Changes for page Data Curation

Last modified by abonard on 2025/06/03 10:55

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edited by ingrreit
on 2023/07/04 15:46

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edited by abonard
on 2025/05/22 15:11

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- EBRAINS-Share-Software-4.pdf
- EBRAINS-Share-Software.pdf
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- Collaboratory.Apps.Collab.Code.CollabClass[0]

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Title

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--test-ir2
++Data Curation

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--CollabClass
++Collabs.WebHome

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--XWiki.ingrreit
++XWiki.abonard

Content

@@ -29,7 +29,7 @@
  == **Information to get started** ==
--**[[REQUEST CURATION>>https://nettskjema.no/a/277393#/]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
++**[[REQUEST CURATION>>https://nettskjema.no/a/386195]] to share data, simulations, computational models, and software, - or to add a new version of an existing one. **
  Have you already published your data somewhere else? You can increase the exposure and impact of your shared dataset by also listing it on EBRAINS.
@@ -67,7 +67,9 @@
  The curation of data, models and software is different. Thus, below we explain the process for sharing for each research product separately.
++**Before you get started, make sure you[[ sign up for a free EBRAINS account>>https://www.ebrains.eu/page/sign-up]]. This is needed to complete the data sharing process. **
++
  ----
  === Step by step - Data ===
@@ -82,7 +82,7 @@
  //with all you need to know//
  //to share data on EBRAINS: //
  // //
--[[[[image:image-20230324171114-2.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
++[[~[~[image:image-20230324171114-2.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/dfd374b9b43a458192e9/]]
  )))
@@ -90,18 +90,13 @@
--(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]]. **
++(% style="margin-right:10px" %)[[image:https://lh3.googleusercontent.com/zh7TvO6w04YGW9jIhfhmdT6CexdGs-AWOLfJXKRq7-tdHOu6ar1rOQx8o4rZevrjXqgPZ7-Ejv4b6X9XpgXuHpdUXi-mBTHIUnv5Vz-DktHt0sP-PZ3gE8XgZid3TV3swV1uTCBhHx11ge0pjP7RVxswGQ=s2048||height="85px;" width="91px;"]](%%)** Fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]]. **
--This form collects preliminary information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track the case.
++The form collects general information about your data, allowing us to assess whether the dataset fits within the scope of EBRAINS. The submission generates a curation ID allowing us to track and follow up on incoming requests.
++You will also be asked to fill in information related to ethics and regulatory compliance, so that we can evaluate whether we can ethically and legally share the data via EBRAINS (earlier, this was recorded via a [[separate form>>https://nettskjema.no/a/224765]]). See below for information about the ethical and legal aspects concerning sharing of human subject data.
--(% style="margin-right:10px" %)[[image:https://lh6.googleusercontent.com/yw442oS6BwZOlY-_0BoVxyCW3DrdcJ5ogCes92iOD16_rgNEVk56aNMDaVWXFfBLYv24bHzmGgBF9wg0szjH70xzuRTqxoQAeuy3knNO7axCHoyZDXwtyTcMgFnYwbOYxOT29LK-zchrUKLW6Mle93kOkQ=s2048||height="94px;" width="94px;"]](%%)**Fill in the [[Ethics and Regulatory compliance form>>https://nettskjema.no/a/224765]]**.
--This form collects the necessary information needed for us to evaluate whether we can ethically and legally share the data via EBRAINS.
--
--See below for information about the ethical and legal aspects concerning sharing of human subject data.
--
--
  ==== **2. Upload data ** ====
  (% class="box floatinginfobox" id="share-data-infographic" %)
@@ -111,8 +111,7 @@
  //with guidelines
  on data organization: //
--(% style="text-align:center" %)
--[[[[image:image-20230621121014-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
++[[~[~[image:image-20230621121014-1.png~|~|data-xwiki-image-style-alignment="center" height="150" width="106"~]~]>>https://drive.ebrains.eu/lib/f5cf4964-f095-49bd-8c34-e4ffda05a497/file/ebrains-infographic-data-organisation.pdf/]]
  )))
  (% style="margin-right:10px" %)[[image:https://lh5.googleusercontent.com/sieKO-kW8O18iPaUyonwyo4UfHBmtc2E9BDnjbx52j6J_uGmm-OzGAo7sloMk3sYwKa6QW3hYQsOA9N4H7uGQpca088Wrk0Nurpt_J3B0-NSbcaPNdZIh21otQcG6jnAxLGiKoEvkTyaDGTMk3fu7me8mQ=s2048||height="94px;" width="94px;"]](%%)**Ensure data is structured consistently prior to upload. **
