Navigate complex neuroanatomy and integrate neuroscience data using 3D brain atlases

Date: 31 August 2019
Venue: Department of Physics, University of Warsaw
            Ludwika Pasteura 5, 02-093 Warsaw, Poland  View map

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Learn how to navigate three-dimensional (3D) brain atlases of the mouse, rat, and human brain, and integrate neuroscience data through use of digital high-resolution human and murine brain atlases.

This full-day course will introduce participants to workflows for spatial integration of morphological features in a 3D reference atlas. Students will be introduced to tools for spatial registration of serial microscopic images or 3D image volumes to three-dimensional reference atlases, learn how to extract labelled features from experimental image data and analyse molecular and gene expression data using the 3D atlases. The course will consist of a combination of lectures and hands-on training sessions. Students will be introduced to key concepts and methods underlying the Human Brain Project (HBP) infrastructure for data sharing, and learn how neuroscience data from different disciplines can be combined, integrated, visualized and analysed using 3D reference atlases.ce atlases, and how the 3D atlases can be utilized for analytic purposes.


  1. Open data sharing and integration using the HBP Neuroinformatics platform (Introduction)
  2. Navigate mouse, rat or human neuroanatomy using 3D brain atlases (hands-on)
  3. Integrate 2D and 3D neuroscience data using digital brain atlases (hands-on)
  4. Atlas-driven data analysis for image series and partial volumes (hands-on)
  5. Scale-up and prepare your data for eternity (Summary and Perspective)

The course is coordinated by Maja A. Puchades1, Camilla H. Blixhavn1and Trygve B. Leergaard1. Course lecturers (Jan G. Bjaalie1, Timo Dickscheid2, Krister Andersson1) and instructors (Sharon Yates1, Lyuba Zehl 2, Ida Aasebø1) are from 1) the Neural Systems laboratory at the University of Oslo (, Norway, and 2) Institute of Neuroscience and Medicine, Structural and Functional Organization of the Brain (INM-1)Forschungszentrum Juelich, Germany.

Requirements for the course

Bring own laptop (Windows) with up to date versions of Chrome or Firefox browsers and pre-installed open source software (information to follow) for the hands-on sessions, which will be distributed to registered participants. If possible, bring a computer mouse. All participants need ORCID accounts.

Prepare for the workshop:
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