Automatic monitoring of neural activity with single-cell resolution in behaving Hydra

Alison Hanson; Raphael Reme; Noah Telerman; Wataru Yamamoto; Jean-Christophe Olivo-Marin; Thibault Lagache; Rafael Yuste

doi:10.1038/s41598-024-55608-2

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Automatic monitoring of neural activity with single-cell resolution in behaving Hydra

Journal article

Peer reviewed

Automatic monitoring of neural activity with single-cell resolution in behaving Hydra

Alison Hanson, Raphael Reme, Noah Telerman, Wataru Yamamoto, Jean-Christophe Olivo-Marin, Thibault Lagache and Rafael Yuste

Scientific reports, Vol.14(1), pp.5083-5083

03/01/2024

DOI: 10.1038/s41598-024-55608-2

PMCID: PMC10907378

PMID: 38429381

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Abstract

The ability to record every spike from every neuron in a behaving animal is one of the holy grails of neuroscience. Here, we report coming one step closer towards this goal with the development of an end-to-end pipeline that automatically tracks and extracts calcium signals from individual neurons in the cnidarian Hydra vulgaris . We imaged dually labeled (nuclear tdTomato and cytoplasmic GCaMP7s) transgenic Hydra and developed an open-source Python platform (TraSE-IN) for the Tracking and Spike Estimation of Individual Neurons in the animal during behavior. The TraSE-IN platform comprises a series of modules that segments and tracks each nucleus over time and extracts the corresponding calcium activity in the GCaMP channel. Another series of signal processing modules allows robust prediction of individual spikes from each neuron’s calcium signal. This complete pipeline will facilitate the automatic generation and analysis of large-scale datasets of single-cell resolution neural activity in Hydra , and potentially other model organisms, paving the way towards deciphering the neural code of an entire animal.

Life Sciences

Details

Title: Subtitle: Automatic monitoring of neural activity with single-cell resolution in behaving Hydra
Creators: Alison Hanson - Columbia University
Raphael Reme - Analyse d'images biologiques - Biological Image Analysis
Noah Telerman - Columbia University
Wataru Yamamoto - Columbia University
Jean-Christophe Olivo-Marin - Analyse d'images biologiques - Biological Image Analysis
Thibault Lagache - Analyse d'images biologiques - Biological Image Analysis
Rafael Yuste - Columbia University
Resource Type: Journal article
Publication Details: Scientific reports, Vol.14(1), pp.5083-5083
DOI: 10.1038/s41598-024-55608-2
PMID: 38429381
PMCID: PMC10907378
NLM abbreviation: Sci Rep
ISSN: 2045-2322
eISSN: 2045-2322
Publisher: Nature Publishing Group
Language: English
Date published: 03/01/2024
Academic Unit: Psychiatry
Record Identifier: 9984823119902771

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