Last modified by robing on 2022/03/25 09:55
From version 32.1
edited by denker
on 2020/04/06 14:27
Change comment: Uploaded new attachment "logos_sga2_sp3_uc002.png", version {1}
To version 37.1
edited by robing
on 2020/04/17 10:34
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -SGA2 SP3 UC002 - Slow Wave Analysis Pipeline
1 +SGA2 SP3 UC002 KR3.2 - Slow Wave Analysis Pipeline
Author
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1 -XWiki.denker
1 +XWiki.robing
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= (% style="color:inherit" %)Slow Wave Analysis Pipeline(%%) =
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="color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002: Integrating multi-scale data in a reproducible and adaptable pipeline**
8 +(% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002: Integrating multi-scale data in a reproducible and adaptable pipeline**
9 9  
10 10  To be discussed Author orders, contributions,...:
11 11  
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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) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Cagliari, Italy,,
20 +,,2) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Roma, Italy,,
21 21  
22 22  
23 23  )))
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31 31  
32 32  This Collab is aimed at experimental and computational neuroscientists interested in the usage of the Neo and Elephant tools in performing data analysis of spiking data.
33 33  
34 -== Executing the pipeline ==
34 +== How the Pipeline works ==
35 35  
36 +The design of the pipeline aims at interfacing a variety of general and specific analysis and processing steps in a flexible modular manner. Hence, it enables the pipeline to adapt to diverse types of data (e.b. electrical EEG, or optical Calcium Imaging recordings) and to different analysis questions. This makes the analyses a) more reproducible and b) comparable amongst each other since they rely on the same stack of algorithms and any differences in the analysis are fully transparent.
37 +The individual processing and analysis steps (//blocks, //see// //the arrow-connected elements below) are organized in sequential //stages (//see the columns below//). //Following along the stages the analysis becomes more specific but also allows to branch off at after any stage as each stage yields useful intermediate results is autonomous so that it can be reused and recombined. Within each stage, there is a collection of blocks from which the user can select and arrange the analysis via a config file. Thus, the pipeline can be thought of as a curated database of methods on which an analysis can be constructed by drawing a path along the blocks and stages.
38 +
39 +(% class="wikigeneratedid" id="H" %)
36 36  [[image:pipeline_flowchart.png]]
37 37  
42 +== Executing the pipeline ==
43 +
38 38  === In the collab (beta) ===
39 39  
40 -* **Copy the collab drive to your drive space**
41 -** Open the Drive from the left menu
42 -** Select the folders 'pipeline' and 'datasets'
43 -** Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
46 +* (((
47 +**Copy the collab drive to your drive space**
48 +
49 +*
50 +
51 +Open the Drive from the left menu
52 +
53 +* Select the folders 'pipeline' and 'datasets'
54 +* Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
44 44  
56 +)))
45 45  * **Start a Jupyter Hub instance **
46 46  In another browser, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
47 47  
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99 99  
100 100  [[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
101 101  
114 +== ==
115 +
102 102  == Acknowledgments ==
103 103  
104 104  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).
119 +
120 +
121 +[[image:logos_sga2_sp3_uc002.png||alt="Logos SP3 Use Case 2"]]
105 105  )))
106 106  
107 107  
125 +== Executing the pipeline ==
126 +
108 108  (% class="col-xs-12 col-sm-4" %)
109 109  (((
110 110  {{box title="**Contents**"}}
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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1 -Space for developing and hosting a showcase pipeline for performing reproducible and adaptable analysis steps.
1 +Space for developing and hosting a showcase pipeline for performing reproducible and adaptable analysis with the focus of slow cortical waves.