Circuit Investigations With Open-Source Miniaturized Microscopes: Past, Present and Future

Interacting neural ensembles in orbitofrontal cortex for social and feeding behaviour

(2019) Joshua H. Jennings et al.   NATURE

A miniature multi-contrast microscope for functional imaging in freely behaving animals

(2019) Janaka Senarathna et al.   Nature Communications

Comparative Evaluation of Genetically Encoded Voltage Indicators

(2019) Yuki Bando et al.   Cell Reports

Single-Neuron Level One-Photon Voltage Imaging With Sparsely Targeted Genetically Encoded Voltage Indicators

(2019) Peter Quicke et al.   Frontiers in Cellular Neuroscience

Three-Dimensional Representation of Motor Space in the Mouse Superior Colliculus

(2018) Jonathan J. Wilson et al.   CURRENT BIOLOGY

Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

(2018) Alessio Paolo Buccino et al.   Journal of Neural Engineering

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

(2018) Kiryl D. Piatkevich et al.   Nature Chemical Biology

High-speed volumetric imaging of neuronal activity in freely moving rodents

(2018) Oliver Skocek et al.   NATURE METHODS

A Hypothalamic Switch for REM and Non-REM Sleep

(2018) Kai-Siang Chen et al.   NEURON

Anxiety Cells in a Hippocampal-Hypothalamic Circuit

(2018) Jessica C. Jimenez et al.   NEURON

Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors

(2018) Tommaso Patriarchi et al.   SCIENCE

Three dimensional two-photon brain imaging in freely moving mice using a miniature fiber coupled microscope with active axial-scanning

(2018) Baris N. Ozbay et al.   Scientific Reports

MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline

(2018) Jinghao Lu et al.   Cell Reports

A theory of how active behavior stabilises neural activity: Neural gain modulation by closed-loop environmental feedback

(2018) Christopher L. Buckley et al.   PLoS Computational Biology

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

(2018) Pengcheng Zhou et al.   eLife

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

(2018) Alexander Mathis et al.   NATURE NEUROSCIENCE

Distinct and Dynamic ON and OFF Neural Ensembles in the Prefrontal Cortex Code Social Exploration

(2018) Bo Liang et al.   NEURON

Simultaneous Optogenetics and Cellular Resolution Calcium Imaging During Active Behavior Using a Miniaturized Microscope

(2018) Alice M. Stamatakis et al.   Frontiers in Neuroscience

Fast animal pose estimation using deep neural networks

(2018) Talmo D. Pereira et al.   NATURE METHODS

All the light that we can see: a new era in miniaturized microscopy

(2018) Daniel Aharoni et al.   NATURE METHODS

Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

(2018) Jonathan S. Marvin et al.   NATURE METHODS

Imaging Cortical Dynamics in GCaMP Transgenic Rats with a Head-Mounted Widefield Macroscope

(2018) Benjamin B. Scott et al.   NEURON

Three-dimensional direct laser written achromatic axicons and multi-component microlenses

(2018) Michael Schmid et al.   OPTICS LETTERS

Efficient cortical coding of 3D posture in freely behaving rats

(2018) Bartul Mimica et al.   SCIENCE

Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction

(2018) Akinori Mitani et al.   Frontiers in Neuroinformatics

An open source, wireless capable miniature microscope system

(2017) William A Liberti et al.   Journal of Neural Engineering

Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology

(2017) Joshua H Siegle et al.   Journal of Neural Engineering

Falcon: a highly flexible open-source software for closed-loop neuroscience

(2017) Davide Ciliberti et al.   Journal of Neural Engineering

Advances in closed-loop deep brain stimulation devices

(2017) Mahboubeh Parastarfeizabadi et al.   Journal of NeuroEngineering and Rehabilitation

NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data

(2017) Eftychios A. Pnevmatikakis et al.   JOURNAL OF NEUROSCIENCE METHODS

Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy

(2017) Tobias Nöbauer et al.   NATURE METHODS

Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice

(2017) Weijian Zong et al.   NATURE METHODS

Flexible Near-Field Wireless Optoelectronics as Subdermal Implants for Broad Applications in Optogenetics

(2017) Gunchul Shin et al.   NEURON

Bidirectional Control of Generalized Epilepsy Networks via Rapid Real-Time Switching of Firing Mode

(2017) Jordan M. Sorokin et al.   NEURON

Rapid Integration of Artificial Sensory Feedback during Operant Conditioning of Motor Cortex Neurons

