Last modified by robing on 2022/03/25 09:55
From version 57.3
edited by debonisg
on 2020/04/27 11:50
Change comment: There is no comment for this version
To version 61.1
edited by robing
on 2020/04/28 10:01
Change comment: There is no comment for this version

Summary

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1 -XWiki.debonisg
1 +XWiki.robing
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23 23  
24 24  ,,4) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
25 25  
26 -,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="color:inherit" %)University of Florence, Florence, Italy(%%),,
26 +,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
27 27  
28 28  ,,6) Istituto di Neuroscienze, CNR, Pisa, Italy,,
29 29  
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44 44  
45 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 46  
47 -== How the Pipeline works ==
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.
50 50  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 and 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.
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120 120  
121 121  == References ==
122 122  
123 -* Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.
124 -* De Bonis, Giulia, et al. "Analysis pipeline for extracting features of cortical slow oscillations." //Frontiers in Systems Neuroscience// 13 (2019): 70.
123 +* [[Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.>>https://doi.org/10.3390/mps3010014]]
124 +* [[De Bonis, Giulia, et al. "Analysis pipeline for extracting features of cortical slow oscillations." //Frontiers in Systems Neuroscience// 13 (2019): 70.>>https://doi.org/10.3389/fnsys.2019.00070]]
125 +* [[Resta, F., Allegra Mascaro, A. L., & Pavone, F. (2020). "Study of Slow Waves (SWs) propagation through wide-field calcium imaging of the right cortical hemisphere of GCaMP6f mice" //EBRAINS//>>https://doi.org/10.25493/3E6Y-E8G]]// //
126 +* [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //Human Brain Project Neuroinformatics Platform//>>https://doi.org/10.25493/WKA8-Q4T]]
125 125  
126 126  == License (to discuss) ==
127 127