Mikkel Elle Lepperød

• Lepperød, Mikkel Elle; Dragly, Svenn-Arne; Buccino, Alessio Paolo; Mobarhan, Milad; Malthe-Sørensen, Anders; Hafting, Torkel & Fyhn, Marianne (2020). Experimental Pipeline (Expipe): A Lightweight Data Management Platform to Simplify the Steps From Experiment to Data Analysis. Frontiers in Neuroinformatics.  ISSN 1662-5196. . doi: https://doi.org/10.3389/fninf.2020.00030 Vis sammendrag

  As experimental neuroscience is moving toward more integrative approaches, with a variety of acquisition techniques covering multiple spatiotemporal scales, data management is becoming increasingly challenging for neuroscience laboratories. Often, datasets are too large to practically be stored on a laptop or a workstation. The ability to query metadata collections without retrieving complete datasets is therefore critical to efficiently perform new analyses and explore the data. At the same time, new experimental paradigms lead to constantly changing specifications for the metadata to be stored. Despite this, there is currently a serious lack of agile software tools for data management in neuroscience laboratories. To meet this need, we have developed Expipe, a lightweight data management framework that simplifies the steps from experiment to data analysis. Expipe provides the functionality to store and organize experimental data and metadata for easy retrieval in exploration and analysis throughout the experimental pipeline. It is flexible in terms of defining the metadata to store and aims to solve the storage and retrieval challenges of data/metadata due to ever changing experimental pipelines. Due to its simplicity and lightweight design, we envision Expipe as an easy-to-use data management solution for experimental laboratories, that can improve provenance, reproducibility, and sharing of scientific projects.

• de Kamps, Marc; Lepperød, Mikkel Elle & Lai, Yi Ming (2019). Computational geometry for modeling neural populations: From visualization to simulation. PLoS Computational Biology.  ISSN 1553-734X.  15(3), s 1- 41 . doi: 10.1371/journal.pcbi.1006729 Fulltekst i vitenarkiv. Vis sammendrag

  The importance of a mesoscopic description level of the brain has now been well established. Rate based models are widely used, but have limitations. Recently, several extremely efficient population-level methods have been proposed that go beyond the characterization of a population in terms of a single variable. Here, we present a method for simulating neural populations based on two dimensional (2D) point spiking neuron models that defines the state of the population in terms of a density function over the neural state space. Our method differs in that we do not make the diffusion approximation, nor do we reduce the state space to a single dimension (1D). We do not hard code the neural model, but read in a grid describing its state space in the relevant simulation region. Novel models can be studied without even recompiling the code. The method is highly modular: variations of the deterministic neural dynamics and the stochastic process can be investigated independently. Currently, there is a trend to reduce complex high dimensional neuron models to 2D ones as they offer a rich dynamical repertoire that is not available in 1D, such as limit cycles. We will demonstrate that our method is ideally suited to investigate noise in such systems, replicating results obtained in the diffusion limit and generalizing them to a regime of large jumps. The joint probability density function is much more informative than 1D marginals, and we will argue that the study of 2D systems subject to noise is important complementary to 1D systems.

• Buccino, Alessio Paolo; Lepperød, Mikkel Elle; Dragly, Svenn-Arne; Häfliger, Philipp; Fyhn, Marianne & Hafting, Torkel (2018). Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai. Journal of Neural Engineering.  ISSN 1741-2560.  15, s 1- 12 . doi: 10.1088/1741-2552/aacf45 Fulltekst i vitenarkiv.
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel & Malthe-Sørenssen, Anders (2018). Experimental directory structure (Exdir): An alternative to HDF5 without introducing a new file format. Frontiers in Neuroinformatics.  ISSN 1662-5196.  12 . doi: 10.3389/fninf.2018.00016
• Aasebø, Ida E. J.; Lepperød, Mikkel Elle; Stavrinou, Maria; Nøkkevangen, Sandra; Einevoll, Gaute; Hafting, Torkel & Fyhn, Marianne (2017). Temporal processing in the visual cortex of the awake and anesthetized rat. eNeuro.  ISSN 2373-2822.  4:e0059-17.2017(4), s 1- 26 . doi: 10.1523/ENEURO.0059-17.2017 Fulltekst i vitenarkiv. Vis sammendrag

