Last modified by robing on 2022/03/25 09:55
From version 72.1
edited by denker
on 2020/05/07 14:22
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To version 82.1
edited by robing
on 2020/05/28 15:45
Change comment: There is no comment for this version

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1 -XWiki.denker
1 +XWiki.robing
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9 9  
10 10  Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2,3^^, Cristiano Capone^^2^^,
11 11  
12 -Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1^^,
12 +Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1,4^^,
13 13  
14 -Pier Stanislao Paolucci^^2^^, Andrew Davison^^4^^
14 +Pier Stanislao Paolucci^^2^^, Andrew Davison^^5^^
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: Anna Letizia Allegra Mascaro^^6,7^^, Francesco Resta^^6^^, Francesco Saverio Pavone^^6^^, Maria-Victoria Sanchez-Vives^^8,9^^
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  
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21 21  
22 22  ,,3) Ph.D. Program in Behavioural Neuroscience, “Sapienza” University of Rome, Rome, Italy,,
23 23  
24 -,,4) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
24 +,,4) Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany,,
25 25  
26 -,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
26 +,,5) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
27 27  
28 -,,6) Istituto di Neuroscienze, CNR, Pisa, Italy,,
28 +,,6) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
29 29  
30 -,,7) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
30 +,,7) Istituto di Neuroscienze, CNR, Pisa, Italy,,
31 31  
32 -,,8) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
32 +,,8) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
33 +
34 +,,9) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
33 33  )))
34 34  )))
35 35  
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71 71  Each stage has config files (//pipeline/<stage_name>/configs/config_<profile>.yaml//) to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can be found in the README and config files of each stage. There are preset configuration profiles for the benchmark datasets IDIBAPS ([[ECoG, anesthetized mouse>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]) and LENS ([[Calcium Imaging, anesthetized mouse>>https://kg.ebrains.eu/search/instances/Dataset/71285966-8381-48f7-bd4d-f7a66afa9d79]]).
72 72  
73 73  * **Run the notebook**
74 -In the jupyter hub, navigate to //drive/My Libraries/My Library/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb//, or where you copied the //pipeline// folder to.
75 -Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake
76 +In the jupyter hub, navigate to //drive/My Libraries/My Library/run_snakemake_in_collab.ipynb//, or where you copied the file to.
77 +Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
76 76  
77 77  === ii) Local execution ===
78 78  
81 +//tested only with Mac OS and Linux!//
82 +
79 79  * **Get the code**
80 80  The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to get started with Github>>https://guides.github.com/activities/hello-world/]]).
81 81  
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84 84  In the wavescalephant git repository, there is an environment file ([[pipeline/environment.yaml>>https://drive.ebrains.eu/smart-link/1a0b15bb-be87-46ee-b838-4734bc320d20/]]) 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 environment.yaml
86 86  conda activate wavescalephant_env##
91 +
92 +Make sure that neo and elephant were installed as their Github development version, and if necessary add them manually to the environment.
93 +##pip install git+https:~/~/github.com/NeuralEnsemble/elephant.git
94 +pip install git+https:~/~/github.com/NeuralEnsemble/python-neo.git##
87 87  
88 88  )))
89 89  * **Edit the settings**
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111 111  
112 112  All results are stored in the path specified in the //settings.py// file. The folder structure reflects the structuring of the pipeline into stages and blocks. All intermediate results are stored as //.nix// files using the [[Neo data format>>https://neo.readthedocs.io/en/stable/]] and can be loaded with ##neo.NixIO('/path/to/file.nix').read_block()##. Additionally, most blocks produce a figure, and each stage a report file, to give an overview of the execution log, parameters, intermediate results, and to help with debugging. The final stage (//stage05_wave_characterization//) stores the results as[[ //pandas.DataFrames//>>https://pandas.pydata.org/]] in //.csv// files, separately for each measure as well as in a combined dataframe for all measures.
113 113  
114 -== Outlook ==
122 +**Examples of the output figures (for IDIBAPS dataset)**
115 115  
124 +* Stage 01 - [[example signal traces and metadata>>https://drive.ebrains.eu/smart-link/cf2fa914-260d-4d61-a2da-03ea07b7f9be/]]
125 +* Stage 02 - [[background substraction>>https://drive.ebrains.eu/smart-link/586d2f3c-591b-4dfb-94ee-8c0e28050dc4/]]
126 +* Stage 02 - [[logMUA estimation>>https://drive.ebrains.eu/smart-link/c92e4b0c-0938-44e8-9f8d-00522796b2fd/]]
127 +* Stage 02 - [[processed signal trace>>https://drive.ebrains.eu/smart-link/26ed27c6-de56-4b48-a57b-f70aab629197/]]
128 +* Stage 03 - [[amplitude distribution>>https://drive.ebrains.eu/smart-link/8ba80293-ba75-4a37-8a8f-05d44cf6f65c/]]
129 +* Stage 03 - [[UP state detection>>https://drive.ebrains.eu/smart-link/ab172be0-178e-4153-a3e6-b4bace32dd50/]]
130 +* Stage 04 - [[trigger clustering>>https://drive.ebrains.eu/smart-link/4a1f0169-8b43-49ce-80c8-f2fa0f4d50d3/]]
131 +* Stage 05 - [[planar velocities>>https://drive.ebrains.eu/smart-link/f4de8073-cb40-47a7-bc82-f97d36dbae25/]]
132 +* Stage 05 - [[directionality>>https://drive.ebrains.eu/smart-link/5485032d-0121-4cde-9ea2-3e0af3f12178/]]
133 +
134 +=== Outlook ===
135 +
116 116  * Using the **KnowledgeGraph API **to insert data directly from the Knowledge Graph into the pipeline and also register and store the corresponding results as Analysis Objects. Such Analysis Objects are to incorporate **Provenance Tracking, **using [[fairgraph>>https://github.com/HumanBrainProject/fairgraph]],** **to record the details of the processing and analysis steps.
117 117  * Adding support for the pipeline to make use of **HPC** resources when running on the collab.
118 118  * Further extending the available **methods** to address a wider variety of analysis objectives and support the processing of other datatypes. Additional documentation and guides should also make it easier for non-developers to contribute new method blocks.
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127 127  * [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //EBRAINS//>>https://doi.org/10.25493/WKA8-Q4T]]
128 128  * [[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]]
129 129  
130 -
131 131  Code developed at:
132 132  
133 133  [[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]]
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