BigBrain Browser

The BigBrain dataset can be viewed and downloaded at various resolutions here.

Full-resolution BigBrain visualization with Atelier3D

During the development of the numerous components for the BigBrain 3D reconstruction, the project collaborators located on different continents must be able to frequently visualize various intermediate versions of the full-size, highest resolution 3D brain model (1 Terabyte).

Atelier3D, a software suite developed at the National Research Council of Canada (NRC), has been used for visualization of this large dataset. This software developed by the Visualization Information Technology group at NRC has been used for visual navigation and analysis of large-scale 3D data in a wide variety of ultra-high resolution applications including cultural and heritage conservation, medical sciences and geomapping projects (see publications below). Louis Borgeat and his research team specializing in visualization of very large 3D models have been customizing Atelier3D to perform full 3D reconstruction of histological brain datasets.

The option of transferring large quantities of information transatlantically each time a new version of the model is created would be both unpractical and costly. In Atelier3D, spatial data which has been pre-processed is streamed on-demand from a remote server at sufficient resolution to render images in precise detail on the client side, making scale issues transparent to the remote users.

atelier_full

bigbrain_a3d_surf

bigbrain_a3d_oblique

BigBrain surface visualization with BrainBrowser

The extremely large size (1 Terabyte) of the full 3D BigBrain dataset currently necessitates that it be viewed with highly specialized software (using Atelier3D, see section above). However, surfaces extracted upon this dataset are smaller in size and allow for an increasing extent of web-based viewing, with no need for any software installation. BrainBrowser, originally developed within our lab for web-based visualization of surfaces extracted from MRI, has been extended to view multiple, conglomerate BigBrain surfaces (cortical as well as subcortical structures, JSON format). In the near future, these surfaces will be made publicly available. Preliminary single cortical surfaces in MNI OBJ format are already available here and can be viewed in the standard BrainBrowser surface viewer or with standard MINC tools (see section below).

bigbrain_BrainBrowser

BigBrain data visualization with standard MINC tools

It also remains possible to download and visualize the BigBrain dataset (available here) either in its entirety at downsampled resolution, or at full resolution but for a limited block of the dataset, using standard MINC tools such as Display or register (available on Github)

Publications

  • Amunts, Katrin, et al., 2013. An ultrahigh-resolution 3D human brain model. Science. [article]
  • Borgeat, Louis, et al., 2009. A framework for the registration of color images with 3D models. Image Processing (ICIP) Proceedings. [article]
  • Borgeat, Louis, et al., 2005. GoLD: Interactive display of huge colored and textured models. In: Proc. of SIGGRAPH 2005. [article]
  • Borgeat, Louis, et al., 2007. Visualizing and Analysing the Mona Lisa. Proc of IEEE Computer Graphics and Applications. [article]
  • Borgeat, Louis, et al., 2007. Visualizing and analyzing large and detailed 3d datasets – Proc of The 3D Virtual Reconstruction and Visualization of Complex Architectures. [article]
  • Borgeat, Louis, et al., 2004. Collaborative visualization and interaction for detailed environment models. In: Proc. of the 10th International Conference on Virtual Systems and Multimedia. [article]