Atlases

• Multilevel Human Brain Atlas

  • Atlases
  A three-dimensional atlas that integrates the different facets of human brain organization at the millimeter and micrometer level

• Rat Brain Atlas

  • Atlases
  Explore open access 3D anatomical atlas for the rat brain

• Mouse Brain Atlas

  • Atlases
  Explore open access 3D anatomical atlas for the mouse brain

• QUINT

  • Atlases
  Extract, quantify and analyse labelled features from rodent histological images

• QuickNII and VisuAlign

  • Atlases
  Spatially register mouse and rat serial 2D brain images to 3D reference atlases

By spatially registering images to a 3D atlas, it becomes possible to perform analyses based on regions of interest that are specified by the atlas maps. The QUINT workflow employs a suite of tools to efficiently extract, locate and quantify labelled features in serial 2D images.

• QUINT

  • Atlases
  Extract, quantify and analyse labelled features from rodent histological images

The first step of integrating neuroscience data is to relate them to a common anatomical location. Image data can be spatially aligned with a 3D reference atlas using linear or non-linear deformations. The transformations needed to bring atlas and images into spatial registration are stored as spatial metadata. EBRAINS provides two tools for registration of 2D images to atlases: QuickNII, tailored for efficient spatial registration of serial 2D (microscopic) image data, and Visualign, tailored for non-linear alignment images to optimize spatial registration after using the QuickNII tool.

• QuickNII and VisuAlign

  • Atlases
  Spatially register mouse and rat serial 2D brain images to 3D reference atlases