Timo Dickscheid, Sebastioan Bludau
Institute for Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany
Understanding the human brain requires access to experimental data that capture relevant aspects of brain organization across a broad range of scales and modalities, and typically originate from a plethora of resources. To make multimodal and multidimensional measures of brain organization accessible, they need to be integrated into a common reference framework and exposed via suitable software interfaces. This tutorial will introduce participants to siibra toolsuite, which provides access to a multilevel atlas of the human brain built from “big data”. The atlas integrates brain reference templates at different spatial scales, complementary parcellation maps, and a wide range of multimodal data features. It links macroanatomical concepts and their inter-subject variability with measurements of the microstructural composition and intrinsic variance of brain regions, using cytoarchitectonic maps as a reference, and integrating the BigBrain model as microscopic reference template. The tool suite includes a web-based 3D viewer (siibra-explorer) and a Python library (siibra-python) to support a broad range of neuroscientific use cases. It makes use of EBRAINS as a data sharing platform and cloud infrastructure and implements interfaces to other neuroscience resources. The focus of this tutorial will be on building reproducible workflows with BigBrain data using the siibra-python library.
Timo Dickscheid is a Professor for Microscopic Image Analysis at Heinrich-Heine University Düsseldorf, and head of the "Big Data Analytics" group at the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany. He is a computer scientist by training and earned his PhD in the field of Computer Vision and Photogrammetry at the University of Bonn in 2011. Dickscheid joined Forschungszentrum Jülich as a post-doc in 2010 to develop image analysis methods for microscopic imaging. After accepting a position as the head of Information Technology at the German Federal Institute of Hydrology in Koblenz in 2012, he returned to Jülich in 2014 to setup his own research group. Aiming to build a cellular resolution multimodal model of the human brain, his work addresses distributed data management for high throughput imaging, AI methods for large-scale biomedical image analysis, and software interfaces for working with very large image data. Dickscheid leads the development of brain atlas
Sebastian Bludau is a senior researcher at at the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich. He graduated with a diploma as a biologist at the Heinrich-Heine University in Duesseldorf and received a PhD in theoretical medicine from the RWTH Aachen University in 2011, where he studied the cytoarchitecture of the frontal pole of the human brain. Subsequently he became post-doc at the INM-1 (Structural and functional organization of the brain) at the Institute of Neuroscience and Medicine at the research center Jülich. His current research is mainly about the cytoarchitecture of the human brain, the integration of different imaging modalities into high resolution reference spaces, high-throughput optical microscopy and developing and testing of new prototype software for the analysis of histological images.
Requirements: A laptop with an up-to-date web browser (Chrome or Firefox is recommended) is required for the hands-on examples. All examples will be run on pre-built Jupyter notebooks, which will be provided for downloading. Please register for an EBRAINS account in advance.
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