SGA2 SP3 UC003 - Temporal Structure in Recorded Ensemble Activity
Temporal Structure in Recorded Ensemble Activity
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
Experiments: Julien Fiorilli2
Implementation: Regimantas Jurkus1, Julien Fiorilli2, Pietro Marchesi2, Thijs Ruikes2
Lead: Michael Denker1, Sonja Grün1,3, Cyriel Pennartz2
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
2) Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
3) Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany
Synopsis of this demonstration
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.
A detailed description is found in the interactive Jupyter notebook.
Executing the analysis notebook
- Copy the collab drive to your drive space
- Open the Drive from the left menu
- Select "Demonstrator_Use_Case_SGA2-SP3-003.ipynb", the "Figures" folder, and the "Data" folder
- Copy the selected items, and select the destination 'My Library' from the dropdown 'Other Libraries'
- Start a Jupyter Hub instance
In another browser, open https://lab.ebrains.eu
- Run the notebook
In the Jupyter Hub, navigate to `drive/My Libraries/My Library/Demonstrator_Use_Case_SGA2-SP3-003.ipynb`, and run the notebook.
Users without an ebrains account can access the notebook by opening: https://drive.ebrains.eu/d/26ee91ed433049278d0e/
License
All text and example data in this collab is licensed under under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. Software code is licensed under a modified BSD license.
Please note that the data in this Collab is preliminary and might therefore still contain inaccuracies in specific event timestamps.
Acknowledgments
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).
