Last modified by robing on 2022/03/25 09:55
From version 67.1
edited by robing
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To version 72.1
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on 2020/05/07 14:22
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1 -XWiki.robing
1 +XWiki.denker
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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)
42 +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  
133 -== License (to discuss) ==
134 134  
135 -All text and example data in this collab is licensed under Creative Commons CC-BY 4.0 license. Software code is licensed under GNU General Public License v3.0.
131 +Code developed at:
136 136  
133 +[[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]]
134 +
135 +== License ==
136 +
137 +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.
138 +
137 137  [[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
138 138  
139 -== ==
141 +[[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  
143 +[[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"]]
144 +
145 +
141 141  == Acknowledgments ==
142 142  
143 143  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).
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152 152  (% class="col-xs-12 col-sm-4" %)
153 153  (((
154 154  {{box title="**Contents**"}}
155 -{{toc/}}
160 +{{toc depth="3"/}}
156 156  {{/box}}
157 157  
158 158  
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