title: Benchmarking Spike Rate Inference in Population Calcium Imaging.
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.
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute of Theoretical Physics, University of Tübingen, 72076 Tübingen, Germany.
authors.forename: Lucas
authors.initials: L
authors.lastname: Theis
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute of Theoretical Physics, University of Tübingen, 72076 Tübingen, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany; Department of Neuroscience, Baylor College of Medicine, Houston, 77030, USA. Electronic address: philipp.berens@uni-tuebingen.de.
authors.forename: Philipp
authors.initials: P
authors.lastname: Berens
authors.affiliation: Department of Neuroscience, Baylor College of Medicine, Houston, 77030, USA.
authors.forename: Emmanouil
authors.initials: E
authors.lastname: Froudarakis
authors.affiliation: Department of Neuroscience, Baylor College of Medicine, Houston, 77030, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Reimer
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany.
authors.forename: Miroslav
authors.initials: M
authors.lastname: Román Rosón
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, 72076 Tübingen, Germany; School of Life Sciences, University of Sussex, Brighton, BN1 9RH, UK.
authors.forename: Tom
authors.initials: T
authors.lastname: Baden
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Euler
authors.affiliation: Bernstein Center for Computational Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Department of Neuroscience, Baylor College of Medicine, Houston, 77030, USA.
authors.forename: Andreas S
authors.initials: AS
authors.lastname: Tolias
authors.affiliation: Centre for Integrative Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Institute of Theoretical Physics, University of Tübingen, 72076 Tübingen, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, 72076 Tübingen, Germany; Max Planck Institute for Biological Cybernetics, 72076 Tübingen, Germany. Electronic address: matthias.bethge@uni-tuebingen.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Bethge
mesh_terms: D000200:Action Potentials / Q000502:physiology*; D000465:Algorithms; D000818:Animals; D002118:Calcium / Q000378:metabolism*; D008297:Male; D051379:Mice; D008959:Models, Neurological; D009474:Neurons / Q000502:physiology*; D012160:Retina / Q000502:physiology; D012815:Signal Processing, Computer-Assisted
chemical_list: D002118:Calcium