Last modified by robing on 2022/03/25 09:55
From version 50.1
edited by debonisg
on 2020/04/24 12:58
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

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1 -XWiki.debonisg
1 +XWiki.robing
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= (% style="--darkreader-inline-color:inherit; color:inherit" %)Slow Wave Analysis Pipeline (SWAP)(%%) =
5 += (% style="--darkreader-inline-color:inherit; color:inherit" %)Slow Wave Analysis Pipeline(%%) =
6 6  
7 7  (% class="wikigeneratedid" id="HUseCaseSGA2-SP3-002:IntegratingmultiscaledataA0inareproducibleandadaptablepipeline" %)
8 -(% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002 KR3.2: Integrating multi-scale data and the output of simulations in a reproducible and adaptable pipeline**
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 -Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2,3^^, Cristiano Capone^^2^^,
10 +Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2^^, Cristiano Capone^^2^^,
11 11  
12 -Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1^^,
12 +Chiara De Luca^^2^^, Marco Celotto^^2^^, Michael Denker^^1^^, Sonja Grün^^1^^,
13 13  
14 -Pier Stanislao Paolucci^^2^^, Andrew Davison^^4^^
14 +Pier Stanislao Paolucci^^2^^, Andrew Davison^^3^^
15 15  
16 -Experiments: Anna Letizia Allegra Mascaro^^5,6^^, Francesco Resta^^5^^, Francesco Saverio Pavone^^5^^, Maria-Victoria Sanchez-Vives^^7,8^^
16 +Experiments: Francesco Pavone^^4^^, Maria-Victoria Sanchez-Vives^^5^^
17 17  
18 18  ,,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,,
19 19  
20 -,,2) Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy,,
20 +,,2) INFN Sezione di Roma, Rome, Italy,,
21 21  
22 -,,3) Ph.D. Program in Behavioural Neuroscience, “Sapienza” University of Rome, Rome, Italy,,
22 +,,3) Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS FRE 3693, Gif-sur-Yvette, France,,
23 23  
24 -,,4) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
24 +,,4) LENS, University of Florence, 50019 Florence, Italy,,
25 25  
26 -,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="color:inherit" %)University of Florence, Florence, Italy(%%),,
27 -
28 -,,6) Istituto di Neuroscienze, CNR, Pisa, Italy,,
29 -
30 -,,7) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
31 -
32 -,,8) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
26 +,,5) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
33 33  )))
34 34  )))
35 35  
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97 97  * **Edit the config files**
98 98  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//.
99 99  //Links are view-only//
100 -** 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/]]
101 101  ** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]], [[config.yaml>>https://drive.ebrains.eu/f/8de751f48d7d47edaec1/]]
102 102  ** stage02_processing: [[README.md>>https://drive.ebrains.eu/f/7f19d89913624425bf63/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468aa43c/]]
103 103  ** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/f/94d12860dde84bbab7b1/]], [[config.yaml>>https://drive.ebrains.eu/f/6dfb712d5fa24f4f9fcf/]]
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118 118  
119 119  == References ==
120 120  
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.
121 121  
122 122  == License (to discuss) ==
123 123