The BigBrain Workshop: From open data to novel applications

Initiated in 2010, by researchers at the McGill Centre for Integrative Neuroscience (MCIN) in Canada and the Jülich Research Centre in Germany, the BigBrain Atlas was digitally and painstakingly reconstructed from 7404 human brain slices. A virtual three-dimensional (3D) brain atlas, BigBrain is the highest-resolution 3D digital map of the human brain produced to date – there are no equivalents. It has an isotropic 3D spatial resolution of 20µm—50 times greater than the 1mm resolution of previous 3D human brain models.

MIT Technology Review ranked BigBrain among the top 10 technological breakthroughs of 2014.

The BigBrain model is available as a free tool from MCIN and offers unequalled neuroanatomical insight as well as the possibility to verify hypotheses, and develop solutions for big data management, visualization and analytics. Visit the European Union Human Brain Project website to learn more about the EU-funded BigBrain project.

Recognizing the potential to revolutionize neuroanatomy teaching, neurosurgical training and cytoarchitectural study, the 1 TByte dataset was made available as free open source data in 2014. It has been downloaded over 25,000 times.

So what have researchers done with the BigBrain dataset?

On November 3, 2018, 17 researchers will present how they have used the BigBrain datasets. The morning will start with a plenary session, with a keynote lecture by Dr Karl Zilles (Germany), followed by presentations and an open forum discussion on the challenges and future directions of the BigBrain data and applications. The afternoon will be dedicated to short presentations from selected projects covering the topics listed below, and will end with poster presentations.

Presentations will cover:

  • Technical or methodological issues related to the BigBrain data, for instance concerning realignment, segmentation, and visualization
  • Neuroinformatics hurdles such as management and storage of large images
  • Scientific and clinical applications of high-resolution reference brains
  • Teaching proposals

Keynote speaker

  • Dr Karl Zilles, PhD, JARA-Senior Professor of Brain Research, Forschungszentrum Jülich, Institute of Neuroscience and Medicine (INM-1), Germany: TBD

An internationally renowned neuroscientist, doctor and professor, Dr. Karl Zilles’ was Director of the C. & O. Vogt Brain Research Institute from 1991 to 2012, and from 1998 to 2012 Director of the Institute of Neuroscience and Medicine, Research Center Jülich, Germany.

He is now a JARA-Senior Professor at the Research Center Jülich and at the RWTH University Aachen, Germany. He is Editor-in-Chief of the journal Brain Structure and Function, and was member of editorial boards of various scientific journals (e.g., Neuroimage). Dr Zilles is a Fellow of the German National Academy of Sciences Leopoldina, and Fellow of the North-Rhine Westphalia Academy of Science and Arts. His research focuses on the analysis of the molecular foundation of signal transmission in the various structural and functional organizational units of the human brain, and in the brains of transgenic animals, that serve as models of mental and neurological diseases.

His groundbreaking work on the expression of transmittor receptors in the human brain lead to a new understanding of the organization of the cerebral cortex at the molecular level. His cytoarchitectonic mapping of the cerebral cortex was an innovative and pioneering contribution to the analysis of structure-function relationships in the brain.

International speakers

  • Nicola Palomero-Gallagher, Post-doctoral Fellow, Forschungszentrum Jülich, INM-1, Germany: 3D reconstruction of the cyto- and receptoarchitecture of the primate brain
  • Hartmut Mohlberg, PhD, Research Fellow, Forschungszentrum Jülich, INM-1, Germany: Workflows and tools for the cytoarchitectonic mapping in BigBrain datasets
  • Hannah Spitzer, PhD Student, Forschungszentrum Jülich, INM-1, Germany: Towards parcellation of visual cortex using convolutional neural networks
  • Vadim Istomin, PhD/Consultant, Imaging and Computer Vision Technology: Brain Imaging Informatics, NY, USA: BigBrain on a small computer: texture-based rendering of sparse 3D data on high-end GPU.
  • Fahmeed Hyder, PhD, Professor of Biomedical Engineering & Radiology and Biomedical Imaging, Yale University, Boston, MA, USA: Human brain gray matter energy map computed on the basis of cellular staining from BigBrain
  • Konrad Wagstyl, PhD Student, University of Cambridge, UK/ Visiting Scholar MCIN/MNI/McGill: Automated segmentation of cortical layers

Canadian Speakers

  • Louis Borgeat, Research officer, National Research Council Canada, Ottawa, Ontario: Big Brain Atlas development with Atelier3D-MCIN
  • Jordan DeKraker, PhD Student, University of Western Ontario, Toronto : Unfolded hippocampal coordinate system in 3D histology
  • Rosanna Olsen, Scientist, Rotman Research Institute, Baycrest Health Sciences, Toronto: Harmonization of hippocampal subfield segmentation

Montreal Canada Speakers

  • Tristan Glatard, PhD, Assistant Professor at the Department of Computer-Science and Software Engineering, Concordia University / Ludmer Centre Researcher: Efficient processing of ultrahigh-resolution 3D images with Apache Spark
  • Dr Abbas Sadikot, PhD, Montreal Neurological Institute and Hospital, McGill University: A 3-D high resolution model of the subcortical structure of BigBrain
  • Sherri L Jones, Post-doctoral Fellow specialized in S, Douglas Hospital and McGill University: The BigBrain as a validation tool in a manual segmentation protocol of the human hypothalamus: Applications on project Ice Storm
  • Alain Dagher, PhD, Montreal Neurological Institute and Hospital, McGill University: Subcortical connectomics from big data
  • Amir Shmuel. PhD, Montreal Neurological Institute and Hospital, McGill University: TBD
  • Marc Fournier, Post-doctoral Fellow, MCIN/Ludmer Centre, Montreal Neurological Institute and Hospital, McGill University: Parcellation of the BigBrain Cortex Using an Adapted K-means Clustering Algorithm
  • Lindsay B Lewis, Research Associate/Developer, MCIN/Ludmer Centre, Montreal Neurological Institute and Hospital, McGill University: Utilizing simulated high-resolution MRIs of the BigBrain for validation of cortical reconstruction pipelines and registration to the Human Connectome Project atlas

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Contact: Joanne Clark | Administrative Director | Ludmer Centre for Neuroinformatics & Mental Health

Montreal Neurological Institute | 3801 Rue University | Montréal, QC | Canada H3A 2B4

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