Last modified by robing on 2022/03/25 09:55
From version 46.1
edited by robing
on 2020/04/24 12:42
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To version 40.1
edited by robing
on 2020/04/21 12:36
Change comment: There is no comment for this version

Summary

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5 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 in a reproducible and adaptable pipeline**
8 +(% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002: Integrating multi-scale data in a reproducible and adaptable pipeline**
9 9  
10 -Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2^^, Cristiano Capone^^2^^,
10 +To be discussed Author orders, contributions,...:
11 11  
12 -Chiara De Luca^^2^^, Marco Celotto^^2^^, Michael Denker^^1^^, Sonja Grün^^1^^,
12 +Experiments: ...?
13 13  
14 -Pier Stanislao Paolucci^^2^^, Andrew Davison^^3^^
14 +Implementation: Robin Gutzen^^1^^, Elena Pastorelli^^2^^, ...
15 15  
16 -Experiments: Francesco Pavone^^4^^, Maria-Victoria Sanchez-Vives^^5^^
16 +Lead: Michael Denker^^1^^, Sonja Grün^^1^^, Pier Stanislao Paolucci^^2^^, Andrew Davison?
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) INFN Sezione di Roma, Rome, Italy,,
20 +,,2) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Roma, Italy,,
21 21  
22 -,,3) Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS FRE 3693, Gif-sur-Yvette, France,,
23 -
24 -,,4) LENS, University of Florence, 50019 Florence, Italy,,
25 -
26 -,,5) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
22 +
27 27  )))
28 28  )))
29 29  
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55 55  
56 56  * Open the Drive from the left menu
57 57  * Select the folders //pipeline// and //datasets,//
58 -and the notebook// run_snakemake_in_collab.ipynb//
54 +and the notebook// run_snakemake_in_collab.ipynb//
59 59  * Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
60 60  
61 61  )))
... ... @@ -81,26 +81,26 @@
81 81  
82 82  * (((
83 83  **Build the Python environment**
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]]).
80 +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]]).
85 85  ##conda env create ~-~-file /envs/wavescalephant_env.yml##
86 86  
87 87  )))
88 88  * **Edit the settings**
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//.
85 +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//.
90 90  
91 91  * **Edit the config files**
92 92  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//.
93 93  //Links are view-only//
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]]
90 +** full pipeline:[[ README.md>>https://drive.ebrains.eu/f/ec474df6919a4089832e/]], config.yaml
91 +** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]], [[config.yaml>>https://drive.ebrains.eu/f/8de751f48d7d47edaec1/]]
92 +** stage02_processing: [[README.md>>https://drive.ebrains.eu/f/7f19d89913624425bf63/]], [[config.yaml>>https://drive.ebrains.eu/f/b1607671f6f2468aa43c/]]
93 +** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/f/94d12860dde84bbab7b1/]], [[config.yaml>>https://drive.ebrains.eu/f/6dfb712d5fa24f4f9fcf/]]
94 +** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/d/9c53abd5eaf543b28615/]], [[config.yaml>>https://drive.ebrains.eu/f/9534e46c4fae41c78f17/]]
95 +** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/f/4d79f3e314474c22a781/]], [[config.yaml>>https://drive.ebrains.eu/f/1689dda03be04251b85f/]]
100 100  
101 101  * **Enter a dataset**
102 102  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.
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/]]//
99 +For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/f/b46ffe259b3a4a51a277/]]//
104 104  
105 105  * **Run the pipeline (-stages)**
106 106  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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112 112  
113 113  == References ==
114 114  
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.
117 117  
118 118  == License (to discuss) ==
119 119