Last modified by robing on 2022/03/25 09:55
From version 57.2
edited by pierstanpaolucci
on 2020/04/26 14:24
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To version 49.1
edited by robing
on 2020/04/24 12:53
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1 -XWiki.pierstanpaolucci
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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40 40  == Flexible workflows to generate multi-scale analysis scenarios ==
41 41  
42 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)
37 +Here, the collab illustrates the tool usage with regards to KR3.2, investigating sleep, anesthesia, and the transition to wakefulness.
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]]
39 +[[image:https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png||height="30" style="float:left" width="30"]]//[[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]]//
46 46  
47 47  == How the Pipeline works ==
48 48  
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99 99  * **Edit the config files**
100 100  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//.
101 101  //Links are view-only//
102 -** full pipeline: [[README.md>>https://drive.ebrains.eu/smart-link/d2e93a2a-09f6-4dce-982d-0370953a4da8/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/7948fbb3-bf8a-4785-9b28-d5c15a1aafa7/]]
103 -** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/smart-link/896f8880-a7d1-4a30-adbf-98759860fed5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/d429639d-b76e-4093-8fad-a25463d41edc/]]
104 -** stage02_processing: [[README.md>>https://drive.ebrains.eu/smart-link/01f21fa5-94f7-4883-8388-cc50957f9c81/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468ahttps://drive.ebrains.eu/smart-link/02a3f92c-dc7d-4b33-94f5-91b00db060d5/a43c/]]
105 -** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/smart-link/18d276cd-a691-4ee1-81c6-7978cef9c1b4/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/76adbb12-7cb4-42df-9fd5-735927ea3ba8/]]
106 -** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/smart-link/a8e80096-06a0-4ff4-b645-90e134e46ac5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/6b0b233f-30b7-4bbd-8564-1abebd27ea6d/]]
107 -** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/471001d5-33f5-488e-a9a4-f03b190e3da7/]]
96 +** full pipeline:[[ README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/README.md]], [[config.yaml>>https://drive.ebrains.eu/f/fd37c5dd8970444fa217/]]
97 +** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage01_data_entry/README.md]], [[config.yaml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage01_data_entry/config_template.yaml]]
98 +** stage02_processing: [[README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage02_processing/README.md]], [[config.yaml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage02_processing/config_template.yaml]]
99 +** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage03_trigger_detection/README.md]], [[config.yaml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage03_trigger_detection/config_template.yaml]]
100 +** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage04_wavefront_detection/README.md]], [[config.yaml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage04_wavefront_detection/config_template.yaml]]
101 +** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage05_wave_characterization/README.md]], [[config.yaml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage05_wave_characterization/config_template.yaml]]
108 108  
109 109  * **Enter a dataset**
110 110  There are two test datasets in the collab drive (IDIBAPS and LENS) for which there are also corresponding config files and scripts in the data_entry stage. So, these datasets are ready to be used and analyzed.
111 -For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/smart-link/d2e93a2a-09f6-4dce-982d-0370953a4da8/]]//
105 +For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/f/b46ffe259b3ahttps://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/stage01_data_entry/README.md4a51a277/]]//
112 112  
113 113  * **Run the pipeline (-stages)**
114 114  To run the pipeline with snakemake ([intro to snakemake]()) activate the Python environment ##conda activate wavescalephant_env,## make sure you are in the working directory `pipeline/`, and call ##snakemake## to run the entire pipeline.
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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.
124 124  * De Bonis, Giulia, et al. "Analysis pipeline for extracting features of cortical slow oscillations." //Frontiers in Systems Neuroscience// 13 (2019): 70.
118 +* Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.
125 125  
126 126  == License (to discuss) ==
127 127