Version 88.1 by jfioril1 on 2020/05/08 17:51
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denker 40.1 5 = Temporal Structure in Recorded Ensemble Activity =
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denker 76.1 7 **Contribution to Use Case SGA2-SP3-003: Pipeline for analyzing the temporal structure in recorded Ensemble Activity and related Systems Neuroscience data in association with behavior, cognitive processing and modeling**
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jurkusr 33.1 9 Experiments: Julien Fiorilli^^2^^
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jurkusr 33.1 11 Implementation: Regimantas Jurkus^^1^^, Julien Fiorilli^^2^^, Pietro Marchesi^^2^^, Thijs Ruikes^^2^^
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denker 75.1 13 Lead: Michael Denker^^1^^, Sonja Grün^^1,3^^, Cyriel Pennartz^^2^^
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15 ,,1) Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany,,
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17 ,,2) Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands,,
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19 ,,3) Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany,,
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denker 67.1 27 == Synopsis of this demonstration ==
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denker 77.1 29 This notebook, aimed at experimental and computational neuroscientists, demonstrates the principles of performing analysis of activity data on a complex dataset using the Neo and Elephant tools. We demonstrate the advantage of a common and shared data representation format for a challenging and complex electrophysiology dataset. Also, we showcase the first part of a pipeline for analysing for population-level data, including parallel spiking activity, paired with behavioural and cognitive state variables.
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denker 66.1 31 A detailed description is found in the interactive Jupyter notebook.
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denker 28.1 33 == Executing the analysis notebook ==
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35 * **Copy the collab drive to your drive space**
jfioril1 82.1 36 ** Open the Drive from the left menu
denker 29.1 37 ** Select "Demonstrator_Use_Case_SGA2-SP3-003.ipynb", the "Figures" folder, and the "Data" folder
38 ** Copy the selected items, and select the destination 'My Library' from the dropdown 'Other Libraries'
jfioril1 84.1 39 \\
denker 27.1 40 * **Start a Jupyter Hub instance **
41 In another browser, open [[https:~~/~~/lab.ebrains.eu>>url:https://lab.ebrains.eu]]
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43 * **Run the notebook**
denker 30.1 44 In the Jupyter Hub, navigate to `drive/My Libraries/My Library/Demonstrator_Use_Case_SGA2-SP3-003.ipynb`, and run the notebook.
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47 Users without an ebrains account can access the notebook by opening: [[https:~~/~~/drive.ebrains.eu/d/26ee91ed433049278d0e/>>url:https://drive.ebrains.eu/d/26ee91ed433049278d0e/]]
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jfioril1 46.1 49 == License ==
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jurkusr 63.1 51 All text and example data in this collab is licensed under under a [[Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License>>url:https://creativecommons.org/licenses/by-nc-nd/4.0/]]. Software code is licensed under [[a modified BSD license>>https://opensource.org/licenses/BSD-3-Clause]].
jfioril1 51.1 52 Please note that the data in this Collab is preliminary and might therefore still contain inaccuracies in specific event timestamps.
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jurkusr 62.1 54 [[image:88x31.png]]
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denker 65.1 57 == Acknowledgments ==
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denker 20.1 59 This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
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denker 44.1 62 [[image:logos_sga2_sp3_uc003.png||alt="Logos SP3 Use Case 3"]]
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68 {{box title="**Contents**"}}
69 {{toc/}}
70 {{/box}}
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