ArticlePLoS computational biology2017
An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed.
- Critical neuronal avalanches arise from excitation-inhibition balanced spontaneous activity.iScience · 2026Article
- LUMIN: an automated graphical analysis toolbox for high-throughput calcium imaging of in vitro neuronal cultures.Scientific reports · 2026Article
- Noise Sources and Strategies for Signal Quality Improvement in Biological Imaging: A Review Focused on Calcium and Cell Membrane Voltage Imaging.Biosensors · 2026Review
- Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism.Nature communications · 2025Article
- Topological analysis of neuronal assemblies reveals low-rank structure modulated by cholinergic activity.bioRxiv : the preprint server for biology · 2025Article
- CRISP: correlation-refined image segmentation process.BMC bioinformatics · 2025Article
- Using in vivo calcium imaging to examine joint neuron spontaneous activity and home cage analysis to monitor activity changes in mouse models of arthritis.Arthritis research & therapy · 2025Article
- Evaluating chemical effects on human neural cells through calcium imaging and deep learning.iScience · 2024Article
- Early and late place cells during postnatal development of the hippocampus.Nature communications · 2024Article
- Nonnegative matrix factorization for analyzing state dependent neuronal network dynamics in calcium recordings.Scientific reports · 2024Article
- Position-independent functional refinement within the vagus motor topographic map.Cell reports · 2024Article
- Ciliogenesis defects after neurulation impact brain development and neuronal activity in larval zebrafish.iScience · 2024Article
- Article
- Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings.bioRxiv : the preprint server for biology · 2024Article
- Position-independent functional refinement within the vagus motor topographic map.bioRxiv : the preprint server for biology · 2024Article
- In-Vivo Calcium Imaging of Sensory Neurons in the Rat Trigeminal Ganglion.Journal of visualized experiments : JoVE · 2024Article
- Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance.Nature communications · 2024Article
- Radial astrocyte synchronization modulates the visual system during behavioral-state transitions.Neuron · 2023Article
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7 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.
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