Goal-Directed Magnetic Resonance Brain Micro Imaging
The Human Brain Project
Caltech Division
General Information
Connectivity Project
Atlas Project
Algorithms Project
Project Images
Atlas Project
The three individual Projects and four Cores revolve around the development, application, interpretation, and presentation of high resolution multidimensional images of the developing nervous system obtained on several model systems both in vitro and in vivo. The collaborators bring a number of different philosophies and types of expertise: computer graphics, modeling and control theory; mapping brain physiology/function and cortical learning; embryology, cell and molecular biology, and digital optical microscopy; microscopic resolution MRI.

In Vivo Atlases of Brain Development Project [Atlas Project] 
Russell Jacobs and John Allman 

The goal of this project is to create, analyze, and distribute in vivo atlases of the developing brain recorded using three dimensional Magnetic Resonance (MR) imaging. These atlases will provide comprehensive three-dimensional images of the developing brain in three different species (avian, rodent, & primate) using MR micro-imaging. The information is being analyzed at a number of different levels ranging from simple annotation to correlating the onset and developing organization of different structures in both space and time. Moreover, cross species comparisons (avian .vs. rodent .vs. primate) will provide information not available from any single species.

There are two major short comings of current published developmental atlases; 1) they require that a different individual specimen be sampled at each time point; 2) the book format is needlessly confining. If different individuals must be examined at different times; then variations in specimen sizes, variations in relative size and orientation of different features, and variations in the timing of development vastly complicate the interpretation of the time course data in terms of real events occurring during embryological development.

Examining a single individual through the time course of development obviates many of these problems. Using the computer as the 'format' for dissemination of the atlas (e.g. via the Web and on CD-ROM) puts at the neuroscientist's disposal all the modern tools for 3D image rendering and morphometric analysis not available when the raw data is presented in planes of section on the pages of a book. For example, the ability to take arbitrarily oriented slices of the 3D data will vastly simplify comparison of the atlas with ones own data. For purposes of comparison with current atlases and to develop hardware and software, in vitro atlases of fixed specimens are also being compiled in this Project. For an example see the preliminary MRI data sets.

MR imaging has several unique aspects which make it ideal for this Project. It is non-invasive making longitudinal studies of the same animal possible. Three dimensional images of optically opaque samples are routinely obtainable. The three dimensional images may be rendered and 'sliced' in any direction. Different MR imaging protocols can are used on the same sample to provide different types of contrast and thus furnish more than simple anatomical information. For example, the diffusion tensor of water in tissue may be measured quantitatively with MRI and is diagnostic for the presence/absence of local anisotropic motion. We take advantage of all these characteristics compiling the data for the atlases of brain development.