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Updated: Oct 17, 2025
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Ratiometric Calcium Imaging of Individual Neurons in Behaving Caenorhabditis Elegans
Published on: February 7, 2018
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Tracking calcium dynamics from individual neurons in behaving animals
Thibault Lagache1,2, Alison Hanson1,2,3, Jesús E Pérez-Ortega1
1Department of Biological Sciences, Columbia University, New York, New York, United States of America.
Plos Computational Biology
|October 8, 2021
Summary
We developed an open-source algorithm, Elastic Motion Correction and Concatenation (EMC2), to track neurons in calcium imaging data. This tool overcomes challenges from animal movement and sensor detectability for robust neuronal activity monitoring.
Area of Science:
- Neuroscience
- Biophysics
- Computational Biology
Background:
- Calcium imaging enables single-cell resolution of neuronal activity in circuits.
- Animal movement and intermittent sensor signals complicate automated neuronal activity monitoring and functional analysis.
Purpose of the Study:
- To develop and implement an open-source algorithm for robust cellular tracking in calcium imaging data.
- To address challenges posed by animal motion and intermittent neuron detectability.
Main Methods:
- Developed the Elastic Motion Correction and Concatenation (EMC2) algorithm, integrating local deformation from detectable neurons.
- Applied EMC2 to two-photon microscopy data from mouse visual cortex and confocal microscopy data from behaving Hydra.
- Validated performance using manual tracking and synthetic data with varying motion and detectability parameters.
Main Results:
- EMC2 accurately tracks neurons across significant body deformations (Hydra) and long-term recordings (mice).
- Demonstrated significant daily turnover in active neurons in mouse visual cortex.
- Identified three distinct neuronal ensembles in Hydra (CB, RP1, RP2) correlated with body movements.
Conclusions:
- EMC2 provides a robust and versatile platform for neuronal tracking in behaving animals.
- The algorithm facilitates long-term monitoring and ensemble characterization of neuronal activity.
