Last modified by robing on 2022/03/25 09:55
From version 50.1
edited by debonisg
on 2020/04/24 12:58
Change comment: There is no comment for this version
To version 46.1
edited by robing
on 2020/04/24 12:42
Change comment: There is no comment for this version

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1 -XWiki.debonisg
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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87 87  
88 88  * (((
89 89  **Build the Python environment**
90 -In the wavescalephant git repository, there is an environment file ([[pipeline/envs/wavescalephant_env.yaml>>https://drive.ebrains.eu/f/efe2ecf0874d4402bb11/]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
84 +In the wavescalephant git repository, there is an environment file ([[pipeline/envs/wavescalephant_env.yml>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/envs/wavescalephant_env.yml]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
91 91  ##conda env create ~-~-file /envs/wavescalephant_env.yml##
92 92  
93 93  )))
94 94  * **Edit the settings**
95 -The settings file specifies the path to the output folder, where results are saved to. Open the template file //[[pipeline/settings_template.py>>https://drive.ebrains.eu/f/b6dbd9f15e4f4d97af17/]]//, set the ##output_path## to the desired path, and save it as //pipeline/settings.py//.
89 +The settings file specifies the path to the output folder, where results are saved to. Open the template file //[[pipeline/settings_template.py>>https://drive.ebrains.eu/lib/905d7321-a16b-4147-8cca-31d710d1f946/file/pipeline/settings_template.py]]//, set the ##output_path## to the desired path, and save it as //pipeline/settings.py//.
96 96  
97 97  * **Edit the config files**
98 98  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//.
99 99  //Links are view-only//
100 -** full pipeline:[[ README.md>>https://drive.ebrains.eu/f/ec474df6919a4089832e/]], config.yaml
101 -** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]], [[config.yaml>>https://drive.ebrains.eu/f/8de751f48d7d47edaec1/]]
102 -** stage02_processing: [[README.md>>https://drive.ebrains.eu/f/7f19d89913624425bf63/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468aa43c/]]
103 -** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/f/94d12860dde84bbab7b1/]], [[config.yaml>>https://drive.ebrains.eu/f/6dfb712d5fa24f4f9fcf/]]
104 -** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/d/9c53abd5eaf543b28615/]], [[config.yaml>>https://drive.ebrains.eu/f/9534e46c4fae41c78f17/]]
105 -** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/f/4d79f3e314474c22a781/]], [[config.yaml>>https://drive.ebrains.eu/f/1689dda03be04251b85f/]]
94 +** 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/]]
95 +** 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]]
96 +** 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]]
97 +** 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]]
98 +** 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]]
99 +** 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]]
106 106  
107 107  * **Enter a dataset**
108 108  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.
109 -For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]]//
103 +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/]]//
110 110  
111 111  * **Run the pipeline (-stages)**
112 112  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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118 118  
119 119  == References ==
120 120  
115 +* De Bonis, Giulia, et al. "Analysis pipeline for extracting features of cortical slow oscillations." //Frontiers in Systems Neuroscience// 13 (2019): 70.
116 +* Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.
121 121  
122 122  == License (to discuss) ==
123 123