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Related Experiment Video

Updated: Oct 17, 2025

Ratiometric Calcium Imaging of Individual Neurons in Behaving Caenorhabditis Elegans
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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
PubMed
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.

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Related Experiment Videos

Last Updated: Oct 17, 2025

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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.