Neuroscience data integration through use of digital brain atlases

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 Neuroscience data integration through use of digital murine brain atlases

This full-day course will introduce participants to a workflow for spatial integration of morphological features in a three-dimensional (3D) reference atlas. Students will be introduced to the QuickNII tool for spatial registration of serial microscopic images from mouse or rat brains to three-dimensional reference atlases, learn how labelled features can be identified and extracted using the machine-learning tool ilastik, and subsequently enumerated in brain regions of interest with the Nutil software. This course will consist of a combination of lectures and hands-on training sessions. This short course will introduce the students to key concepts and methods underlying the Human Brain Project (HBP) infrastructure for data sharing, and the 3D mouse and rat brain reference atlases used for spatial data integration in HBP. The course will focus on how neuroscience data from different disciplines can be combined and integrated using 3D reference atlases, and how the 3D atlases can be utilized for analytic purposes.

Short plenary lectures

  1. Welcome and introduction to HBP Neuroinformatics platform
  2. Data integration through use of digital brain atlases
  3. Analytical workflows for image series
  4. Scale-up and prepare your data for eternity

Practical hands-on sessions (individual and group work)

  1. Registration of 2D images to a reference atlas
  2. Segmentation of labelled features in images
  3. Quantification and analysis of features of interest

Requirements for the course

Bring own laptop (Windows) with pre-installed open source software necessary for the hands-on sessions, which will be distributed to registered participants

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