@@ -126,7 +126,7 @@
  **Opt. 2. **For larger datasets or datasets with a large amount of files, we recommend using a programmatic approach. The [[python script>>https://github.com/eapapp/ebrains-data-storage/tree/main/data-proxy]] is interactive and does not require any additional programming.
--EBRAINS offers secure, long-term storage at [[CSCS Swiss National Supercomputing Centre>>url:https://www.cscs.ch/]], with currently no upper limit of storage capacity.
++EBRAINS offers secure, long-term storage at FENIX Supercomputing Centres in Europe.
  If a data collection is already uploaded elsewhere, we may link to the already existing repository.
@@ -144,7 +144,7 @@
  * [[Fairgraph>>https://fairgraph.readthedocs.io/en/stable/]]: This is the recommended software tool for programmatic interaction with the KG. It allows you to programmatically upload openMINDS compliant metadata into your KG space and interact with existing metadata.
  * [[KG Core Python SDK>>https://github.com/HumanBrainProject/kg-core-sdks]]: This python package gives you full freedom in interacting with he KG. It allows you to upload any JSON-LD with metadata into your private space. Note, for dataset publications in EBRAINS, the JSON-LD metadata files have to comply to openMINDS.
--Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/lib/47995dbc-f576-4008-a76c-eefbfd818529/file/ebrains-minimum-required-metadata.xlsx]] on EBRAINS.
++Datasets published through the EBRAINS Knowledge Graph have to be registered using **openMINDS compliant metadata** delivered as JSON-LD files. See this summary table for an overview of [[the minimally required openMINDS properties for publishing>>https://drive.ebrains.eu/f/3e226ad165054b35b456/||rel="noopener noreferrer" target="_blank"]] on EBRAINS.
  ==== **4. Write a Data Descriptor** ====
@@ -169,7 +169,7 @@
  about the EBRAINS Data//
  //Descriptor//
  // //
--[[[[image:image-20230324171109-1.png||height="150" width="106"]]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
++[[~[~[image:image-20230324171109-1.png~|~|height="150" width="106"~]~]>>https://drive.ebrains.eu/f/c1ccb78be52e4bdba7cf/]]
  )))
  ==== **5. Preview and publish** ====
@@ -211,9 +211,9 @@
  We recommend storing model code and/or configuration files in an online Git repository, for example on GitHub.
  This repository should be public when you publish the model, but a private repository can be used for model development.
--Alternatively, you can upload code to the Collab Drive or Bucket storage.
++Alternatively, you can upload code to the Collab Drive (in this case, curators will copy it to a read-only Bucket upon publication) or Bucket storage.
--==== 4.Submit metadata ====
++==== 4. Submit metadata ====
  We recommend submitting metadata using the Model Catalog app, installed in your collab.
@@ -230,7 +230,7 @@
  As development of your model proceeds, you can easily register new versions of the code,
  and new parameterizations, by clicking "Add new version".
--If you prefer not to use the app, you can instead fill in the [[Curation request form>>https://nettskjema.no/a/277393#/]].,
++If you prefer not to use the app, you can instead fill in the [[EBRAINS Curation Request Form>>https://nettskjema.no/a/386195]].,
  and you will be contacted by e-mail with further instructions.
  ==== 5. Provide a reference dataset ====
@@ -274,26 +274,15 @@
  === Step by Step - Software ===
++We ask software developers to provide their metadata in the "CodeMeta" format. [[CodeMeta>>https://codemeta.github.io/]] is a common format for software metadata, supported by GitHub, Zenodo, FigShare, DataCite, and the US National Science Foundation.
--(% class="box floatinginfobox" id="software-curation-infographic" %)
--(((
--(% style="text-align:center" %)
--//Software curation at a glance//
--// //
--[[[[image:Thumb2.png||alt="EBRAINS-Share-Software.pdf" height="287" width="197"]]>>attach:EBRAINS-Share-Software-4.pdf]]
--)))
++1. Create a codemeta.json file for your software. There are several [[tools>>https://codemeta.github.io/tools/]] to help you do this, for example the [[CodeMeta generator>>https://codemeta.github.io/codemeta-generator]] app. Please fill in as many of the fields as possible.
++1. Place this file in the root folder of your code repository.
