Featured
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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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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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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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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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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 |
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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News & Views |
Deep learning reaches the motor system
A new article by Pandarinath et al. describes an artificial neural network model that captures some key aspects of the activity of populations of neurons in the primary motor cortex.
- Aaron P. Batista
- & James J. DiCarlo
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Article |
Inferring single-trial neural population dynamics using sequential auto-encoders
LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to these dynamics.
- Chethan Pandarinath
- , Daniel J. O’Shea
- & David Sussillo
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Brief Communication |
Optogenetic inhibition of behavior with anion channelrhodopsins
Anion channelrhodopsins are light-sensitive chloride channels that can be used as optogenetic inhibitors. Mohammad et al. report their application in Drosophila, showing that various behaviors can be inhibited in a light-dependent manner.
- Farhan Mohammad
- , James C Stewart
- & Adam Claridge-Chang
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Correspondence |
Light-sheet functional imaging in fictively behaving zebrafish
- Nikita Vladimirov
- , Yu Mu
- & Misha B Ahrens
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Article |
Chronic, wireless recordings of large-scale brain activity in freely moving rhesus monkeys
Movable volumetric three-dimensional multielectrode implants coupled to a modular headcap with wireless capabilities allow simultaneous recording of nearly 500 cortical neurons in freely behaving rhesus monkeys.
- David A Schwarz
- , Mikhail A Lebedev
- & Miguel A L Nicolelis
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Methods in Brief |
Clearing the way to spinal cord regeneration
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Brief Communication |
Embryonic stem cell–based mapping of developmental transcriptional programs
Presented is a study of gene regulation during development using a combination of chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) and directed differentiation of mouse embryonic stem cells inducibly expressing epitope-tagged transcription factors.
- Esteban O Mazzoni
- , Shaun Mahony
- & Hynek Wichterle
A large-scale neural network training framework for generalized estimation of single-trial population dynamics