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Open Access
Featured
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News & Views |
LiMCA: Hi-C gets an RNA twist
A multiomics method measures both the cellular three-dimensional genome and transcriptome at the single-cell level.
- Jane Kawaoka
- & Stavros Lomvardas
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Article
| Open Access
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice
LiMCA offers a tool for co-profiling 3D genome structure and gene expression at the single-cell level, enabling researchers to elucidate the olfactory receptor gene selection process.
- Honggui Wu
- , Jiankun Zhang
- & X. Sunney Xie
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News & Views |
Accessible computing platforms democratize neuroimaging data analysis
Several research groups are making it easier for other neuroscientists to analyze large datasets by providing tools that can be accessed and used from anywhere in the world.
- Lucina Q. Uddin
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Brief Communication
| Open Access
brainlife.io: a decentralized and open-source cloud platform to support neuroscience research
brainlife.io is a one-stop cloud platform for data management, visualization and analysis in human neuroscience. It is web-based and provides access to a variety of tools in a reproducible and reliable manner.
- Soichi Hayashi
- , Bradley A. Caron
- & Franco Pestilli
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Article
| Open Access
Spike sorting with Kilosort4
Kilosort4 is a spike-sorting algorithm with improved performance compared to previous versions, owing to the use of a graph-based clustering approach. The tool extracts the activity of individual neurons from electrophysiological recordings acquired with, for example, Neuropixels electrodes.
- Marius Pachitariu
- , Shashwat Sridhar
- & Carsen Stringer
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Research Briefing |
Building an automated three-dimensional flight agent for neural network reconstruction
RoboEM, an artificial intelligence (AI)-based flight agent, automatically steers through three-dimensional electron microscopy (3D-EM) images of brain tissue to follow neurites. RoboEM substantially improves state-of-the-art automated reconstructions, eliminating manual proofreading needs in complex connectomic analysis problems and paving the way for high-throughput, cost-effective, large-scale mapping of neuronal networks — connectomes.
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Article
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RoboEM: automated 3D flight tracing for synaptic-resolution connectomics
RoboEM enables automated proofreading of electron microscopy datasets using a strategy akin to that of self-steering cars. This decreases the need for manual proofreading of segmented datasets and facilitates connectomic analyses.
- Martin Schmidt
- , Alessandro Motta
- & Moritz Helmstaedter
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Article
| Open Access
A multicolor suite for deciphering population coding of calcium and cAMP in vivo
Improved green cAMP and red calcium sensors were developed to facilitate dual-color imaging in vivo. These sensors will allow studying the relationship between calcium and cAMP signaling.
- Tatsushi Yokoyama
- , Satoshi Manita
- & Masayuki Sakamoto
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Article |
Improved green and red GRAB sensors for monitoring spatiotemporal serotonin release in vivo
Deng et al. expand the toolbox of neurotransmitter sensors with high-sensitivity green and red genetically encoded serotonin sensors. These are suitable for in vivo applications, as demonstrated in a variety of applications in mice.
- Fei Deng
- , Jinxia Wan
- & Yulong Li
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Research Highlight |
Predicting neural activity from facial expressions
Facemap tracks keypoints on the mouse face and feeds the information into a deep neural network to predict neural activity.
- Nina Vogt
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Article |
Real-time visualization of structural dynamics of synapses in live cells in vivo
SynapShot combines ddFPs with engineered synaptic adhesion molecules for real-time observation of the structural plasticity of synapses in cultured cells and animals.
- Seungkyu Son
- , Kenichiro Nagahama
- & Won Do Heo
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Brief Communication |
Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging
Neurodesk is a platform for analyzing human neuroimaging data, which provides numerous tools in a containerized form, thereby ensuring reproducibility and portability.
- Angela I. Renton
- , Thuy T. Dao
- & Steffen Bollmann
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This Month |
If at first you don’t succeed
Scientists have successes to celebrate but must also cope with the sting of failures. In the way she handles both, Nobel laureate Katalin Karikó inspires others.
- Vivien Marx
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Research Briefing |
Ultra-long-working-distance multiphoton objective unlocks new possibilities for imaging
In 1858, the first standard for microscope objectives was established to encourage interchangeable components. Over the following 150 years, standards have evolved to constrain the size of objectives, which limits the parameters of working distance, field of view and resolution. A new design breaks out of this conventional envelope, offering an ultra-long working distance in air and enabling new neuroscience experiments.
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Article
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The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo
The Cousa objective is an ultra-long working distance air objective optimized for two- and three-photon imaging. Bypassing challenges caused by water immersion and short working distances, the Cousa enables and improves imaging of diverse specimens.
- Che-Hang Yu
- , Yiyi Yu
- & Spencer LaVere Smith
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Method to Watch |
Human brain mapping
High-resolution connectomics of the human brain is the next frontier in neuroscience.
- Nina Vogt
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Research Briefing |
Inferring how animals deform improves cell tracking
Tracking cells is a time-consuming part of biological image analysis, and traditional manual annotation methods are prohibitively laborious for tracking neurons in the deforming and moving Caenorhabditis elegans brain. By leveraging machine learning to develop a ‘targeted augmentation’ method, we substantially reduced the number of labeled images required for tracking.