++1. Contact [[EBRAINS support>>https://www.ebrains.eu/contact/]] to request curation of your software, letting us know the URL of your code repository. If you need help hosting your code online, please also let us know.
++1. After a quality check, we integrate and publish the information contained in your codemeta.json file to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
--(% style="margin-left:15px" %)[[[[image:Screenshot 2023-06-06 1122082.png||alt="swc-flow.png" height="136" width="637"]]>>https://www.ebrains.eu/tools/ebrains-curation-request-form||rel="noopener noreferrer" target="_blank"]]
++When you release a new version of your software, just update the codemeta.json file in your repository. We will check the repository on a regular basis, and if the version identifier has changed the Knowledge Graph will be updated accordingly.
--1. Fill in the [[request form>>https://www.ebrains.eu/tools/ebrains-curation-request-form]]. You'll be contacted by a curator with further instructions. In these instructions, you will find the links to your software and software version entries in the Knowledge Graph.
--1. Enter the metadata of your software in your private space of the [[Knowledge Graph Editor>>url:https://editor.kg.ebrains.eu/]] by using the links provided by the curator. Please provide the metadata for your software as complete as possible. This makes it easier for users to find and use your software. If you have questions feel free to contact the curation support. After you have finished editing your entries, please let the curators know by replying to your ticket. We curate your metadata and get back to you, if necessary.
--1. After a quality check, we integrate and publish the information to the Knowledge Graph. Your software is then searchable and usable for the neuroscience community.
--
--If you want to add a new version to an already curated software, please request this via the [[curation request form>>https://nettskjema.no/a/277393]].
--
--For more information, visit our [[Guide to Software Curation in the EBRAINS Knowledge Graph>>url:https://wiki.ebrains.eu/bin/view/Collabs/swc-guide]] or see our infographic on the right.
--
--
  ----
  === Sharing human subject data ===
@@ -330,104 +330,23 @@
  (% class="box floatinginfobox" %)
  (((
--[[[[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png||alt="openMINDS logo" height="87" width="164"]]>>https://github.com/HumanBrainProject/openMINDS]]
++[[~[~[image:https://github.com/HumanBrainProject/openMINDS/raw/main/img/light_openMINDS-logo.png~|~|alt="openMINDS logo" height="87" width="164"~]~]>>https://github.com/HumanBrainProject/openMINDS]]
  )))
--openMINDS (open Metadata Initiative for Neuroscience Data Structures) is a community-driven, open-source metadata framework for graph database systems, such as the EBRAINS Knowledge Graph. It is composed of linked metadata models, libraries of serviceable metadata instances, and supportive tooling ([[openMINDS Python>>url:https://pypi.org/project/openMINDS/]], openMINDS Matlab). For exploring the openMINDS schemas, go to the [[HTML documentation>>url:https://humanbrainproject.github.io/openMINDS/]]. For a full overview of the framework, go to [[the openMINDS collab>>url:https://wiki.ebrains.eu/bin/view/Collabs/openminds/]] or the [[GitHub repository>>https://github.com/HumanBrainProject/openMINDS]].
++openMINDS is a community-driven, open-source metadata framework for linked data, as used in graph database systems, such as the EBRAINS Knowledge Graph. It is composed of multiple metadata models with interlinked schemas, libraries of serviceable metadata instances, and supportive tooling (e.g., [[openMINDS Python>>https://github.com/openMetadataInitiative/openMINDS_Python]] or [[openMINDS Matlab>>https://github.com/openMetadataInitiative/openMINDS_MATLAB]]). A full documentation (for users and contributors) of the openMINDS framework can be found on [[ReadTheDocs>>https://openminds-documentation.readthedocs.io||rel="noopener noreferrer" target="_blank"]].
  For feedback, requests, or contributions, please get in touch with the openMINDS development team via
--* the support-email: [[openminds@ebrains.eu>>path:mailto:openminds@ebrains.eu]]
--* the [[GitHub issue tracker>>url:https://github.com/HumanBrainProject/openMINDS/issues]]
--* the INCF NeuroStars [[openMINDS Community Forum>>url:https://neurostars.org/t/openminds-community-forum-virtual/20156]]
++* [[support@openmetadatainitiative.org>>mailto:mailto:support@openmetadatainitiative.org]]
++* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS/issues]] (for metadata schemas)
++* [[GitHub Issues>>https://github.com/openMetadataInitiative/openMINDS_instances/issues]] (for metadata instances)
++* [[openMINDS Community Forum>>https://neurostars.org/t/openminds-community-forum-virtual]]
  ----
--== **The curation team: meet the curators** ==
--
--The EBRAINS curators help researchers publish their research using the EBRAINS Research Infrastructure. A curator’s job is similar to the job of an editor of a scientific journal, checking the data is organized, understandable, accessible and sufficiently described.
--
--The curators in EBRAINS are located in Oslo, Jülich, Trier and Paris.
--
--
--**Located in Norway**
--
--|(% style="width:303px" %)(((
--[[image:My project2.jpg||height="209" width="167"]]
--
--**Archana Golla**
--
--(% class="small" %)Curation Scientist
--Neuroscience (PhD)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Behavioral neuroscience and microscopy**
--)))|(% style="width:303px" %)(((
--[[image:Camilla.jpg||alt="My project.jpg" height="209" width="167"]]
--
--**Camilla H. Blixhavn**
--
--(% class="small" %)Curation Scientist,
--Phd Student
--Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and data integration**
--)))|(% style="width:303px" %)(((
--[[image:My project (1).jpg||height="209" width="167"]]
--
--**Ingrid Reiten**
--
--(% class="small" %)Curation Scientist,
--Phd Student
--Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and structural connectivity**
--)))|(% style="width:303px" %)(((
--[[image:My project1.jpg||height="209" width="167"]]
--
--**Sophia Pieschnik**
--
--(% class="small" %)Curation Scientist
--Neurocognitive Psychology (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroimaging **
--)))
--
--|(% style="width:303px" %)(((
--[[image:My project.jpg||height="209" width="167"]]
--
--**Heidi Kleven**
--
--(% class="small" %)Curation Scientist,
--Phd Student
--Neuroscience (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Neuroanatomy and brain atlases**
--)))| | |
--
--
--\\**Located in Germany**
--
--|(% style="width:303px" %)(((
--[[image:My project (2).jpg||height="209" width="167"]]
--
--**Jan Gündling**
--
--(% class="small" %)Curation Scientist,
--Phd Student
--Sensors and Cognitive Psychology (M. Sc.)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Human-Computer Interaction**
--)))|(% style="width:303px" %)(((
--[[image:Lyuba.jpg||height="209" width="167"]]
--
--**Lyuba Zehl**
--
--(% class="small" %)Knowledge Systems Engineer
--Dr. rer. nat. (Systems Neuroscience)(%%)
--(% class="small" style="--darkreader-inline-color:#d3cbbf; color:#4a5568" %)**Standard development, data & knowledge management, interdisciplinary communication, data analysis**
--)))|(% style="width:303px" %) |(% style="width:303px" %)
--
------
--
  == **Add practical value to your shared data, model or software** ==
------
--
  === **Showcase shared data, models or software in other services** ===
  Below is a list of additional services that data, models or software shared via EBRAINS can benefit from.  EBRAINS is continuously looking to increase the number of interoperable services.
@@ -434,7 +434,7 @@
  |(% colspan="2" %)**Viewer for 2D images**
--|[[image:MIO_screenshot.PNG]]|Integrate image data with //the Mio viewer//: EBRAINS Multi-Image OpenSeadragon viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[Mio viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example. MioViewer user manual is found [[here>>https://multi-image-osd.readthedocs.io/en/latest/index.html]].
++|[[image:MIO_screenshot.PNG]]|Integrate image data with //SeriesZoom viewer//: EBRAINS viewer provides an intuitive way of navigating high-resolution 2D image series. It has browser-based classic pan and zoom capabilities. A collection can be displayed as a filmstrip (Filmstrip Mode) or as a table (Collection Mode) with adjustable number of row and columns. See [[viewer links available for this dataset>>https://search.kg.ebrains.eu/?category=Dataset&q=nr2f1#9677359c-73fa-4425-b8fa-3de794e9017a]] as an example.
  |(% colspan="2" %)**Viewer for sequential atlas-registered 2D images with annotation options**
