Supplemental Material for:
Microscopic Diffusion Tensor Imaging of the Mouse Brain
Yi Jiang, G. Allan Johnson
Diffusion tensor imaging (DTI) data at 43 μm isotropic resolution has been acquired
on the intact adult mouse brain in 28-hour scan time by using a streamlined protocol,
including specimen fixation and staining, image acquisition, reconstruction,
post-processing, and distribution. An intermediate registration of each component
image is required to achieve the desired microscopic resolution. Multiple parameters
have been derived including fractional anisotropy, axial and radial diffusivity, and a
color-coded orientation map of the primary eigenvector. Each DTI dataset was mapped
to a common reference space to facilitate future standardized analysis. Fiber tracking
has also been demonstrated, providing 3D connection information. This protocol to
acquire high-resolution DTI data in a robust and repeatable fashion will serve as a
foundation to quantitatively study mouse brain integrity and white matter architecture,
at what we believe to be the highest spatial resolution yet attained.
Files in This Data Supplement
All datasets associated with this publication are available from CIVMSpace, our
Web-based data portal.
|Tensor_090430_reg_re.dat ||tensor, 4-byte (float), little-endian, xyzc, 256x256x512x6, 43 micron/voxel|
|va0_090430_re.dat||primary eigenvalue, axial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel|
|T2_090430_reg.dat||T2 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel|
|T1_090430_reg.dat||T1 contrast, 2-byte (unsigned int), little-endian, 256x256x512, 43 micron/voxel|
|RD_090430_re.dat||Radial diffusivity, 4-byte (float), little-endian, 256x256x512, 43 micron/voxel|
|FA_090430_re.dat||fractional anisotropy, 4 byte (float), little-endian, 256x256x512, 43 micron/voxel|
|ev0_090430_re.dat||primary eigenvector, 3x4 byte (float), little-endian, cxyz, 3x256x256x512, 43 micron/voxel|
|ClrMap_0430_re.dat||RGB color map, 3x1 byte/voxel, 256x256x512, 43 micron/voxel|
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On the Mac, Safari versions 1.3 and above and Mozilla Firefox versions 1.0 and above are supported.
VoxStation requires a working Java installation. It has been tested with Java 1.4, 1.5 and 1.6 on Windows, and Java 1.4 and 1.5 on Mac OS X.
From CIVMSpace, select any thumbnail to browse slices from the corresponding dataset. To view
structure labels, select "Open in VoxStation" from the pull-down menu at the
upper right corner of the CIVMSpace page, then select the "Go" button; this
will launch VoxStation, a Java Web Start application that lets you view datasets
in three planes.
Below is an example of a volume dataset (ClrMap_0430_re.dat)
that can be found in CIVMSpace.
We are grateful to Boma Fubara for assistance in specimen preparation and
anatomical region definition, Gary Cofer for assistance in MR acquisition,
Jeffrey Brandenburg for assistance in 3D visualization, Alexandra Badea
for assistance in anatomical region definition and fiber tracking, and
Sally Zimney for assistance in manuscript preparation. All work was
performed at the Duke Center for In Vivo Microscopy, an NCRR National
Biomedical Technology Research Center (P41 RR005959) and Small Animal
Imaging Resource Program (U24 CA092656), with specific support from
he Mouse Bioinformatics Research Network (U24 RR021760).