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debonisg 50.1 5 = (% style="--darkreader-inline-color:inherit; color:inherit" %)Slow Wave Analysis Pipeline (SWAP)(%%) =
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debonisg 50.1 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**
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robing 85.1 10 Robin Gutzen^^1,4^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2,3^^, Cristiano Capone^^2^^,
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denker 73.1 12 Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1,4^^,
denker 25.1 13
denker 73.1 14 Pier Stanislao Paolucci^^2^^, Andrew Davison^^5^^
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denker 73.1 16 Experiments: Anna Letizia Allegra Mascaro^^6,7^^, Francesco Resta^^6^^, Francesco Saverio Pavone^^6^^, Maria-Victoria Sanchez-Vives^^8,9^^
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denker 25.1 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,,
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debonisg 50.1 20 ,,2) Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy,,
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debonisg 50.1 22 ,,3) Ph.D. Program in Behavioural Neuroscience, “Sapienza” University of Rome, Rome, Italy,,
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denker 73.1 24 ,,4) Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany,,
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denker 73.1 26 ,,5) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
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denker 73.1 28 ,,6) European Laboratory for Non-linear Spectroscopy (LENS), (% style="--darkreader-inline-color:inherit; color:inherit" %)University of Florence, Florence, Italy(%%),,
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denker 73.1 30 ,,7) Istituto di Neuroscienze, CNR, Pisa, Italy,,
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denker 73.1 32 ,,8) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
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34 ,,9) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
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denker 23.1 42 == Flexible workflows to generate multi-scale analysis scenarios ==
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denker 71.1 44 This collab illustrates the usage of the [[Neo>>https://neo.readthedocs.io/en/stable/]] and [[Elephant>>https://elephant.readthedocs.io/en/latest/]] tools in performing data analysis 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). For details on the datasets used in this collab, please see the References below.
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robing 84.1 46 [[See the introduction video>>https://www.youtube.com/watch?v=uuAiY6HScM0]]
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robing 61.1 48 == How the pipeline works ==
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robing 39.1 50 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.
debonisg 57.3 51 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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54 [[image:pipeline_flowchart.png]]
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robing 10.1 56 == Executing the pipeline ==
robing 6.1 57
debonisg 57.3 58 There are two ways of getting started and testing the pipeline, i) online using the collab drive and jupyter hub, or ii) downloading the code and data from GitHub and the collab storage and running it locally.
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robing 38.1 60 === i) In the collab ===
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robing 36.1 62 * (((
robing 38.1 63 **Copy the collab drive to your personal drive space**
robing 36.1 64
robing 38.1 65 * Open the Drive from the left menu
robing 40.1 66 * Select the folders //pipeline// and //datasets,//
denker 41.1 67 and the notebook// run_snakemake_in_collab.ipynb//
robing 36.1 68 * Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
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robing 36.1 70 )))
robing 19.1 71 * **Start a Jupyter Hub instance **
robing 38.1 72 In another browser tab, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
robing 40.1 73
robing 10.1 74 * **Edit the config files**
robing 64.1 75 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]]).
robing 10.1 76
robing 20.1 77 * **Run the notebook**
robing 82.1 78 In the jupyter hub, navigate to //drive/My Libraries/My Library/run_snakemake_in_collab.ipynb//, or where you copied the file to.
robing 80.1 79 Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
robing 10.1 80
robing 38.1 81 === ii) Local execution ===
robing 10.1 82
robing 80.1 83 //tested only with Mac OS and Linux!//
robing 75.1 84
robing 10.1 85 * **Get the code**
robing 64.1 86 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/]]).
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robing 38.1 88 * (((
89 **Build the Python environment**
robing 64.1 90 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]]).
91 ##conda env create ~-~-file environment.yaml
92 conda activate wavescalephant_env##
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94 Make sure that neo and elephant were installed as their Github development version, and if necessary add them manually to the environment.
95 ##pip install git+https:~/~/github.com/NeuralEnsemble/elephant.git
96 pip install git+https:~/~/github.com/NeuralEnsemble/python-neo.git##
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robing 38.1 98 )))
robing 10.1 99 * **Edit the settings**
robing 51.1 100 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//.
robing 10.1 101
102 * **Edit the config files**
robing 64.1 103 Each stage uses 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>/configs/config_template.yaml// according to your dataset and analysis goal, and save them as //pipeline/stageXX_<stage_name>/configs/config_<profile>.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//.
