Last modified by robing on 2022/03/25 09:55
From version 70.1
edited by denker
on 2020/05/02 16:46
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To version 73.1
edited by denker
on 2020/05/08 15:19
Change comment: There is no comment for this version

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9 9  
10 10  Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2,3^^, Cristiano Capone^^2^^,
11 11  
12 -Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1^^,
12 +Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1,4^^,
13 13  
14 -Pier Stanislao Paolucci^^2^^, Andrew Davison^^4^^
14 +Pier Stanislao Paolucci^^2^^, Andrew Davison^^5^^
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: Anna Letizia Allegra Mascaro^^6,7^^, Francesco Resta^^6^^, Francesco Saverio Pavone^^6^^, Maria-Victoria Sanchez-Vives^^8,9^^
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  
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21 21  
22 22  ,,3) Ph.D. Program in Behavioural Neuroscience, “Sapienza” University of Rome, Rome, Italy,,
23 23  
24 -,,4) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
24 +,,4) Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany,,
25 25  
26 -,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
26 +,,5) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
27 27  
28 -,,6) Istituto di Neuroscienze, CNR, Pisa, Italy,,
28 +,,6) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
29 29  
30 -,,7) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
30 +,,7) Istituto di Neuroscienze, CNR, Pisa, Italy,,
31 31  
32 -,,8) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
32 +,,8) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
33 +
34 +,,9) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
33 33  )))
34 34  )))
35 35  
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39 39  (((
40 40  == Flexible workflows to generate multi-scale analysis scenarios ==
41 41  
42 -This Collab is aimed at experimental and computational neuroscientists interested in the usage of the [[Neo>>https://neo.readthedocs.io/en/stable/]] and [[Elephant>>https://elephant.readthedocs.io/en/latest/]] tools in performing data analysis of spiking data.
43 -Here, the collab illustrates the tool usage with regards to the SGA2-SP3-UC002 KR3.2, investigating sleep, anesthesia, and the transition to wakefulness: see Chapter 1 and Figure 2  of SGA2[[ Deliverable D3.2.1.>>https://drive.ebrains.eu/smart-link/17ac0d6e-e050-4a49-8ca2-e223b70a3121/]], for an overview of the scientific motivations and a description of the UseCase workflow; Chapter 2 (same document) for an introduction to KR3.2; Chapter 3, for a description of the mice ECoG data sets; Chapter 5, about the Slow Wave Analysis Pipeline and Chapter 6 for the mice wide-field GECI data)
44 +This collab illustrates the usage of the [[Neo>>https://neo.readthedocs.io/en/stable/]] and [[Elephant>>https://elephant.readthedocs.io/en/latest/]] tools in performing data analysis with regards to the SGA2-SP3-UC002 KR3.2, investigating sleep, anesthesia, and the transition to wakefulness: see Chapter 1 and Figure 2  of SGA2[[ Deliverable D3.2.1.>>https://drive.ebrains.eu/smart-link/17ac0d6e-e050-4a49-8ca2-e223b70a3121/]], for an overview of the scientific motivations and a description of the UseCase workflow; Chapter 2 (same document) for an introduction to KR3.2; Chapter 3, for a description of the mice ECoG data sets; Chapter 5, about the Slow Wave Analysis Pipeline and Chapter 6 for the mice wide-field GECI data). For details on the datasets used in this collab, please see the References below.
44 44  
45 -[[image:https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png||height="35" width="35"]][[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]]
46 -
47 47  == How the pipeline works ==
48 48  
49 49  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.g., electrical ECoG, 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.
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130 130  * [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //EBRAINS//>>https://doi.org/10.25493/WKA8-Q4T]]
131 131  * [[Sanchez-Vives, M. (2019). "Cortical activity features in transgenic mouse models of cognitive deficits (Fragile X Syndrome).//" EBRAINS//>>https://doi.org/10.25493/ANF9-EG3]]
132 132  
132 +Code developed at:
133 +
134 +[[image:https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png||height="35" width="35"]][[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]]
135 +
133 133  == License ==
134 134  
135 135  Text is licensed under the Creative Commons CC-BY 4.0 license. LENS data is licensed under the Creative Commons CC-BY-NC-ND 4.0 license. IDIBAPS data is licensed under the Creative Commons CC-BY-NC-SA 4.0 license. Software code is licensed under GNU General Public License v3.0.
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136 136  
137 137  [[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
138 138  
139 - [[image:https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
142 +[[image:https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
140 140  
141 141  [[image:https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
142 142  
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 with the focus of slow cortical waves.
1 +Use Case SGA2-SP3-002 KR3.2: Integrating multi-scale data and the output of simulations in a reproducible and adaptable pipeline