Biology subjects

Pnevmatikakis, E.

Publications and source records attributed to Pnevmatikakis, E..

4 recordsLinked to original sources

bioRxiv2021

improv: A flexible software platform for adaptive neuroscience experiments

Current neuroscience research is often limited to testing predetermined hypotheses and post hoc analysis of already collected data. Adaptive experimental designs, in which modeling drives ongoing data collection and selects experimental manipulations, offer a promising alternative. Still, tight integration between models and data collection requires coordinating diverse hardware configurations and complex computations under real-time constraints. Here, we introduce improv, a software platform that allows users to fully integrate custom modeling, analysis, and visualization with data collection and experimental control. We demonstrate both in silico and in vivo how improv enables more efficient experimental designs for discovery and validation across various model organisms and data types. Improv can orchestrate custom real-time behavioral analyses, rapid functional typing of neural responses from large populations via calcium microscopy, and optimal visual stimulus selection. We incorporate real-time machine learning methods for dimension reduction and predictive modeling of latent neural and behavioral features. Finally, we demonstrate how improv can perform model-driven interactive imaging and simultaneous optogenetic photostimulation of visually responsive neurons in the larval zebrafish brain expressing GCaMP6s and the red-shifted opsin rsChRmine. Together, these results demonstrate the power of improv to integrate modeling with data collection and experimental control to achieve next-generation adaptive experiments.

neuroscience↗

bioRxiv2019

Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila

Sensory pathways are typically studied by starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of activity towards the earliest layers of processing. Here, we present new methods for volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila and make comparisons across trials, individuals, and sexes. We discover that auditory activity is present in most central brain regions and in neurons known to carry responses to other modalities. Auditory responses are temporally diverse, but the majority of activity, regardless of brain region, is tuned to aspects of courtship song. We find that auditory responses are stereotyped across trials and animals in early mechanosensory regions, becoming more variable at higher layers of the putative pathway, and that this variability is largely independent of spontaneous movements. This study highlights the power of using an unbiased, brain-wide approach for mapping the functional organization of sensory activity.

neuroscience↗

bioRxiv2018

Emergence of stable sensory and dynamic temporal representations in the hippocampus during working memory

Hippocampal networks form maps of experience through spiking sequences that encode sensory cues, space or time. But whether distinct rules govern the emergence, stability and plasticity of externally driven and internally-generated representations remains unclear. Using two-photon calcium imaging, we recorded CA1 pyramidal populations across multiple days, while mice learned and performed an olfactory, delayed, working-memory task. We observed anatomically intermixed spiking sequences, comprised of odor-cells encoding olfactory cues, followed by time-cells encoding odor-specific delay time-points. Odor-cells were reliably activated across trials and retained stable fields over days and different delays. In contrast, time-cells exhibited sparse, unreliable activation and labile fields that remapped over days and extended delays. Moreover, the number of odor-cells remained stable, whereas time-cells increased over days during learning of the task, but not during passive exposure. Therefore, multi-modal representations with distinct learning-related dynamics and stability can co-exist in CA1, likely driven by different neurophysiological and plasticity mechanisms.

neuroscience↗

bioRxiv2018

Inhibitory and excitatory populations in parietal cortex are equally selective for decision outcome in both novices and experts

Inhibitory neurons, which play a critical role in decision-making models, are often simplified as a single pool of non-selective neurons lacking connection specificity. This assumption is supported by observations in primary visual cortex: inhibitory neurons are broadly tuned in vivo, and show non-specific connectivity in slice. Selectivity of excitatory and inhibitory neurons within decision circuits, and hence the validity of decision-making models, is unknown. We simultaneously measured excitatory and inhibitory neurons in posterior parietal cortex of mice judging multisensory stimuli. Surprisingly, excitatory and inhibitory neurons were equally selective for the animals choice, both at the single cell and population level. Further, both cell types exhibited similar changes in selectivity and temporal dynamics during learning, paralleling behavioral improvements. These observations, combined with modeling, argue against circuit architectures assuming non-selective inhibitory neurons. Instead, they argue for selective subnetworks of inhibitory and excitatory neurons that are shaped by experience to support expert decision-making.

neuroscience↗