Featured
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Article
| Open Access
Multi-layered maps of neuropil with segmentation-guided contrastive learning
SegCLR automatically annotates segmented electron microscopy datasets of the brain with information such as cellular subcompartments and cell types, using a self-supervised contrastive learning approach.
- Sven Dorkenwald
- , Peter H. Li
- & Viren Jain
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Resource
| Open Access
Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration
An updated version of the Waxholm Space atlas of the rat brain includes more detailed annotations of several brain regions, including the cortex, striatopallidal region, midbrain and thalamus, expanding the previous version with 112 new and 57 revised structures.
- Heidi Kleven
- , Ingvild E. Bjerke
- & Trygve B. Leergaard
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Article
| Open Access
Voltage-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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Research Briefing |
LIONESS enables 4D nanoscale reconstruction of living brain tissue
We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.
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Article
| Open Access
Dense 4D nanoscale reconstruction of living brain tissue
A combination of gentle stimulated emission depletion microscopy imaging and deep-learning-based improvements in signal-to-noise ratio enables high-resolution reconstruction of neuronal architecture in living tissue.
- Philipp Velicky
- , Eder Miguel
- & Johann G. Danzl
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Article
| Open Access
Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression
SELECTIV is an efficient method for tissue-specific AAV-mediated transgene expression in mice mediated by AAV receptor overexpression.
- James Zengel
- , Yu Xin Wang
- & Jan E. Carette
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Brief Communication
| Open Access
High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics
For EM-based connectomics applications, a staining protocol for large tissue samples in the range of a centimeter has been developed, which avoids artifacts common with established protocols.
- Kun Song
- , Zhihui Feng
- & Moritz Helmstaedter
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Research Briefing |
Deep-brain photoactivation of an opioid peptide shapes mouse behavior within seconds
Light-activated drugs and signaling molecules have therapeutic potential and are valuable experimental tools. Photoactivation of a mu opioid receptor agonist in the mouse brain rapidly triggered pain relief and locomotion, demonstrating that in vivo photopharmacology can drive dynamic studies into animal behavior.
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Brief Communication |
In vivo photopharmacology with a caged mu opioid receptor agonist drives rapid changes in behavior
CNV-Y-DAMGO enables photopharmacological manipulations of mu opioid receptor signaling in behaving mice with high temporal resolution.
- Xiang Ma
- , Desiree A. Johnson
- & Matthew R. Banghart
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News & Views |
Linking connectome with transcriptome using a self-inactivating rabies virus
A self-inactivating rabies virus tracer allows long-term monitoring and transcriptomic profiling of synaptically connected cells.
- Shenqin Yao
- & Boaz P. Levi
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Research Highlight |
A cell’s growth rings
Two research groups independently develop tools to record the history of cellular dynamics.
- Hui Hua
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Article |
Sensitive genetically encoded sensors for population and subcellular imaging of cAMP in vivo
cAMPFIREs are genetically encoded cAMP sensors that are suitable for in vivo imaging of cAMP signaling, as demonstrated in Drosophila larvae and behaving mice.
- Crystian I. Massengill
- , Landon Bayless-Edwards
- & Haining Zhong
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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 |
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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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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This Month |
Jonathan Sweedler
Scuba diving and jazz bring together chemistry, neuroscience and life inland.
- Vivien Marx
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Article
| Open Access
Image-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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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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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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Brief Communication |
Deep three-photon imaging of the brain in intact adult zebrafish
Three-photon microscopy provides access to most of the adult zebrafish brain for both structural and functional imaging, as well as to the Danionella dracula brain.
- Dawnis M. Chow
- , David Sinefeld
- & Joseph R. Fetcho
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Article |
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations
Light-dependent variants of Cre, Dre and Flp enable targeted sparse or single-cell labeling in mouse and zebrafish.
- Shenqin Yao
- , Peng Yuan
- & Ali Cetin
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This Month |
Na Ji
How joy and wide-ranging curiosity leads to neurobiology tools for new types of questions.
- Vivien Marx
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Brief Communication |
Rapid mesoscale volumetric imaging of neural activity with synaptic resolution
Integrating a Bessel focus module into a two-photon fluorescence mesoscope enables high-speed volumetric imaging of neuronal activity in soma, dendrites and spines.
- Rongwen Lu
- , Yajie Liang
- & Na Ji
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Comment |
Imaging whole nervous systems: insights into behavior from worms to fish
The development of systems combining rapid volumetric imaging with three-dimensional tracking has enabled the measurement of brain-wide dynamics in freely behaving animals such as worms, flies, and fish. These advances provide an exciting opportunity to understand the organization of neural circuits in the context of voluntary and natural behaviors. In this Comment, we highlight recent progress in this burgeoning area of research.
- John A. Calarco
- & Aravinthan D. T. Samuel
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Article |
Fast, in vivo voltage imaging using a red fluorescent indicator
VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined with blue-light-sensitive tools for dual-color applications.
- Madhuvanthi Kannan
- , Ganesh Vasan
- & Vincent A. Pieribone
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Article |
All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition
The synOptopatch approach enables all-optical access to synaptic communication via mutually exclusive expression of an optogenetic actuator and a voltage sensor in pre- and postsynaptic neurons, respectively.
- Linlin Z. Fan
- , Ralda Nehme
- & Adam E. Cohen
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Research Highlight |
Transcript constellations in a tissue’s universe
The STARmap method advances RNA sequencing in intact tissues.
- Tal Nawy
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Tools in Brief |
Cell-type-specific proteomics in the in vivo mouse brain
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Brief Communication |
Massively parallel single-nucleus RNA-seq with DroNc-seq
DroNc-seq enables low-cost, high-throughput single-nucleus RNA-seq of tissues that are archived or difficult to dissociate, such as post-mortem human brain.
