Whole Brain Catalog

From NoskeWiki
Jump to navigation Jump to search


The Whole Brain Catalog (WBC) is a free, open source, downloadable, multi-scale, virtual catalog of the mouse brain and its cellular constituents. This project is bring undertaken at the National Center for Microscopy and Imaging Research at the University of California, San Diego, and the project lead is Stephen Larson. On this page I have my own personal notes to help me remember stuff about WBC, including hyperlinks etc!

WBC Programming

WBC has been programmed in Java (cross-platform), however they are currently developing a web-based version as well.

WBC Resources

How to Extract Meshes

Stephen showed me how to extract/download the 3D meshes as ".obj" files, but I'm writing it here so I remember. The steps are:

  1. Download and execute WBC (Java version).
  2. On the left hand side of the WBC interface, right click any mesh under "Mesh Models" (eg: "Retina, Eyes") and select "Display properties".
  3. Copy the "ID" tag URL (eg: "http://data.wholebraincatalog.org/tangibles/meshmodels/eyesc") into a web browser.
    • NOTE: Firefox works best, because it displays XML files nicely.
  4. Within the web browser, right click then go: View Source. Here you want to locate and copy the URI between the "ns2:dataWrapperId" tags (eg: "http://data.wholebraincatalog.org/datawrappers/generic/eyesc"), then go to that URL.
  5. Find the "location" tags (which should be right at the end), and it should give a URL to a ".obj" file (eg: "http://data.wholebraincatalog.org/content/eyes.obj"). Download this file and then it should then open in most 3D animation/modelling programs, such as Cinema 4D or Blender.

Other Brain Projects

  • Allen's Brain Explorer - Brain Explorer is a free program for viewing the Allen Mouse Brain Atlas gene expression data in the 3D framework of the Allen Reference Atlas (ARA). The software works on Mac or Windows, and the project is part of the Allen Institute for Brain Science. Interestingly the default view is one side of the brain only - it doesn't seem to include the eyes or allow you to download the model.
  • Brain Navigator - A online atlas and visualization program by Elsevier and The Allen Institute for Brain Science. Video looks pretty good, but is not free!