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Article |
Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation
Targettrack is a deep-learning-based pipeline for automatic tracking of neurons within freely moving C. elegans. Using targeted augmentation, the pipeline has a reduced need for manually annotated training data.
- Core Francisco Park
- , Mahsa Barzegar-Keshteli
- & Sahand Jamal Rahi
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Article
| Open Access
In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids
MISCOs are spatially arranged ventral midbrain–striatum–cortical organoids that enable investigations into the human dopaminergic system.
- Daniel Reumann
- , Christian Krauditsch
- & Jürgen A. Knoblich
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Article |
Improved green and red GRAB sensors for monitoring dopaminergic activity in vivo
Next-generation red and green G-protein-coupled receptor-based dopamine sensors with improved properties have been developed. Their performance is demonstrated in cell culture, in brain slices and in vivo in the mouse.
- Yizhou Zhuo
- , Bin Luo
- & Yulong Li
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This Month |
Sizing a lab
Labs range in size, and no one size is likely to fit all. Here some researchers share their lab size experiences and preferences.
- Vivien Marx
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Article
| Open Access
Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla
A combination of hardware developments has increased the achievable spatial resolution in 7 Tesla human neuroimaging to about 0.4 mm.
- David A. Feinberg
- , Alexander J. S. Beckett
- & Peter Dietz
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Article
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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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Technology Feature |
A sound solution for deep-brain imaging
Ultrasound-based modalities are revealing the brain’s inner workings with steadily increasing speed, resolution and depth.
- Michael Eisenstein
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Article |
Fatigue-resistant hydrogel optical fibers enable peripheral nerve optogenetics during locomotion
Flexible and fatigue-resistant optical fibers made from hydrogel allow optogenetic manipulations in the periphery in freely behaving mice.
- Xinyue Liu
- , Siyuan Rao
- & Xuanhe Zhao
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Research Highlight |
Droplet-based power sources for modulating neural activity
Miniaturized power sources consisting of a few droplets can generate enough power to modulate neuronal activity.
- Nina Vogt
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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
D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry
D-LMBmap is a fully automated pipeline for mesoscale connectomics including deep-learning modules for axon segmentation, brain region segmentation and whole-brain registration. D-LMBmap works accurately across cell types and modalities.
- Zhongyu Li
- , Zengyi Shang
- & Jing Ren
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Article |
FIOLA: an accelerated pipeline for fluorescence imaging online analysis
FIOLA is a pipeline for processing calcium or voltage imaging data. Its advantages include the fast speed and online processing.
- Changjia Cai
- , Cynthia Dong
- & Andrea Giovannucci
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Editorial |
Let’s talk about diversity in human neuroscience
Diversity in human neuroscience studies is an important and recurring topic of discussion. Though slow, progress is being made.
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This Month |
How to make double affiliations work
Some researchers have the good fortune of two academic affiliations. Sometimes these affiliations are not exactly within easy commuting distance.
- Vivien Marx
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Research Briefing |
Ultrafast nLight indicators for sensitive and specific in vivo imaging of norepinephrine
We developed, characterized and validated nLight sensors, a new family of genetically encoded green and red fluorescent norepinephrine indicators based on an alpha-1 adrenergic receptor. nLight probes can detect norepinephrine in living animals with superior sensitivity, ligand specificity and temporal resolution as compared with previous tools.
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Article
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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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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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Research Briefing |
A method to map single-cell lineages in the mouse brain by CRISPR-based barcoding
We developed CREST (CRISPR editing-based lineage-specific tracing) to enable high-throughput mapping of single-cell lineages in any Cre lineage of interest in mice. In addition, we delineated a comprehensive lineage landscape of the developing mouse ventral midbrain, revealing novel differentiation trajectories and molecular programs underlying neural specification.
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Article |
Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding
CREST is a dual-recorder single-cell lineage tracing method for spatiotemporal mapping of the mouse brain.
- Lianshun Xie
- , Hengxin Liu
- & Yuejun Chen
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Correspondence |
Addgene AAV Data Hub: a platform for sharing AAV experimental data
- Jason S. Nasse
- , Rachel Leeson
- & Melina Fan
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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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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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Technology Feature |
To share is to be a scientist
Wrangling big data is now part of being a biomedical scientist, and mandates on data sharing have entered the scene. Mandates can alter behavior, but data sharing also needs incentives and shifts in science culture.
- Vivien Marx
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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 |
ReX: an integrative tool for quantifying and optimizing measurement reliability for the study of individual differences
The Reliability eXplorer is a tool for assessing measurement reliability in neuroimaging studies.
- Ting Xu
- , Gregory Kiar
- & Michael P. Milham
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This Month |
Languages in the lab
Members of a lab often have a varied language background. This rich language diversity leads to lab dynamics that take mindful handling.
- Vivien Marx
Virtual reality-empowered deep-learning analysis of brain cells
Modeling locomotion from environment to neurons
Development of the human head
Imaging behavior with a camera arrayBrowse broader subjects
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