  The activity pattern and temporal dynamics within and between neuron ensembles are essential features of information processing and believed to be profoundly affected by anesthesia. Much of our general understanding of sensory information processing, including computational models aimed at mathematically simulating sensory information processing, rely on parameters derived from recordings conducted on animals under anesthesia. Due to the high variety of neuronal subtypes in the brain, population-based estimates of the impact of anesthesia may conceal unit- or ensemble-specific effects of the transition between states. Using chronically implanted tetrodes into primary visual cortex (V1) of rats, we conducted extracellular recordings of single units and followed the same cell ensembles in the awake and anesthetized states. We found that the transition from wakefulness to anesthesia involves unpredictable changes in temporal response characteristics. The latency of single-unit responses to visual stimulation was delayed in anesthesia, with large individual variations between units. Pair-wise correlations between units increased under anesthesia, indicating more synchronized activity. Further, the units within an ensemble show reproducible temporal activity patterns in response to visual stimuli that is changed between states, suggesting state-dependent sequences of activity. The current dataset, with recordings from the same neural ensembles across states, is well suited for validating and testing computational network models. This can lead to testable predictions, bring a deeper understanding of the experimental findings and improve models of neural information processing. Here, we exemplify such a workflow using a Brunel network model.

• Lensjø, Kristian Kinden; Lepperød, Mikkel Elle; Dick, Gunnar; Hafting, Torkel & Fyhn, Marianne (2017). Removal of perineuronal nets unlocks juvenile plasticity through network mechanisms of decreased inhibition and increased gamma Activity. Journal of Neuroscience.  ISSN 0270-6474.  37(5), s 1269- 1283 . doi: 10.1523/JNEUROSCI.2504-16.2016
• Tyvand, Peder A. & Lepperød, Mikkel Elle (2015). Doppler effects of an oscillating line source in shear flow with a free surface. Wave motion.  ISSN 0165-2125.  52, s 103- 119 . doi: 10.1016/j.wavemoti.2014.09.005
• Tyvand, Peder A. & Elle Lepperød, Bjørn Mikkel (2014). Oscillatory line source for water waves in shear flow. Wave motion.  ISSN 0165-2125.  51(3), s 505- 516 . doi: 10.1016/j.wavemoti.2013.12.001

