Last modified by robing on 2022/03/25 09:55
From version 41.1
edited by denker
on 2020/04/21 15:26
Change comment: There is no comment for this version
To version 45.1
edited by robing
on 2020/04/24 12:34
Change comment: There is no comment for this version

Summary

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1 -XWiki.denker
1 +XWiki.robing
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7 7  (% class="wikigeneratedid" id="HUseCaseSGA2-SP3-002:IntegratingmultiscaledataA0inareproducibleandadaptablepipeline" %)
8 8  (% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002 KR3.2: Integrating multi-scale data in a reproducible and adaptable pipeline**
9 9  
10 -Experiments: ...?
10 +Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2^^, Cristiano Capone^^2^^,
11 11  
12 -Implementation: Robin Gutzen^^1^^, Elena Pastorelli^^2^^, ...
12 +Chiara De Luca^^2^^, Marco Celotto^^2^^, Michael Denker^^1^^, Sonja Grün^^1^^,
13 13  
14 -Lead: Michael Denker^^1^^, Sonja Grün^^1^^, Pier Stanislao Paolucci^^2^^, Andrew Davison?
14 +Pier Stanislao Paolucci^^2^^, Andrew Davison^^3^^
15 15  
16 +Experiments: Francesco Pavone^^4^^, Maria-Victoria Sanchez-Vives^^5^^
17 +
16 16  ,,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,,
17 17  
18 -,,2) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Roma, Italy,,
20 +,,2) INFN Sezione di Roma, Rome, Italy,,
19 19  
20 -
22 +,,3) Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS FRE 3693, Gif-sur-Yvette, France,,
23 +
24 +,,4) LENS, University of Florence, 50019 Florence, Italy,,
25 +
26 +,,5) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
21 21  )))
22 22  )))
23 23  
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85 85  * **Edit the config files**
86 86  Each stage has a config file to specify which analysis/processing blocks to execute and which parameters to use. Edit the config template files //pipeline/stageXX_<stage_name>/config_template.yaml// according to your dataset and analysis goal, and save them as //pipeline/stageXX_<stage_name>/config.yaml//. A detailed description of the available parameter settings and their meaning is commented in the template files, and a more general description of the working mechanism of each stage can be found in the respective README file //pipeline/stageXX_<stage_name>/README.md//.
87 87  //Links are view-only//
88 -** full pipeline:[[ README.md>>https://drive.ebrains.eu/f/ec474df6919a4089832e/]], config.yaml
94 +** full pipeline:[[ README.md>>https://drive.ebrains.eu/f/ec474df6919a4089832e/]], [[config.yaml>>https://drive.ebrains.eu/f/fd37c5dd8970444fa217/]]
89 89  ** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]], [[config.yaml>>https://drive.ebrains.eu/f/8de751f48d7d47edaec1/]]
90 90  ** stage02_processing: [[README.md>>https://drive.ebrains.eu/f/7f19d89913624425bf63/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468aa43c/]]
91 91  ** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/f/94d12860dde84bbab7b1/]], [[config.yaml>>https://drive.ebrains.eu/f/6dfb712d5fa24f4f9fcf/]]
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106 106  
107 107  == References ==
108 108  
115 +* De Bonis, Giulia, et al. "Analysis pipeline for extracting features of cortical slow oscillations." //Frontiers in Systems Neuroscience// 13 (2019): 70.
116 +* Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.
109 109  
110 110  == License (to discuss) ==
111 111