ArticlePLoS computational biology2021
Tracking calcium dynamics from individual neurons in behaving animals.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Stars2Cells: Astrometric Tracking of Neurons Across Imaging Sessions.bioRxiv : the preprint server for biology · 2026Article
- Deep neural networks to register and annotate cells in moving and deforming nervous systems.eLife · 2026Article
- A Semi-Automatic Tool for the Standardized Analysis of Fluorescent Intensity Changes in Polarized Cells.International journal of molecular sciences · 2025Article
- A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging.Nature communications · 2025Article
- Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration.PLoS computational biology · 2024Article
- Automatic monitoring of neural activity with single-cell resolution in behaving Hydra.Scientific reports · 2024Article
- Automatic monitoring of whole-body neural activity in behavingbioRxiv : the preprint server for biology · 2023Article
- Effects of Nonthermal Radiofrequency Stimulation on Neuronal Activity and Neural Circuit in Mice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- A complete biomechanical model ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis.Journal of visualized experiments : JoVE · 2022Article
- Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans.PLoS computational biology · 2022Article
- Correcting motion induced fluorescence artifacts in two-channel neural imaging.PLoS computational biology · 2022Article
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- Antiocclusion Visual Tracking Algorithm Combining Fully Convolutional Siamese Network and Correlation Filtering.Computational intelligence and neuroscience · 2022Article
- High-Power Electromagnetic Pulse Exposure of Healthy Mice: Assessment of Effects on Mice Cognitions, Neuronal Activities, and Hippocampal Structures.Frontiers in cellular neuroscience · 2022Article
- Two-photon calcium imaging of neuronal activity.Nature reviews. Methods primers · 2022Article
- Translational neuronal ensembles: Neuronal microcircuits in psychology, physiology, pharmacology and pathology.Frontiers in systems neuroscience · 2022Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behaving Hydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. As a demonstration of the utility of the algorithm, we monitor for several days calcium activity of the same neurons in layer 2/3 of mouse visual cortex in vivo, finding significant turnover within the active neurons across days, with only few neurons that remained active across days. Also, combining automatic tracking of single neuron activity with statistical clustering, we characterize and map neuronal ensembles in behaving Hydra, finding three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results show that the EMC2 algorithm can be used as a robust and versatile platform for neuronal tracking in behaving animals.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.