes viral
Viral tools are a mainstay in mammalian neuroscience, but there is room for improvement.
- Nina Vogt
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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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News & Views |
New dual-channel system records lineage in high definition
Introducing iTracer, a system for long-term measurement of lineage dynamics at high resolution.
- Kunal Jindal
- , Sadie VanHorn
- & Samantha A. Morris
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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 |
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 |
Cross-modal coherent registration of whole mouse brains
mBrainAligner is a cross-modal registration platform for whole mouse brains imaged with different modalities. In addition, a fluorescence micro-optical sectioning tomography-based mouse brain atlas has been generated.
- Lei Qu
- , Yuanyuan Li
- & Hanchuan Peng
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News & Views |
A repurposed vaccine grants durable anterograde access to neural circuits
How a decades-old vaccine for yellow fever may help scientists study the brain connectome.
- Jennifer B. Treweek
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Article |
Anterograde transneuronal tracing and genetic control with engineered yellow fever vaccine YFV-17D
Anterograde transneuronal tracing can be achieved with engineered variants of the yellow fever vaccine YFV-17D. Both monosynaptic and polysynaptic tracing are demonstrated in different circuits of the mouse brain.
- Elizabeth Li
- , Jun Guo
- & Wei Xu
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Article
| Open AccessDeep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
Tangram is a versatile tool for aligning single-cell and single-nucleus RNA-seq data to spatially resolved transcriptomics data using deep learning.
- Tommaso Biancalani
- , Gabriele Scalia
- & Aviv Regev
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Perspective |
Time for NanoNeuro
This Perspective discusses how neuroscience can benefit from harnessing nanoscience-based tools for manipulating and recording neuronal activity.
- Aitzol Garcia-Etxarri
- & Rafael Yuste
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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 |
Spike inference with CASCADE
A deep-learning-based tool and a large ground truth dataset enable spike inference from calcium imaging data acquired in a variety of experimental conditions.
- Nina Vogt
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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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This Month |
Jonathan Sweedler
Scuba diving and jazz bring together chemistry, neuroscience and life inland.
- Vivien Marx
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Article
| Open AccessImage-guided MALDI mass spectrometry for high-throughput single-organelle characterization
This article presents a workflow for image-guided MALDI MS characterization of peptide and lipid content in single organelles.
- Daniel C. Castro
- , Yuxuan Richard Xie
- & Jonathan V. Sweedler
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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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Technology Feature |
Neuroscientists go wireless
To study the neural complexities of animals moving though physical and social space, labs increasingly turn to wireless technology.
- Vivien Marx
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Article |
Chronically implantable LED arrays for behavioral optogenetics in primates
An implantable array of LEDs called the Opto-Array facilitates optogenetic manipulations in the nonhuman primate brain.
- Rishi Rajalingham
- , Michael Sorenson
- & Arash Afraz
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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 |
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising
DeepCAD is a self-supervised deep-learning approach for denoising calcium imaging data. DeepCAD improved SNR and facilitates neuron extraction and spike inference.
- Xinyang Li
- , Guoxun Zhang
- & Qionghai Dai
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This Month |
Pavan Ramdya
A neuroscientist who jams, plays and builds a way to capture animal movement.
- Vivien Marx
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Article |
LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals
LiftPose3D infers three-dimensional poses from two-dimensional data or from limited three-dimensional data. The approach is illustrated for videos of behaving Drosophila, mice, rats and macaques.
- Adam Gosztolai
- , Semih Günel
- & Pavan Ramdya
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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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Correspondence |
CloudReg: automatic terabyte-scale cross-modal brain volume registration
- Vikram Chandrashekhar
- , Daniel J. Tward
- & Joshua T. Vogelstein
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Research Highlight |
Optogenetic silencing at synaptic terminals
GPCR-based opsins can be harnessed to inhibit neurotransmission via inhibitory G protein signaling.
- Nina Vogt
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Correspondence |
The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets
- Sara Larivière
- , Casey Paquola
- & Boris C. Bernhardt
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Correspondence |
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
- Joshua Orvis
- , Brian Gottfried
- & Ronna Hertzano
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Brief Communication |
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set
A deep-learning-based approach enables automatic identification of synaptically connected neurons in electron microscopy datasets of the fly brain.
- Julia Buhmann
- , Arlo Sheridan
- & Jan Funke
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Brief Communication |
QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data
QSIPrep is a software platform for processing of most diffusion MRI datasets and ensures that adequate workflows are used.
- Matthew Cieslak
- , Philip A. Cook
- & Theodore D. Satterthwaite
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Research Highlight |
Cell–cell interactions revealed with RABID-seq
An approach involving barcoded viral tracing provides insights into cell–cell interactions at single-cell resolution.
- Nina Vogt
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Brief Communication |
L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma
L1CAM was presumed to be a marker for neuron-derived extracellular vesicles, but this is now shown not to be the case.
- Maia Norman
- , Dmitry Ter-Ovanesyan
- & David R. Walt
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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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News & Views |
The DANNCE of the rats: a new toolkit for 3D tracking of animal behavior
A new approach tracks animal movements in 3D from multiple camera views using volumetric triangulation, reconciling occlusions and ambiguities present in any one camera view.
- Pierre Karashchuk
- , John C. Tuthill
- & Bingni W. Brunton
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Article |
Geometric deep learning enables 3D kinematic profiling across species and environments
DANNCE enables robust 3D tracking of animals’ limbs and other features in naturalistic environments by making use of a deep learning approach that incorporates geometric reasoning. DANNCE is demonstrated on behavioral sequences from rodents, marmosets, and chickadees.
- Timothy W. Dunn
- , Jesse D. Marshall
- & Bence P. Ölveczky
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Article |
Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice
The mini-mScope is a miniature microscope that can image neural activity at the mesoscale in most of the dorsal cortex of freely behaving mice.
- Mathew L. Rynes
- , Daniel A. Surinach
- & Suhasa B. Kodandaramaiah
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Brief Communication |
A three-dimensional virtual mouse generates synthetic training data for behavioral analysis
Bolaños et al. present a realistic three-dimensional virtual mouse model that can be animated and that facilitates the training of pose estimation algorithms.
- Luis A. Bolaños
- , Dongsheng Xiao
- & Timothy H. Murphy
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This Month |
Tiago Ferreira
How computational neuroanatomy, vintage gear and fado fit together.
- Vivien Marx
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Brief Communication |
SNT: a unifying toolbox for quantification of neuronal anatomy
SNT is a toolbox neuronal morphometry and connectomics and provides various analysis, visualization, quantification and modeling tools.
- Cameron Arshadi
- , Ulrik Günther
- & Tiago A. Ferreira
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Correspondence |
Chunkflow: hybrid cloud processing of large 3D images by convolutional nets
- Jingpeng Wu
- , William M. Silversmith
- & H. Sebastian Seung
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Article |
Single-molecule FRET imaging of GPCR dimers in living cells
A suite of generally applicable methods and tools, developed to enable single-molecule FRET-based studies of transmembrane proteins diffusing in the cell membrane of living cells, was used to study the oligomerization and dynamics of GPCRs.
- Wesley B. Asher
- , Peter Geggier
- & Jonathan A. Javitch
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