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1		-XWiki.moritzkern
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Content

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7	7	(% style="color:#4e5f70" %)Interactive video tutorials on
8	8	neuronal data analysis using Elephant
9	9
10		-
	10	+(% style="color:#e74c3c" %)**~-~- in beta  ~-~-**
11	11	)))
12	12	)))
13	13
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15	15	(((
16	16	(% class="col-xs-12 col-sm-8" %)
17	17	(((
18		-== Upcoming training events ==
19		-
20		-{{info}}
21		-
22		-
23		-
24		-
25		-{{/info}}
26		-
27	27	== A resource for kick-starting work with the Elephant library ==
28	28
29	29	The Python library [[Electrophysiology Analysis Toolkit (Elephant)>>https://python-elephant.org||rel="noopener noreferrer" target="_blank"]] provides tools for the analysis of neuronal activity data, such as spike trains, local field potentials and intracellular data. In addition to providing a platform for sharing analysis codes from different laboratories, Elephant provides a consistent and homogeneous framework for data analysis, built on a modular foundation. The underlying data model is the Neo library, a framework which easily captures a wide range of neuronal data types and methods, including dozens of file formats and network simulation tools. A common data description, as provided by the Neo library, is essential for developing interoperable analysis workflows.
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30	30
31	31	In this collaborative space, we provide hands on video tutorials based on Jupyter notebooks that showcase various types of data analysis, from simple to advanced. Most notebooks are based on a common dataset published at [[https:~~/~~/gin.g-node.org/INT/multielectrode_grasp>>https://gin.g-node.org/INT/multielectrode_grasp]] (for details cf. Brochier et al (2018) Scientific Data 5, 180055. [[https:~~/~~/doi.org/10.1038/sdata.2018.55>>url:https://doi.org/10.1038/sdata.2018.55]]). All video tutorials are approximately 30 minutes in length.
32	32
33		-In addition, tutorials presented at various workshops and schools are collected in this collab.
34	34
35		-
36	36	== Access to the tutorials ==
37	37
38	38	To access the tutorials, check out the drive space of this collab. The Jupyter notebooks are available in the (% style="color:#f39c12" %)notebooks(%%) folder, and links to the (% style="color:#f39c12" %)videos(%%) are embedded within each notebook. Notebooks can either be run directly on the EBRAINS Collaboratory's JupyterLab service (currently limited to HBP-affiliated members), or downloaded and run locally. For local execution, please use the provided (% style="color:#f39c12" %)requirements.txt(%%) file to generate an appropriate Python environment.
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66	66	Alessandra Stella|(% style="width:626px" %)Highlights two methods for detecting hidden spatio-temporal patterns in spike data.
67	67	|(% style="width:300px" %)GPFA|(% style="width:267px" %)Simon Essink|(% style="width:626px" %)Extract low-dimensional rate trajectories from the population spike activity.
68	68	|(% style="width:300px" %)Surrogate_techniques|(% style="width:267px" %)Peter Bouss|(% style="width:626px" %)Learn how to use different surrogate methods for spike trains to assist in formulating statistical null hypotheses in the presence of non-stationarity.
69		-|(% style="width:300px" %)NEST-Elephant|(% style="width:267px" %)(((
70		-Jessica Mitchell
71	71
72		-Moritz Kern
73		-)))|(% style="width:626px" %)Learn how to simulate a neural network with NEST, analyse data with Elephant and visualize results with Viziphant.
74		-
75		-== List of past events ==
76		-
77		-
78		-April 5, 2023 **Data Analysis using Elephant (Hybrid), SMHB General Assembly**
79		-Location: Forschungszentrum Juelich, Germany
80		-
81		-
82		-(((
83		-November 10, 2022** Simulate with EBRAINS (Online)**
84		-Agenda: [[https:~~/~~/flagship.kip.uni-heidelberg.d/jss/HBPm?m=showAgenda&meetingID=242>>https://flagship.kip.uni-heidelberg.de/jss/HBPm?m=showAgenda&meetingID=242]]
85		-
86		-
87		-July 1, 2022 **Satellite tutorial at the annual CNS meeting (Online)**
88		-Program: [[https:~~/~~/ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-cns-2022.html>>https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-cns-2022.html]]
89		-
90		-
91		-June 13-15, 2022 **BASSES workshop (Rome, Italy)**
92		-Program: [[https:~~/~~/www.humanbrainproject.eu/en/education/ebrains- workshops/basses/>>https://www.humanbrainproject.eu/en/education/ebrains-workshops/basses/]]
93		-
94		-
95	95
96	96	)))
97		-)))
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100	100	(((
101	101	{{box title="**Contents**"}}