- Naomi Habib
- , Inbal Avraham-Davidi
- & Aviv Regev
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Article |
Large-scale mapping of cortical synaptic projections with extracellular electrode arrays
Combining multielectrode arrays with an ex vivo preparation of the turtle brain allows identification of neurons as excitatory or inhibitory and mapping of their axonal projections.
- Mark Shein-Idelson
- , Lorenz Pammer
- & Gilles Laurent
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Brief Communication |
webKnossos: efficient online 3D data annotation for connectomics
webKnossos is a browser-based tracing and annotation tool for 3D electron microscopy data sets that is optimized for seamless data viewing. The tool’s flight-mode view facilitates fast neurite tracing because of its egocentric viewpoint.
- Kevin M Boergens
- , Manuel Berning
- & Moritz Helmstaedter
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Brief Communication |
DeActs: genetically encoded tools for perturbing the actin cytoskeleton in single cells
DeActs are genetically encoded tools that perturb the actin cytoskeleton. In contrast to drugs such as latrunculin, they can be targeted to specific cell types, which is demonstrated in the developing mouse brain and in Caenorhabditis elegans.
- Martin Harterink
- , Marta Esteves da Silva
- & J Bradley Zuchero
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Article |
Automated synaptic connectivity inference for volume electron microscopy
SyConn is a computational framework that infers the synaptic wiring of neurons in volume electron microscopy data sets with machine learning. It has been applied to zebra finch, mouse and zebrafish neuronal tissue samples.
- Sven Dorkenwald
- , Philipp J Schubert
- & Joergen Kornfeld
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Article |
Control of cerebral ischemia with magnetic nanoparticles
Stroke is often modeled in rodents by surgically occluding vessels. SIMPLE is an alternative approach that involves the magnet-induced accumulation of nanoparticles. Because of its reversible nature, this method can be used to study both occlusion and subsequent reperfusion of blood vessels.
- Jie-Min Jia
- , Praveen D Chowdary
- & Woo-Ping Ge
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Research Highlights |
Mapmaking with barcoded neurons
In the mouse brain, researchers use sequencing to map long-range neuronal projections...a lot of projections.
- Tal Nawy
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Brief Communication |
Random-access scanning microscopy for 3D imaging in awake behaving animals
Random-access line scanning enables neural activity to be monitored at high speed in neurons and dendrites that are sparsely distributed in three dimensions. The approach is demonstrated in behaving mice.
- K M Naga Srinivas Nadella
- , Hana Roš
- & R Angus Silver
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Research Highlights |
Automating brain mapping
Two new platforms allow single neurons to be imaged throughout the mouse brain.
- Brigitta B Gundersen
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Brief Communication |
Simultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain
Frame-projected independent-fiber photometry (FIP) enables the concurrent monitoring and manipulation of neural activity at multiple sites in the brains of freely behaving mice.
- Christina K Kim
- , Samuel J Yang
- & Karl Deisseroth
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Research Highlights |
Fast track to neurons
New protocols generate neurons directly from fibroblasts using only chemical cocktails.
- Tal Nawy
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Article |
Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging
The photoactivatable calcium sensors reported in this paper allow simultaneous highlighting of cellular morphology and recording of calcium activity, which is demonstrated in neuronal cultures, in Drosophila and in zebrafish.
- Shai Berlin
- , Elizabeth C Carroll
- & Ehud Y Isacoff
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Article |
Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture
A method for 3D differentiation of human pluripotent stem cells yields brain cortical spheroids with functional neurons and astrocytes. The spheroids can be sliced for imaging and electrophysiological studies.
- Anca M Paşca
- , Steven A Sloan
- & Sergiu P Paşca
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Article |
High-resolution whole-brain staining for electron microscopic circuit reconstruction
An improved method for preparing mouse brains for electron microscopy allows reliable tracing of neurites and identification of synapses and appears suitable for whole-brain connectomic reconstruction.
- Shawn Mikula
- & Winfried Denk
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Technology Feature |
Microscopy: seeing through tissue
Tissue samples scatter light and shut out a deeper gaze. Tissue-clearing agents have changed that, but scientists must consider optimizing the optics when using these methods.
- Vivien Marx
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Article |
Rational design of a high-affinity, fast, red calcium indicator R-CaMP2
An improved genetically encoded red calcium sensor enables the monitoring of neuronal activity in cell culture and in vivo. R-CaMP2 has fast kinetics and a high affinity to calcium and can follow action potentials up to 40 Hz.
- Masatoshi Inoue
- , Atsuya Takeuchi
- & Haruhiko Bito
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Correspondence |
In vivo imaging of oligodendrocytes with sulforhodamine 101
- Robert A Hill
- & Jaime Grutzendler
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Brief Communication |
Quantum dot–based multiphoton fluorescent pipettes for targeted neuronal electrophysiology
Quantum dot–coated pipettes facilitate targeted electrophysiological recordings in deep brain tissue because they are readily visible owing to the strong two-photon fluorescence of the quantum dots.
- Bertalan K Andrásfalvy
- , Gregorio L Galiñanes
- & Igor L Medintz
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Correspondence |
Neuronal morphometry directly from bitmap images
- Tiago A Ferreira
- , Arne V Blackman
- & Donald J van Meyel
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Article |
Targeting cells with single vectors using multiple-feature Boolean logic
This paper describes a single-vector strategy for flexible intersectional expression of genetically encoded reporters and tools in precisely defined cell types in the mouse.
- Lief E Fenno
- , Joanna Mattis
- & Karl Deisseroth
Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation