Software interfaces to the human brain atlas in EBRAINS
Speakers: Timo Dickscheid (Forschungszentrum Juelich)
Where: Zoom meeting: https://kth-se.zoom.us/j/63073903565
When: Monday, June 14, 2021, 2-3 pm
Abstract: The EBRAINS multilevel human brain atlas integrates maps that capture different facets of human brain organisation, in a common framework. It is defined across multiple reference spaces, zooming in from the millimetre scale in the MNI space to the micrometer level of the BigBrain. The atlas currently links cytoarchitectonic areas with ultra-high resolution BigBrain data, fibre bundles from MRI tractography, maps of functional modules, and a whole range of multimodal data features associated to various brain regions. The range and scope of available maps and features is constantly increasing. As the amount of data constituting the human atlas exceeds the disk capacity of most computers, it is designed as an online framework that you can access in a number of ways through the siibra toolsuite. The main entry point is an interactive 3D viewer (siibra explorer), which allows to explore the different facets of the atlas in 3D and to select specific data features for download. Programmatic interfaces, including a Python library (siibra-python) and HTTP API (siibra-API) are in development, with pre-releases now available. An interactive web-application (VoluBA) provides an intuitive way of integrating volumes of interest from imaging experiments to Altas reference space.
We will talk about the development of key parts of this atlas, demonstrate main features of the different software interfaces, and introduce participants to typical scientific use cases.
Speaker’s Bio: Timo Dickscheid is heading the “Big Data Analytics” group at the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany. He graduated in Computer Science at the University of Koblenz in 2006, and earned his PhD in Computer Vision and Photogrammetry at the University of Bonn in 2011 under the supervision of Prof. Wolfgang Förstner. In 2010, he joined Forschungszentrum Jülich as a post-doc in the lab of Katrin Amunts to work on medical image registration and segmentation for histological brain sections. After accepting a position as the head of Information Technology at the German Federal Institute of Hydrology in Koblenz in 2012, Timo returned to Jülich in 2014. His research group focuses on biomedical image analysis and neuroinformatics methods for building high-resolution 3D models of the human brain, and constitutes a local pillar of the national artificial intelligence research network “Helmholtz AI”. In the Human Brain Project (HBP), Timo leads the EBRAINS atlas service category (SC2), which includes the development of brain reference atlases and the corresponding software interfaces for exploration, data integration and data analysis.