ArticleFrontiers in neural circuits2020
Calcium Imaging and the Curse of Negativity.
Article in Frontiers in neural circuits, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Target-dependent routing of sensory information in the olfactory system.Communications biology · 2026Article
- Visual Threat Location Impacts Brain-Wide Visual Adaptation Networks.The Journal of comparative neurology · 2026Article
- Whole-brain cellular-resolution functional network properties of seizure susceptibility.bioRxiv : the preprint server for biology · 2026Article
- Deriving functional network topology frombioRxiv : the preprint server for biology · 2026Article
- Cellular multipoint adaptive technology for two-photon mesoscope.Neurophotonics · 2026Article
- A competitive disinhibitory network for robust optic flow processing in Drosophila.Nature neuroscience · 2025Article
- Hierarchical competing inhibition circuits govern motor stability in C. elegans.Nature communications · 2025Article
- Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis.PLoS computational biology · 2025Article
- Brain-Wide Impacts of Sedation on Spontaneous Activity and Auditory Processing in Larval Zebrafish.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Evidence for Auditory Stimulus-Specific Adaptation But Not Deviance Detection in Larval Zebrafish Brains.The Journal of comparative neurology · 2025Article
- The development of functional glutamatergic and GABAergic synaptic connections between vestibulo-ocular projection neurons and oculomotor motoneurons in the chicken embryo.Frontiers in neurology · 2025Article
- Article
- Nonnegative matrix factorization for analyzing state dependent neuronal network dynamics in calcium recordings.Scientific reports · 2024Article
- Functional networks of inhibitory neurons orchestrate synchrony in the hippocampus.PLoS biology · 2024Article
- Spontaneous Brain Activity Emerges from Pairwise Interactions in the Larval Zebrafish Brain.Physical review. X · 2024Article
- Mixed Representations of Sound and Action in the Auditory Midbrain.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- EVIDENCE FOR AUDITORY STIMULUS-SPECIFIC ADAPTATION BUT NOT DEVIANCE DETECTION IN LARVAL ZEBRAFISH BRAINS.bioRxiv : the preprint server for biology · 2024Article
- Stimulus encoding by specific inactivation of cortical neurons.Nature communications · 2024Article
- Amplitude- and frequency-dependent activation of layer II/III neurons by intracortical microstimulation.iScience · 2023Article
- Orbitofrontal cortex conveys stimulus and task information to the auditory cortex.Current biology : CB · 2023Article
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3 authors.
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Abstract
The imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, CaImAn, suite2p, and CellSort, finding that suite2p may be the best suited to large datasets. We also tested the spike inference algorithms included in CaImAn, suite2p, and Cellsort, as well as the dedicated inference algorithms MLspike and CASCADE, and found each to have limitations in dealing with inhibited neurons. Among these spike inference algorithms, FOOPSI, from CaImAn, performed the best on inhibited neurons, but even this algorithm inferred spurious spikes upon the return of the fluorescence signal to baseline. As such, new approaches will be needed before spikes can be sensitively and accurately inferred from calcium data in inhibited neurons. We further suggest avoiding data analysis approaches that, by assuming non-negativity, ignore inhibited responses. Instead, we suggest a first exploratory step, using k-means or PCA for example, to detect whether meaningful negative deviations are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
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