ArticleNature communications2016
Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed.
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- Precise calcium-to-spike inference using biophysical generative models.bioRxiv : the preprint server for biology · 2026Article
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- The Geometry of Layer 2/3 Cortical Sound Processing in Slow Wave Sleep.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dissecting neuronal circuit function and dysfunction in Alzheimer's disease mouse models: from conventional calcium imaging analysis to machine learning-based approaches.Frontiers in aging neuroscience · 2026Review
- Levodopa Disrupts Activity Patterns and Encoding of Movement in Striatal Cholinergic Interneurons of Behaving Mice.Movement disorders : official journal of the Movement Disorder Society · 2025Article
- Improved inference of latent neural states from calcium imaging data.bioRxiv : the preprint server for biology · 2025Article
- Exposure to COVID-19 virus-like particles modulates firing patterns of cortical neurons in the mouse brain.Communications biology · 2025Article
- The medial prefrontal cortex encodes procedural rules as sequential neuronal activity dynamics.Molecular brain · 2025Article
- Unraveling the neural code: analysis of large-scale two-photon microscopy data.Microscopy (Oxford, England) · 2025Review
- Predicting neuronal firing from calcium imaging using a control theoretic approach.PLoS computational biology · 2025Article
- Amplification of Olfactory Transduction Currents Implements Sparse Stimulus Encoding.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Precise calcium-to-spike inference using biophysical generative models.Research square · 2025Article
- Spike rate inference from mouse spinal cord calcium imaging data.bioRxiv : the preprint server for biology · 2025Article
- Discretized representations in V1 predict suboptimal orientation discrimination.Nature communications · 2025Article
75 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo.
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