(2017) Mario Prsa et al.   NEURON

The Spatiotemporal Organization of the Striatum Encodes Action Space

(2017) Andreas Klaus et al.   NEURON

Beam switching and bifocal zoom lensing using active plasmonic metasurfaces

(2017) Xinghui Yin et al.   Light-Science & Applications

Single-frame 3D fluorescence microscopy with ultraminiature lensless FlatScope

(2017) Jesse K. Adams et al.   Science Advances

Cell-Type-Specific Optical Recording of Membrane Voltage Dynamics in Freely Moving Mice

(2016) Jesse D. Marshall et al.   CELL

Virtual reality systems for rodents

(2016) Kay Thurley et al.   Current Zoology

A shared neural ensemble links distinct contextual memories encoded close in time

(2016) Denise J. Cai et al.   NATURE

Fast volumetric calcium imaging across multiple cortical layers using sculpted light

(2016) Robert Prevedel et al.   NATURE METHODS

Unstable neurons underlie a stable learned behavior

(2016) William A Liberti et al.   NATURE NEUROSCIENCE

Two-photon direct laser writing of ultracompact multi-lens objectives

(2016) Timo Gissibl et al.   Nature Photonics

Spatially Compact Neural Clusters in the Dorsal Striatum Encode Locomotion Relevant Information

(2016) Giovanni Barbera et al.   NEURON

Ultra-compact on-chip LED collimation optics by 3D femtosecond direct laser writing

(2016) Simon Thiele et al.   OPTICS LETTERS

A Markerless 3D Computerized Motion Capture System Incorporating a Skeleton Model for Monkeys

(2016) Tomoya Nakamura et al.   PLoS One

Ventral CA1 neurons store social memory

(2016) T. Okuyama et al.   SCIENCE

Virtual reality systems for rodents

(2016) Kay Thurley et al.   Current Zoology

Sensitive red protein calcium indicators for imaging neural activity

(2016) Hod Dana et al.   eLife

moco: Fast Motion Correction for Calcium Imaging

(2016) Alexander Dubbs et al.   Frontiers in Neuroinformatics

Gradient Index Microlens Implanted in Prefrontal Cortex of Mouse Does Not Affect Behavioral Test Performance over Time

(2016) Seon A. Lee et al.   PLoS One

Wireless inertial measurement of head kinematics in freely-moving rats

(2016) Matthieu O. Pasquet et al.   Scientific Reports

Soft, stretchable, fully implantable miniaturized optoelectronic systems for wireless optogenetics

(2015) Sung Il Park et al.   NATURE BIOTECHNOLOGY

Wirelessly powered, fully internal optogenetics for brain, spinal and peripheral circuits in mice

(2015) Kate L Montgomery et al.   NATURE METHODS

Mapping Sub-Second Structure in Mouse Behavior

(2015) Alexander B. Wiltschko et al.   NEURON

Minimally invasive microendoscopy system for in vivo functional imaging of deep nuclei in the mouse brain

(2015) Miriam E. Bocarsly et al.   Biomedical Optics Express

Mesoscopic Patterns of Neural Activity Support Songbird Cortical Sequences

(2015) Jeffrey E. Markowitz et al.   PLOS BIOLOGY

Bonsai: an event-based framework for processing and controlling data streams

(2015) Gonçalo Lopes et al.   Frontiers in Neuroinformatics

Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo

(2014) Adam M Packer et al.   NATURE METHODS

Volitional modulation of optically recorded calcium signals during neuroprosthetic learning

(2014) Kelly B Clancy et al.   NATURE NEUROSCIENCE

Big behavioral data: psychology, ethology and the foundations of neuroscience

(2014) Alex Gomez-Marin et al.   NATURE NEUROSCIENCE

Enhancing the performance of the light field microscope using wavefront coding

(2014) Noy Cohen et al.   OPTICS EXPRESS

Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons

(2014) Nicholas C. Flytzanis et al.   Nature Communications

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

A 3D-Video-Based Computerized Analysis of Social and Sexual Interactions in Rats

(2013) Jumpei Matsumoto et al.   PLoS One

Brain-wide neuronal dynamics during motor adaptation in zebrafish

(2012) Misha B. Ahrens et al.   NATURE

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

Investigating Neural Correlates of Behavior in Freely Behaving Rodents Using Inertial Sensors

(2010) Subramaniam Venkatraman et al.   JOURNAL OF NEUROPHYSIOLOGY

Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data

(2009) Eran A. Mukamel et al.   NEURON

Visually evoked activity in cortical cells imaged in freely moving animals

(2009) J. Sawinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated correction of fast motion artifacts for two-photon imaging of awake animals

(2008) David S. Greenberg et al.   JOURNAL OF NEUROSCIENCE METHODS

High-speed, miniaturized fluorescence microscopy in freely moving mice

(2008) Benjamin A Flusberg et al.   NATURE METHODS