robing 38.1 104 //Links are view-only//
robing 52.1 105 ** 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/]]
robing 64.1 106 ** stage01_data_entry: [[README.md>>https://drive.ebrains.eu/smart-link/896f8880-a7d1-4a30-adbf-98759860fed5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/9bef8f59-1007-48c4-b5ba-30de4ff18f34/]]
107 ** stage02_processing: [[README.md>>https://drive.ebrains.eu/smart-link/01f21fa5-94f7-4883-8388-cc50957f9c81/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/7e75caf6-e2d6-4393-a97c-4f481c908cf8/]]
108 ** stage03_trigger_detection: [[README.md>>https://drive.ebrains.eu/smart-link/18d276cd-a691-4ee1-81c6-7978cef9c1b4/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/dfa375c0-cc80-4f95-b3ed-40140acbd96b/]]
109 ** stage04_wavefront_detection: [[README.md>>https://drive.ebrains.eu/smart-link/a8e80096-06a0-4ff4-b645-90e134e46ac5/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/3a54be8c-b9f4-4698-a85d-6ad97990b40a/]]
110 ** stage05_wave_characterization: [[README.md>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]], [[config.yaml>>https://drive.ebrains.eu/smart-link/83f68955-0ca8-4123-9734-6e93349ca3e3/]]
robing 10.1 111
112 * **Enter a dataset**
robing 38.1 113 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.
robing 52.1 114 For adding new datasets see //[[pipeline/stage01_data_entry/README.md>>https://drive.ebrains.eu/smart-link/d2e93a2a-09f6-4dce-982d-0370953a4da8/]]//
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116 * **Run the pipeline (-stages)**
robing 64.1 117 To run the pipeline with [[snakemake>>https://snakemake.readthedocs.io/en/stable/]]), 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.
118 For a more detailed executed guide and how to execute individual stages and blocks see the pipeline [[Readme>>https://drive.ebrains.eu/smart-link/3009a214-a11f-424c-8a6e-13e7506545eb/]].
robing 10.1 119
120 == Accessing and using the results ==
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robing 38.1 122 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.
robing 10.1 123
robing 74.1 124 **Examples of the output figures (for IDIBAPS dataset)**
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robing 74.1 126 * Stage 01 - [[example signal traces and metadata>>https://drive.ebrains.eu/smart-link/cf2fa914-260d-4d61-a2da-03ea07b7f9be/]]
127 * Stage 02 - [[background substraction>>https://drive.ebrains.eu/smart-link/586d2f3c-591b-4dfb-94ee-8c0e28050dc4/]]
128 * Stage 02 - [[logMUA estimation>>https://drive.ebrains.eu/smart-link/c92e4b0c-0938-44e8-9f8d-00522796b2fd/]]
129 * Stage 02 - [[processed signal trace>>https://drive.ebrains.eu/smart-link/26ed27c6-de56-4b48-a57b-f70aab629197/]]
130 * Stage 03 - [[amplitude distribution>>https://drive.ebrains.eu/smart-link/8ba80293-ba75-4a37-8a8f-05d44cf6f65c/]]
131 * Stage 03 - [[UP state detection>>https://drive.ebrains.eu/smart-link/ab172be0-178e-4153-a3e6-b4bace32dd50/]]
132 * Stage 04 - [[trigger clustering>>https://drive.ebrains.eu/smart-link/4a1f0169-8b43-49ce-80c8-f2fa0f4d50d3/]]
133 * Stage 05 - [[planar velocities>>https://drive.ebrains.eu/smart-link/f4de8073-cb40-47a7-bc82-f97d36dbae25/]]
134 * Stage 05 - [[directionality>>https://drive.ebrains.eu/smart-link/5485032d-0121-4cde-9ea2-3e0af3f12178/]]
135
robing 83.1 136 == Outlook ==
robing 74.1 137
robing 65.1 138 * 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.
139 * Adding support for the pipeline to make use of **HPC** resources when running on the collab.
140 * 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.
141 * Extending the **application** of the pipeline to the analysis of other types of activity waves and oscillations.
142 * Integrating and co-developing new features of the underlying **software tools **[[Elephant>>https://elephant.readthedocs.io/en/latest/]], [[Neo>>https://neo.readthedocs.io/en/stable/]], [[Nix>>https://github.com/G-Node/nix]], [[Snakemake>>https://snakemake.readthedocs.io/en/stable/]].
143
robing 10.1 144 == References ==
145
robing 59.1 146 * [[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]]
147 * [[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]]
148 * [[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]]// //
robing 62.1 149 * [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //EBRAINS//>>https://doi.org/10.25493/WKA8-Q4T]]
robing 63.1 150 * [[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]]
robing 10.1 151
denker 71.1 152 Code developed at:
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154 [[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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denker 70.1 156 == License ==
denker 22.1 157
denker 70.1 158 Text is licensed under the Creative Commons CC-BY 4.0 license. LENS data is licensed under the Creative Commons CC-BY-NC-ND 4.0 license. IDIBAPS data is licensed under the Creative Commons CC-BY-NC-SA 4.0 license. Software code is licensed under GNU General Public License v3.0.
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denker 29.1 160 [[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
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denker 71.1 162 [[image:https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
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denker 70.1 164 [[image:https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
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robing 10.1 167 == Acknowledgments ==
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denker 22.1 169 This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
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172 [[image:logos_sga2_sp3_uc002.png||alt="Logos SP3 Use Case 2"]]
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