Research Highlight |
Featured
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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
| Open Access
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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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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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 |
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
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 |
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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Resource |
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
This resource describes a collection of neurons from a variety of light microscopy-based datasets, which can serve as a gold standard for testing automated tracing algorithms, as shown by comparison of the performance of 35 algorithms.
- Linus Manubens-Gil
- , Zhi Zhou
- & Hanchuan Peng
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Article |
High-speed low-light in vivo two-photon voltage imaging of large neuronal populations
A suite of tools including positive-going voltage indicators, a high-speed two-photon microscope, and denoising software enables prolonged imaging of electrical activity in neurons with limited toxicity.
- Jelena Platisa
- , Xin Ye
- & Jerry L. Chen
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Brief Communication |
A modular architecture for organizing, processing and sharing neurophysiology data
A modular architecture for managing and sharing electrophysiology, behavior, colony management and other data has been built to support individual laboratories or large consortia.
- Luigi Acerbi
- , Valeria Aguillon-Rodriguez
- & Miles J. Wells
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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 Access
Multifaceted 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 Access
Local shape descriptors for neuron segmentation
During segmentation of neurons in electron microscopy datasets, auxiliary learning via the prediction of local shape descriptors increases efficiency, which is important for the processing of datasets of ever-increasing size.
- Arlo Sheridan
- , Tri M. Nguyen
- & Jan Funke
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Brief Communication
| Open Access
TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models
TemplateFlow is a repository for human and other brain templates and atlases, which operates under the FAIR principles.
- Rastko Ciric
- , William H. Thompson
- & Oscar Esteban
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Brief Communication |
A large-scale neural network training framework for generalized estimation of single-trial population dynamics
AutoLFADS models neural population activity via a deep learning-based approach with automated hyperparameter optimization.
- Mohammad Reza Keshtkaran
- , Andrew R. Sedler
- & Chethan Pandarinath
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News & Views |
Mapping of the zebrafish brain takes shape
The generation of a whole larval zebrafish brain electron microscopy volume in tandem with automated tools lays the groundwork for producing the first vertebrate brain connectome.
- Paul Brooks
- , Andrew Champion
- & Marta Costa
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Article
| Open Access
Estimation of skeletal kinematics in freely moving rodents
Pose estimation in combination with an anatomically constrained model allows inferring skeletal kinematics in rodents.
- Arne Monsees
- , Kay-Michael Voit
- & Jason N. D. Kerr
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News & Views |
The data science future of neuroscience theory
An approach for integrating the wealth of heterogeneous brain data — from gene expression and neurotransmitter receptor density to structure and function — allows neuroscientists to easily place their data within the broader neuroscientific context.
- Bradley Voytek
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Article
| Open Access
neuromaps: structural and functional interpretation of brain maps
neuromaps is a toolbox for accessing, transforming and comparing human neuroimaging data.
- Ross D. Markello
- , Justine Y. Hansen
- & Bratislav Misic
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Research Highlight |
Neuroscience data analysis in the cloud
The NeuroCAAS platform simplifies data analysis in the neuroscience space for users and enhances reproducibility.
- Nina Vogt
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This Month |
When labs welcome under-represented groups
To diversify science, some labs open summer doors wide to reach out to under-represented groups.
- Vivien Marx
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Brief Communication |
ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion
ASLPrep is a software suite for reproducible processing of arterial spin labeled magnetic resonance imaging data.
- Azeez Adebimpe
- , Maxwell Bertolero
- & Theodore D. Satterthwaite
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Research Briefing |
NeuroMechFly: an integrative simulation testbed for studying Drosophila behavioral control
Neuromechanical simulations enable the study of how interactions between organisms and their physical surroundings give rise to behavior. NeuroMechFly is an open-source neuromechanical model of adult Drosophila, with data-driven morphological biorealism that enables a synergistic cross-talk between computational and experimental neuroscience.
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Article |
NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster
NeuroMechFly enables simulations of adult Drosophila melanogaster. The platform combines a biomechanical representation of the fly body, models of the muscles, a neural controller and a physics-based simulation of the environment.
- Victor Lobato-Rios
- , Shravan Tata Ramalingasetty
- & Pavan Ramdya
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News & Views |
Tracking together: estimating social poses
Two new toolkits that leverage deep-learning approaches can track the positions of multiple animals and estimate poses in different experimental paradigms.
- Sena Agezo
- & Gordon J. Berman
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This Month |
Mackenzie Weygandt Mathis
Building a sustainable open source toolbox to track social behavior and how to get in the zone.
- Vivien Marx
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Article
| Open Access
Multi-animal pose estimation, identification and tracking with DeepLabCut
DeepLabCut is extended to enable multi-animal pose estimation, animal identification and tracking, thereby enabling the analysis of social behaviors.
- Jessy Lauer
- , Mu Zhou
- & Alexander Mathis
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Article
| Open Access
SLEAP: 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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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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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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Correspondence |
CloudReg: automatic terabyte-scale cross-modal brain volume registration
- Vikram Chandrashekhar
- , Daniel J. Tward
- & Joshua T. Vogelstein
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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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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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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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Comment |
Quantum computing at the frontiers of biological sciences
Computing plays a critical role in the biological sciences but faces increasing challenges of scale and complexity. Quantum computing, a computational paradigm exploiting the unique properties of quantum mechanical analogs of classical bits, seeks to address many of these challenges. We discuss the potential for quantum computing to aid in the merging of insights across different areas of biological sciences.
- Prashant S. Emani
- , Jonathan Warrell
- & Aram W. Harrow
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Article |
A temporal decomposition method for identifying venous effects in task-based fMRI
Temporal decomposition through manifold fitting (TDM) is an analysis technique that decomposes blood oxygenation level dependent (BOLD) responses in task-based fMRI into different components that likely correspond to microvasculature- and macrovasculature-driven signals.
- Kendrick Kay
- , Keith W. Jamison
- & Kamil Uğurbil
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Article |
A virtual reality system to analyze neural activity and behavior in adult zebrafish
Complex behaviors and the underlying neural activity in adult zebrafish can be accessed through a virtual reality system in combination with two-photon microscopy.
- Kuo-Hua Huang
- , Peter Rupprecht
- & Rainer W. Friedrich
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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 animal pose estimation using deep neural networks
LEAP is a deep-learning-based approach for the analysis of animal pose. LEAP’s graphical user interface facilitates training of the deep network. The authors illustrate the method by analyzing Drosophila and mouse behavior.
- Talmo D. Pereira
- , Diego E. Aldarondo
- & Joshua W. Shaevitz
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Article |
fMRIPrep: a robust preprocessing pipeline for functional MRI
fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
- Oscar Esteban
- , Christopher J. Markiewicz
- & Krzysztof J. Gorgolewski
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Article |
Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function
Imaging of neuronal activity across the whole zebrafish brain in combination with online analysis allows for manipulating neuronal activity according to function. This approach is used to ablate or activate neurons in fictively swimming zebrafish larvae.
- Nikita Vladimirov
- , Chen Wang
- & Misha B. Ahrens
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Correspondence |
A community-developed open-source computational ecosystem for big neuro data
- Joshua T. Vogelstein
- , Eric Perlman
- & Randal Burns
Modeling locomotion from environment to neurons