Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience

L Paninski, JP Cunningham - Current opinion in neurobiology, 2018 - Elsevier
Highlights•Modern recording technologies are creating data at a scale and complexity that
demand rigorous data analytical approaches.•Neural data science is an essential bridge …

CaImAn an open source tool for scalable calcium imaging data analysis

A Giovannucci, J Friedrich, P Gunn, J Kalfon, BL Brown… - elife, 2019 - elifesciences.org
Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer
time resolution. The resulting data rates require reproducible analysis pipelines that are …

Fast online deconvolution of calcium imaging data

J Friedrich, P Zhou, L Paninski - PLoS computational biology, 2017 - journals.plos.org
Fluorescent calcium indicators are a popular means for observing the spiking activity of
large neuronal populations, but extracting the activity of each neuron from raw fluorescence …

Compartment-specific tuning of dendritic feature selectivity by intracellular Ca2+ release

JK O'Hare, KC Gonzalez, SA Herrlinger, Y Hirabayashi… - Science, 2022 - science.org
Dendritic calcium signaling is central to neural plasticity mechanisms that allow animals to
adapt to the environment. Intracellular calcium release (ICR) from the endoplasmic reticulum …

Sexual arousal gates visual processing during Drosophila courtship

T Hindmarsh Sten, R Li, A Otopalik, V Ruta - Nature, 2021 - nature.com
Long-lasting internal arousal states motivate and pattern ongoing behaviour, enabling the
temporary emergence of innate behavioural programs that serve the needs of an animal …

Stimulus encoding by specific inactivation of cortical neurons

J Pérez-Ortega, A Akrouh, R Yuste - Nature Communications, 2024 - nature.com
Neuronal ensembles are groups of neurons with correlated activity associated with sensory,
motor, and behavioral functions. To explore how ensembles encode information, we …

Long-term stability of cortical ensembles

J Pérez-Ortega, T Alejandre-García, R Yuste - Elife, 2021 - elifesciences.org
Neuronal ensembles, coactive groups of neurons found in spontaneous and evoked cortical
activity, are causally related to memories and perception, but it is still unknown how stable or …

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

P Berens, J Freeman, T Deneux… - PLoS computational …, 2018 - journals.plos.org
In recent years, two-photon calcium imaging has become a standard tool to probe the
function of neural circuits and to study computations in neuronal populations. However, the …

Fast nonconvex deconvolution of calcium imaging data

SW Jewell, TD Hocking, P Fearnhead, DM Witten - Biostatistics, 2020 - academic.oup.com
Calcium imaging data promises to transform the field of neuroscience by making it possible
to record from large populations of neurons simultaneously. However, determining the exact …

Multifocal fluorescence video-rate imaging of centimetre-wide arbitrarily shaped brain surfaces at micrometric resolution

H **e, X Han, G **ao, H Xu, Y Zhang, G Zhang… - Nature Biomedical …, 2024 - nature.com
Fluorescence microscopy allows for the high-throughput imaging of cellular activity across
brain areas in mammals. However, capturing rapid cellular dynamics across the curved …