Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Changes for page SGA3 D1.1 Showcase 1

Last modified by dicksche on 2022/05/23 22:24
From version 10.1
edited by dicksche
on 2020/12/17 07:33
Change comment: There is no comment for this version
To version 11.1
edited by dicksche
on 2020/12/17 07:36
Change comment: There is no comment for this version

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16 -//This collab hosts a jupyter notebook which demonstrates a first prototype coupling of the [[EBRAINS human brain atlas>>https://ebrains.eu/services/atlases]] with the [[The VirtualBrain simulator>>https://ebrains.eu/service/the-virtual-brain]] in a purely programmatic fashion, using a pre-release of the `brainscapes` Python client. The notebook is accessible from the [[JupyterLab>>https://lab.ebrains.eu/user/dicksche/lab/tree/drive/Shared%20with%20groups/SGA3%20D1.1%20Showcase%201/D1.1%20Showcase%201%20TVB%20Atlas%20Integration%20Prototype.ipynb]] of this collaboratory.//
16 +//This collab hosts a jupyter notebook which demonstrates a first prototype coupling of the [[EBRAINS human brain atlas>>https://ebrains.eu/services/atlases]] with the [[The VirtualBrain simulator>>https://ebrains.eu/service/the-virtual-brain]] in a purely programmatic fashion. The notebook is accessible from the [[JupyterLab>>https://lab.ebrains.eu/user/dicksche/lab/tree/drive/Shared%20with%20groups/SGA3%20D1.1%20Showcase%201/D1.1%20Showcase%201%20TVB%20Atlas%20Integration%20Prototype.ipynb]] of this collaboratory.//
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18 18  == Prototype coupling of TVB and EBRAINS atlas services ==
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20 -The demo showcases how data services and computing can interact in a well-structured and meaningful way in the collaboratory. It is the first use case for purely programmatic access to EBRAINS atlases. While not all datasets and functionalities are yet accessible through the client, it makes data formats, region specifications and access patterns explicit, thereby fertilizing co-design and boosting the collaboration between WP1 and WP4.
20 +The demo showcases how data services and computing can interact in a well-structured and meaningful way in the collaboratory. It is the first use case for purely programmatic access to EBRAINS atlases using a new Python client, //brainscapes//. While not all datasets and functionalities are yet accessible through the client, it makes data formats, region specifications and access patterns explicit, thereby fertilizing co-design and boosting the collaboration between WP1 and WP4.
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22 22  The atlas client gives direct programmatic access to typical patterns of interaction with EBRAINS human brain atlas. It supports the multilevel character of this atlas, which defines cytoarchitectonic maps in multiple reference template spaces at different spatial resolutions (namely the MNI Colin, ICBM152 asymmetric as well as the BigBrain microscopic space), and links them with complementary maps related to brain function, connectivity and fibre architecture. The functionality of the Python client matches common patterns known from browsing the interactive atlas viewer: Selecting a parcellation, browsing and searching brain region hierarchies, downloading maps, selecting regions, and requesting manifold information and features associated with brain regions.
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