Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Survey of spiking in the mouse visual system reveals functional hierarchy

(2021) Joshua H. Siegle et al.   NATURE

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

(2021) Lawrence Huang et al.   eLife

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology

(2020) Ziqiang Wei et al.   PLoS Computational Biology

High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification

(2019) Xiaoxuan Jia et al.   JOURNAL OF NEUROPHYSIOLOGY

Volumetric Ca2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy

(2019) Siegfried Weisenburger et al.   CELL

Spontaneous behaviors drive multidimensional, brainwide activity

(2019) Carsen Stringer et al.   SCIENCE

High-dimensional geometry of population responses in visual cortex

(2019) Carsen Stringer et al.   NATURE

Kilohertz frame-rate two-photon tomography

(2019) Abbas Kazemipour et al.   NATURE METHODS

Kilohertz two-photon brain imaging in awake mice

(2019) Tong Zhang et al.   NATURE METHODS

A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

(2019) Saskia E. J. de Vries et al.   NATURE NEUROSCIENCE

In vivo imaging of neuronal calcium during electrode implantation: Spatial and temporal mapping of damage and recovery

(2018) James R. Eles et al.   BIOMATERIALS

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

(2018) Oliver Skocek et al.   NATURE METHODS

Community-based benchmarking improves spike rate inference from two-photon calcium imaging data

(2018) Philipp Berens et al.   PLoS Computational Biology

Robustness of Spike Deconvolution for Neuronal Calcium Imaging

(2018) Marius Pachitariu et al.   JOURNAL OF NEUROSCIENCE

Exact spike train inference via $\ell_{0}$ optimization

(2018) Sean Jewell et al.   Annals of Applied Statistics

Distinct descending motor cortex pathways and their roles in movement

(2018) Michael N. Economo et al.   NATURE

A Cell Atlas for the Mouse Brain

(2018) Csaba Erö et al.   Frontiers in Neuroinformatics

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

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

Fully integrated silicon probes for high-density recording of neural activity

(2017) James J. Jun et al.   NATURE

In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain

(2017) Dimitre G Ouzounov et al.   NATURE METHODS

Fast online deconvolution of calcium imaging data

(2017) Johannes Friedrich et al.   PLoS Computational Biology

A comparison of computational methods for detecting bursts in neuronal spike trains and their application to human stem cell-derived neuronal networks

(2016) Ellese Cotterill et al.   JOURNAL OF NEUROPHYSIOLOGY

Anatomy and function of an excitatory network in the visual cortex

(2016) Wei-Chung Allen Lee et al.   NATURE

Improving data quality in neuronal population recordings

(2016) Kenneth D Harris et al.   NATURE NEUROSCIENCE

Simultaneous Multi-plane Imaging of Neural Circuits

(2016) Weijian Yang et al.   NEURON

Benchmarking Spike Rate Inference in Population Calcium Imaging

(2016) Lucas Theis et al.   NEURON

Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo

(2016) Thomas Deneux et al.   Nature Communications

A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging

(2016) Nicholas James Sofroniew et al.   eLife

Arousal and Locomotion Make Distinct Contributions to Cortical Activity Patterns and Visual Encoding

(2015) Martin Vinck et al.   NEURON

Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance

(2015) Linda Madisen et al.   NEURON

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging

(2014) Nicolas Renier et al.   CELL

Topography and Areal Organization of Mouse Visual Cortex

(2014) M. E. Garrett et al.   JOURNAL OF NEUROSCIENCE

Orientation columns in the mouse superior colliculus

(2014) Evan H. Feinberg et al.   NATURE

Emergence of reproducible spatiotemporal activity during motor learning

(2014) Andrew J. Peters et al.   NATURE

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

Cortico-cortical projections in mouse visual cortex are functionally target specific

(2013) Lindsey L Glickfeld et al.   NATURE NEUROSCIENCE

Strain Background Influences Neurotoxicity and Behavioral Abnormalities in Mice Expressing the Tetracycline Transactivator

(2012) H. J. Han et al.   JOURNAL OF NEUROSCIENCE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Quality Metrics to Accompany Spike Sorting of Extracellular Signals

(2011) D. N. Hill et al.   JOURNAL OF NEUROSCIENCE

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

Functional specificity of local synaptic connections in neocortical networks

(2011) Ho Ko et al.   NATURE

Imaging Voltage in Neurons

(2011) Darcy S. Peterka et al.   NEURON

Molecular and Cellular Approaches for Diversifying and Extending Optogenetics

(2010) Viviana Gradinaru et al.   CELL

Fast Nonnegative Deconvolution for Spike Train Inference From Population Calcium Imaging

(2010) Joshua T. Vogelstein et al.   JOURNAL OF NEUROPHYSIOLOGY

Functional imaging of hippocampal place cells at cellular resolution during virtual navigation

(2010) Daniel A Dombeck et al.   NATURE NEUROSCIENCE

Modulation of Visual Responses by Behavioral State in Mouse Visual Cortex

(2010) Cristopher M. Niell et al.   NEURON

A self-adapting approach for the detection of bursts and network bursts in neuronal cultures

(2009) Valentina Pasquale et al.   JOURNAL OF COMPUTATIONAL NEUROSCIENCE

PINP: A New Method of Tagging Neuronal Populations for Identification during In Vivo Electrophysiological Recording

(2009) Susana Q. Lima et al.   PLoS One