CaImAn an open source tool for scalable calcium imaging data analysis

Analysis pipelines for calcium imaging data

(2019) Eftychios A Pnevmatikakis   CURRENT OPINION IN NEUROBIOLOGY

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

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

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

(2018) Pengcheng Zhou et al.   eLife

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

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

Tracking the Same Neurons across Multiple Days in Ca 2+ Imaging Data

(2017) Liron Sheintuch et al.   Cell Reports

Multi-scale approaches for high-speed imaging and analysis of large neural populations

(2017) Johannes Friedrich et al.   PLoS Computational Biology

Fast online deconvolution of calcium imaging data

(2017) Johannes Friedrich et al.   PLoS Computational Biology

The Serotonergic System Tracks the Outcomes of Actions to Mediate Short-Term Motor Learning

(2016) Takashi Kawashima et al.   CELL

Resolution of High-Frequency Mesoscale Intracortical Maps Using the Genetically Encoded Glutamate Sensor iGluSnFR

(2016) Y. Xie et al.   JOURNAL OF NEUROSCIENCE

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

(2016) Denise J. Cai et al.   NATURE

Benchmarking Spike Rate Inference in Population Calcium Imaging

(2016) Lucas Theis et al.   NEURON

Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data

(2016) Eftychios A. Pnevmatikakis 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

Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms

(2015) Matthew B. Bouchard et al.   Nature Photonics

Mapping brain activity at scale with cluster computing

(2014) Jeremy Freeman et al.   NATURE METHODS

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

(2014) Adam M Packer et al.   NATURE METHODS

Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy

(2014) Robert Prevedel et al.   NATURE METHODS

SIMA: Python software for analysis of dynamic fluorescence imaging data

(2014) Patrick Kaifosh et al.   Frontiers in Neuroinformatics

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

Whole-brain functional imaging at cellular resolution using light-sheet microscopy

(2013) Misha B Ahrens et al.   NATURE METHODS

Kernel density estimation via diffusion

(2010) Z. I. Botev et al.   ANNALS OF STATISTICS

Automatic Identification of Fluorescently Labeled Brain Cells for Rapid Functional Imaging

(2010) Ilya Valmianski et al.   JOURNAL OF NEUROPHYSIOLOGY

Fast Nonnegative Deconvolution for Spike Train Inference From Population Calcium Imaging

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

Parallel processing of visual space by neighboring neurons in mouse visual cortex

(2010) Spencer L Smith et al.   NATURE NEUROSCIENCE

In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons

(2010) Hongbo Jia et al.   Nature Protocols

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

(2009) Eran A. Mukamel et al.   NEURON

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

High-speed, miniaturized fluorescence microscopy in freely moving mice

(2008) Benjamin A Flusberg et al.   NATURE METHODS