  |[[image:LZ_screenshot.PNG]]|Integrate atlas-registered 2D image data with //the LocaliZoom viewer//: The EBRAINS LocaliZoom serial section viewer displays series of registered 2D section images with atlas overlay, allowing the users to zoom into high-resolution images and have information about the brain regions. See the [[LocaliZoom links available for this dataset>>https://doi.org/10.25493/T686-7BX]] as an example. LocaliZoom user manual is found [[here>>https://localizoom.readthedocs.io/en/latest/index.html]].
  |(% colspan="2" %)**Interactive 3D atlas viewer with options for data visualization**
@@ -457,8 +457,19 @@
  ----
--=== **The benefits of sharing data ** ===
++== **EBRAINS commits to the FAIR principles** ==
++In 2016, the 'FAIR Guiding Principles for the management and guardianship of scientific data'{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}} were introduced to the scientific community. The objective of the authors was to provide a set of general recommendations aimed at enhancing the Findability, Accessibility, Interoperability, and Reusability of digital resources (data). They emphasize the importance of making data more open, discoverable, and usable, ultimately facilitating collaboration and knowledge sharing within the scientific community. Today, the FAIR principles are widely recognized and adopted as best practices in data management and stewardship across scientific fields.
++
++In EBRAINS, all datasets, models and software shared go through a streamlined curation process that ensures relevant annotation of the data using the [[openMINDS>>url:https://github.com/HumanBrainProject/openMINDS]] metadata framework and integration into the [[EBRAINS Knowledge Graph>>url:https://docs.kg.ebrains.eu/]] metadata management system. The research products are Findable and Accessible through the [[Knowledge Graph Search>>url:https://search.kg.ebrains.eu/?category=Dataset]] as dataset/model/software cards that display further information regarding the dataset's Interoperability and Reusability.
++
++To further specify how EBRAINS aligns with the FAIR principles, we have assessed the FAIRness of datasets shared in the EBRAINS Knowledge Graph following the [[FAIRsFAIR Data Object Assessment Metrics>>https://zenodo.org/record/6461229||style="background-color: rgb(255, 255, 255); --darkreader-inline-bgcolor: #1c1e1f;"]]: see our **[[FAIR assessment of EBRAINS datasets>>doc:.FAIR assessment of EBRAINS datasets.WebHome]]. **
++
++
++----
++
++== **General benefits of sharing data ** ==
++
  By sharing your data via EBRAINS, you gain access to the following benefits:
  [[image:image-20230324170841-3.png]]
@@ -465,19 +465,13 @@
--We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship{{footnote}}Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18 {{/footnote}}.  Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
++We support you to better follow the [[FAIR^^ ^^guiding principles>>https://www.nature.com/articles/sdata201618]] for data management and stewardship. Publishing data, models or code via EBRAINS will provide you with a citeable [[DataCite DOI>>https://www.doi.org/the-identifier/resources/handbook/]] for your research product.
  ----
--=== **Frequently asked questions ** ===
++== **Frequently asked questions ** ==
--(((
--====  ====
--
--(((
  >Is the curation process time consuming and difficult?
--)))
--)))
  No, if communication is on a regular basis, we are able to finish curation within two weeks. Publishing your data naturally takes some effort but we will support you as much as possible.
@@ -502,23 +502,22 @@
  No, publishing your data does not mean that others can use it however they want. Use of your data will require citation, and by choosing an appropriate Creative Commons licence you decide what others are allowed to do with it. If you still feel worried, you can publish your data under embargo, and in this way delay the date of data release, but still make it possible for others to find the information about the data.
------
--
  == Contact ==
  [[curation-support@ebrains.eu>>mailto:curation-support@ebrains.eu]]
++----
  == Affiliated laboratories ==
--
  //Institute of Basic Medical Sciences,** **University of Oslo, Norway (PI: Jan G. Bjaalie, Trygve B. Leergaard)//
--//Human-Computer Interaction, University of Trier, Germany  //
--
  //Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Germany (PI: Timo Dicksheid)//
++//Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, France (PI: Andrew P. Davison)//
++----
++
  == References ==
  {{putFootnotes/}}

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