ArticlePLoS computational biology2018
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
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- A mouse model for cerebral/cortical visual impairment (CVI) impairs vision and disrupts the spatial frequency tuning of neurons in visual cortex.Experimental neurology · 2026Article
- Enhancing Experience-Dependent Plasticity Accelerates Vision Loss in a Murine Model of Retinitis Pigmentosa.Investigative ophthalmology & visual science · 2026Article
- Voltage imaging as a window into neural computation.Neurophotonics · 2026Article
- Pre-existing and emergent cortical neuronal assembly sequences during learning.bioRxiv : the preprint server for biology · 2025Article
- A mouse model for cerebral/cortical visual impairment (CVI) impairs vision and disrupts the spatial frequency tuning of neurons in visual cortex.bioRxiv : the preprint server for biology · 2025Article
- Representational drift gates critical-period plasticity in mouse visual cortex.Current biology : CB · 2025Article
- Enhancing experience-dependent plasticity accelerates vision loss in a murine model of retinitis pigmentosa.bioRxiv : the preprint server for biology · 2025Article
- Predicting neuronal firing from calcium imaging using a control theoretic approach.PLoS computational biology · 2025Article
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- Machine learning in healthcare citizen science: A scoping review.International journal of medical informatics · 2025Article
- Compartmentalized dendritic plasticity in the mouse retrosplenial cortex links contextual memories formed close in time.Nature neuroscience · 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
- Contrast gain control is a reparameterization of a population response curve.Journal of neurophysiology · 2024Article
31 more citing papers are in PubMed but not listed here.
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29 authors.
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Abstract
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.
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