EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data

CaImAn an open source tool for scalable calcium imaging data analysis

(2019) Andrea Giovannucci et al.   eLife

Reinforcement Learning Recruits Somata and Apical Dendrites across Layers of Primary Sensory Cortex

(2019) Clay O. Lacefield et al.   Cell Reports

Cell-type-Specific Patterned Stimulus-Independent Neuronal Activity in the Drosophila Visual System during Synapse Formation

(2019) Orkun Akin et al.   NEURON

Neuromodulatory control of localized dendritic spiking in critical period cortex

(2019) Courtney E. Yaeger et al.   NATURE

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

(2019) Ahmed S. Abdelfattah et al.   SCIENCE

A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

(2018) Pierre Yger et al.   eLife

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

(2018) Pengcheng Zhou et al.   eLife

In vivo measurement of afferent activity with axon-specific calcium imaging

(2018) Gerard Joey Broussard et al.   NATURE NEUROSCIENCE

Impaired perceptual learning in a mouse model of Fragile X syndrome is mediated by parvalbumin neuron dysfunction and is reversible

(2018) Anubhuti Goel et al.   NATURE NEUROSCIENCE

A Versatile Method for Viral Transfection of Calcium Indicators in the Neonatal Mouse Brain

(2018) Cynthia X. He et al.   Frontiers in Neural Circuits

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

(2018) Daniel Aharoni et al.   NATURE METHODS

An open source, wireless capable miniature microscope system

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

Tactile Defensiveness and Impaired Adaptation of Neuronal Activity in the Fmr1 Knock-Out Mouse Model of Autism

(2017) Cynthia X. He et al.   JOURNAL OF NEUROSCIENCE

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

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

In vivo imaging of neural activity

(2017) Weijian Yang et al.   NATURE METHODS

A Fully Automated Approach to Spike Sorting

(2017) Jason E. Chung et al.   NEURON

Enhanced Spatial Resolution During Locomotion and Heightened Attention in Mouse Primary Visual Cortex

(2016) Patrick J. Mineault et al.   JOURNAL OF NEUROSCIENCE

Genetically encoded indicators of neuronal activity

(2016) Michael Z Lin et al.   NATURE NEUROSCIENCE

New Transgenic Mouse Lines for Selectively Targeting Astrocytes and Studying Calcium Signals in Astrocyte Processes In Situ and In Vivo

(2016) Rahul Srinivasan et al.   NEURON

Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data

(2016) Eftychios A. Pnevmatikakis et al.   NEURON

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

(2016) Nicholas James Sofroniew et al.   eLife

Branch-specific dendritic Ca2+ spikes cause persistent synaptic plasticity

(2015) Joseph Cichon et al.   NATURE

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

(2014) Adam M Packer et al.   NATURE METHODS

Detecting cells using non-negative matrix factorization on calcium imaging data

(2014) Ryuichi Maruyama et al.   NEURAL NETWORKS

SIMA: Python software for analysis of dynamic fluorescence imaging data

(2014) Patrick Kaifosh et al.   Frontiers in Neuroinformatics

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

An optimized fluorescent probe for visualizing glutamate neurotransmission

(2013) Jonathan S Marvin et al.   NATURE METHODS

Imaging Calcium in Neurons

(2012) Christine Grienberger et al.   NEURON

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

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

Optical probing of neuronal ensemble activity

(2009) Benjamin F Grewe et al.   CURRENT OPINION IN NEUROBIOLOGY

Internally Mediated Developmental Desynchronization of Neocortical Network Activity

(2009) P. Golshani et al.   JOURNAL OF NEUROSCIENCE

Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window

(2009) Anthony Holtmaat et al.   Nature Protocols

Sparsification of neuronal activity in the visual cortex at eye-opening

(2009) N. L. Rochefort 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