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Hanson A, Reme R, Telerman N, Yamamoto W, Olivo-Marin JC, Lagache T, Yuste R. Automatic monitoring of neural activity with single-cell resolution in behaving Hydra. Sci Rep 2024; 14:5083. [PMID: 38429381 PMCID: PMC10907378 DOI: 10.1038/s41598-024-55608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/26/2024] [Indexed: 03/03/2024] Open
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.
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Affiliation(s)
- Alison Hanson
- Department of Biological Sciences, Neurotechnology Center, Columbia University, New York, NY, USA.
- Department of Psychiatry, New York State Psychiatric Institute, Columbia University, New York, NY, USA.
| | - Raphael Reme
- UMR3691, BioImage Analysis Unit, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Noah Telerman
- Department of Biological Sciences, Neurotechnology Center, Columbia University, New York, NY, USA
| | - Wataru Yamamoto
- Department of Biological Sciences, Neurotechnology Center, Columbia University, New York, NY, USA
| | | | - Thibault Lagache
- UMR3691, BioImage Analysis Unit, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Rafael Yuste
- Department of Biological Sciences, Neurotechnology Center, Columbia University, New York, NY, USA
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Hanson A, Reme R, Telerman N, Yamamoto W, Olivo-Marin JC, Lagache T, Yuste R. Automatic monitoring of whole-body neural activity in behaving Hydra. bioRxiv 2023:2023.09.22.559063. [PMID: 37790332 PMCID: PMC10542483 DOI: 10.1101/2023.09.22.559063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
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.
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Affiliation(s)
- Alison Hanson
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Psychiatry, New York State Psychiatric Institute, Columbia University, New York, NY, USA
| | - Raphael Reme
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, BioImage Analysis Unit, Paris, France
| | - Noah Telerman
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Wataru Yamamoto
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Thibault Lagache
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, BioImage Analysis Unit, Paris, France
| | - Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
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