Kyle Lepage

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  Allen Brain Observatory: 2P Calcium Imaging Inference
  Kyle Lepage

  As a portion of the Allen Brain Observatory, a major initiative at the Allen Institute for Brain Science, head fixed adult mice are shown both artificial and natural visual stimuli while high-throughput 2- photon calcium imaging data are recorded from the mouse visual cortex, allowing assessment of stimulus processing across cortical layers, cortical areas, and Cre lines. In support of this effort, to assess the accuracy of statistical inference, cell-attached electrophysiological (ephys) data are collected simultaneously with two-photon calcium imaging (ophys). This latter experiment reveals, particularly when imaging at the lower magnification required to cover the mouse cortex, that a large number of spikes are not represented by the fluorescence signal, and conversely, an upward transient in the fluorescence signal does not always correspond with the occurrence of a neuron action potential. Despite considerable methodological effort, it remains a challenge to associate fluorescence signal with neural spiking. In this presentation, I will describe a a three-part approach to estimate neural receptive- fields and filters: (i) generalized linear models of spiking are estimated directly from fluorescence signal without direct knowledge of spike times, (ii) methods of estimation make explicit use of the calcium moments to facilitate (iii) the incorporation of calcium models derived from the joint ephys/ophys experiment.