ArticlePLoS computational biology2017
Fast online deconvolution of calcium imaging data.
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 331 papers.
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Who cites it
331 citing papers in PubMed.
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- Overlapping representations in the ventral hippocampus support rapid fear memory retrieval.Nature neuroscience · 2026Article
- Learning induces activation-mechanism-dependent neural plasticity in an intracortical microstimulation task.Science advances · 2026Article
- A cortical output channel for perceptual categorization.Science advances · 2026Article
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- Graph theory identifies altered prefrontal microcircuit organization in Shank3 mice, a mouse Model of autism.Cell reports · 2026Article
- Crosstalk-free optical indicator-actuator combinations for bidirectional optogenetics.npj biomedical innovations · 2026Review
- Inferring brain-wide interactions using data-constrained recurrent neural network models.Neuron · 2026Article
- Spike inference from calcium imaging data acquired with GCaMP8 indicators.Nature methods · 2026Article
- Parvalbumin interneurons contribute to spontaneous hemodynamic fluctuations.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Article
- NMDA receptor-dependent Hebbian plasticity refines hippocampal spatial representations during two-dimensional navigation learning.bioRxiv : the preprint server for biology · 2026Article
- Midazolam Exerts Sedative Effects by Differentially Modulating Cortical Pyramidal Neurons and PV Interneurons.CNS neuroscience & therapeutics · 2026Article
- Noise-invariant representations of sound emerge along the canonical cortical hierarchy.PLoS biology · 2026Article
- Article
- Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish.Science advances · 2026Article
- Adaptive reorganization of history encoding in the retrosplenial cortex supports flexible decision-making strategies.Neuron · 2026Article
- Precise calcium-to-spike inference using biophysical generative models.bioRxiv : the preprint server for biology · 2026Article
271 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting the activity of each neuron from raw fluorescence calcium imaging data is a nontrivial problem. We present a fast online active set method to solve this sparse non-negative deconvolution problem. Importantly, the algorithm 3progresses through each time series sequentially from beginning to end, thus enabling real-time online estimation of neural activity during the imaging session. Our algorithm is a generalization of the pool adjacent violators algorithm (PAVA) for isotonic regression and inherits its linear-time computational complexity. We gain remarkable increases in processing speed: more than one order of magnitude compared to currently employed state of the art convex solvers relying on interior point methods. Unlike these approaches, our method can exploit warm starts; therefore optimizing model hyperparameters only requires a handful of passes through the data. A minor modification can further improve the quality of activity inference by imposing a constraint on the minimum spike size. The algorithm enables real-time simultaneous deconvolution of O(105) traces of whole-brain larval zebrafish imaging data on a laptop.
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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.