UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Pachitariu, M; Stringer, C; Dipoppa, M; Schröder, S; Rossi, LF; Dalgleish, H; Carandini, M; (2017) Suite2p: beyond 10,000 neurons with standard two-photon microscopy. BioRxiv: Cold Spring Harbor, NY, USA. Green open access

[thumbnail of PachitariuStringerDipoppaSchroderRossiDalgleishCarandiniHarris_2017.pdf]
Preview
Text
PachitariuStringerDipoppaSchroderRossiDalgleishCarandiniHarris_2017.pdf - Published Version

Download (3MB) | Preview

Abstract

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.

Type: Working / discussion paper
Title: Suite2p: beyond 10,000 neurons with standard two-photon microscopy
Open access status: An open access version is available from UCL Discovery
DOI: 10.1101/061507
Publisher version: https://doi.org/10.1101/061507
Language: English
Additional information: The copyright holder for this preprint is the author/funder. It is made available under a CC-BY 4.0 International license (http://creativecommons.org/licenses/by/4.0/).
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > Institute of Ophthalmology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > The Sainsbury Wellcome Centre
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine > Wolfson Inst for Biomedical Research
URI: https://discovery.ucl.ac.uk/id/eprint/10049507
Downloads since deposit
1,350Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item