Journal
JOURNAL OF NEUROSCIENCE
Volume 38, Issue 37, Pages 7976-7985Publisher
SOC NEUROSCIENCE
DOI: 10.1523/JNEUROSCI.3339-17.2018
Keywords
calcium imaging; spike deconvolution; spike inference
Categories
Funding
- Wellcome Trust [95668, 95669, 108726]
- Simons Foundation [325512]
- Gatsby Foundation
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Calcium imaging is a powerful method to record the activity of neural populations in many species, but inferring spike times from calcium signals is a challenging problem. We compared multiple approaches using multiple datasets with ground truth electrophysiology and found that simple non-negative deconvolution (NND) outperformed all other algorithms on out-of-sample test data. We introduce a novel benchmark applicable to recordings without electrophysiological ground truth, based on the correlation of responses to two stimulus repeats, and used this to show that unconstrained NND also outperformed the other algorithms when run on zoomed out datasets of similar to 10,000 cell recordings from the visual cortex of mice of either sex. Finally, we show that NND-based methods match the performance of a supervised method based on convolutional neural networks while avoiding some of the biases of such methods, and at much faster running times. We therefore recommend that spikes be inferred from calcium traces using simple NND because of its simplicity, efficiency, and accuracy.
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