ArticleNeuron2016
Benchmarking Spike Rate Inference in Population Calcium Imaging.
Article in Neuron, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed.
- Spike inference from calcium imaging data acquired with GCaMP8 indicators.Nature methods · 2026Article
- Evaluating linear model frameworks for directed predictive influence estimation from hypothalamic calcium imaging.Journal of neuroscience methods · 2026Article
- Precise calcium-to-spike inference using biophysical generative models.bioRxiv : the preprint server for biology · 2026Article
- Large-scale electrophysiology at single-spike resolution.Nature reviews. Neuroscience · 2026Review
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- Dynamic neuronal ensembles encode burst-suppression revealed by cortex-wide optical-electrical interfaces.Nature communications · 2026Article
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- Cerebellar climbing fibers impact experience-dependent plasticity in the mouse primary somatosensory cortex.eLife · 2025Article
- Cerebellar climbing fibers impact experience-dependent plasticity in the mouse primary somatosensory cortex.bioRxiv : the preprint server for biology · 2025Article
- Temporal coding carries more stable cortical visual representations than firing rate over time.Nature communications · 2025Article
- Predicting neuronal firing from calcium imaging using a control theoretic approach.PLoS computational biology · 2025Article
- Article
- Window into the Brain: In Vivo Multiphoton Imaging.ACS photonics · 2025Review
- Spike rate inference from mouse spinal cord calcium imaging data.bioRxiv : the preprint server for biology · 2025Article
- Multimodal Characterization of Cortical Neuron Response to Permanent Magnetic Field Induced Nanomagnetic Force Maps.ACS nano · 2024Article
- A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo.bioRxiv : the preprint server for biology · 2024Article
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- Automatic monitoring of neural activity with single-cell resolution in behaving Hydra.Scientific reports · 2024Article
- A Semi-supervised Pipeline for Accurate Neuron Segmentation with Fewer Ground Truth Labels.eNeuro · 2024Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
A fundamental challenge in calcium imaging has been to infer spike rates of neurons from the measured noisy fluorescence traces. We systematically evaluate different spike inference algorithms on a large benchmark dataset (>100,000 spikes) recorded from varying neural tissue (V1 and retina) using different calcium indicators (OGB-1 and GCaMP6). In addition, we introduce a new algorithm based on supervised learning in flexible probabilistic models and find that it performs better than other published techniques. Importantly, it outperforms other algorithms even when applied to entirely new datasets for which no simultaneously recorded data is available. Future data acquired in new experimental conditions can be used to further improve the spike prediction accuracy and generalization performance of the model. Finally, we show that comparing algorithms on artificial data is not informative about performance on real data, suggesting that benchmarking different methods with real-world datasets may greatly facilitate future algorithmic developments in neuroscience.
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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.