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• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Stasik, Alexander Johannes; Fyhn, Marianne; Hafting, Torkel & Malthe-Sørenssen, Anders (2018). Exdir An alternative to HDF5 that uses Numpy files for data, YAML for metadata and simple directories to define the hierarchy.
• Christensen, Ane Charlotte; Lensjø, Kristian Kinden; Lepperød, Mikkel Elle; Fyhn, Marianne & Hafting, Torkel (2017). The role of extracellular matrix molecules for spatial representations in medial entorhinal cortex.
• Lepperød, Mikkel Elle; Lai, Yi Ming; Fyhn, Marianne; Einevoll, Gaute; Solstad, Trygve; Hafting, Torkel & de Kamps, Marc (2017). Population density model of the entorhinal stellate-cell network with adaptation.
• Lensjø, Kristian Kinden; Lepperød, Mikkel Elle; Dick, Gunnar; Hafting, Torkel & Fyhn, Marianne (2016). Removal of perineuronal nets affects information processing and plasticity in the primary visual cortex.
• Lepperød, Mikkel Elle; Wigestrand, Mattis B; Frey, M.M.; Lensjø, Kristian Kinden; Einevoll, Gaute; Solstad, Trygve; Fyhn, Marianne & Hafting, Torkel (2016). Role of input-specific perturbations of medial septal projections to the grid cell network.
• Lepperød, Mikkel Elle; Wigestrand, Mattis B; Frey, Mina Martine; Lensjø, Kristian Kinden; Einevoll, Gaute; Solstad, Trygve; Fyhn, Marianne & Hafting, Torkel (2016). On the role of input-specific perturbations of medial septal projections to the grid cell network.
• Lepperød, Mikkel Elle; Wigestrand, Mattis B; Lensjø, Kristian Kinden; Frey, M.M.; Dragly, Svenn-Arne; Einevoll, Gaute; Solstad, Trygve; Fyhn, Marianne & Hafting, Torkel (2016). Grid cell network resilient to input-specific medial septum perturbations.
• Tennøe, Simen; Halnes, Geir; Lepperød, Mikkel Elle; Feinberg, Jonathan; Einevoll, Gaute & Langtangen, Hans Petter (2016). UncertainPy: A Python toolbox for uncertainty quantification in neural and neural-network models..
• Wigestrand, Mattis B; Aasebø, Ida E. J.; Tully, Annabelle; Dinh, Vy To; Lepperød, Mikkel Elle; Hafting, Torkel & Fyhn, Marianne (2016). Lateral hypothalamic outputs control innate defensive responses.
• Wigestrand, Mattis B; Aasebø, Ida E. J.; Tully, Annabelle; Lepperød, Mikkel Elle; Hafting, Torkel & Fyhn, Marianne (2016). Lateral hypothalamic outputs control innate defensive responses. Vis sammendrag

  When facing a threat, animals display defensive behaviors that are critical for survival. The hypothalamus is believed to mediate such defensive responses, but the prevailing view includes a medial/lateral separation, where medial hypothalamus is thought to influence defensive responses, while the lateral hypothalamic area (LHA) regulates feeding and arousal. Here we identify two distinct neural populations in the LHA with surprising survival functions in rats. The two neural populations, defined by their output projections to either the periaqueductal gray (PAG) or the lateral habenula (LHb) have distinct anatomical placements along the anterior-posterior axis of the LHA and express distinct biochemical markers. Optogenetic stimulation of the two LHA populations robustly induced opposite active- or passive defensive responses. Further, chemogenetic silencing of LHA and optogenetic silencing of the LHA-PAG projection disrupted innate defensive responses to a predator-like looming shadow. Using single-unit recordings in the downstream LHb and PAG, we show that the LHA-LHb projection is largely excitatory, while the LHA-PAG projection is mainly inhibitory. We are currently using a miniaturized microscope to image the calcium activity of the two LHA populations during threat processing in behaving rats. Overall, our findings identify a novel LHA circuit that is critical for appropriate defensive responses to innate visual threats. The location of the LHA defense circuits, intermingled within circuitry that governs feeding, suggests that this circuit may provide rapid cross-talk between circuits that govern foraging- and anti-predator behaviors.

• Aasebø, Ida E. J.; Hafting, Torkel; Maria, Stavrinou; Sandra, Nøkkevangen; Lepperød, Bjørn Mikkel Elle & Fyhn, Marianne (2015). Temporal processing in the visual cortex in the awake and anesthetized rat.
• Christensen, Ane Charlotte; Lensjø, Kristian Kinden; Lepperød, Bjørn Mikkel Elle; Fyhn, Marianne & Hafting, Torkel (2015). The role of extracellular matrix molecules for spatial representations and plasticity in entorhinal cortex.
• Lensjø, Kristian Kinden; Lepperød, Bjørn Mikkel Elle; Dick, Gunnar; Hafting, Torkel & Fyhn, Marianne (2015). Removal of perineuronal nets in the visual cortex leads to a reduced inhibition and mimics critical period plasticity.
• Lepperød, Mikkel Elle; Lensjø, Kristian Kinden; Christensen, Ane Charlotte; Fyhn, Marianne; Hafting, Torkel & Einevoll, Gaute (2015). Building an entorhinal cortex network.

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