Digimouse: a 3D whole body mouse atlas from CT and cryosection data

Abstract

We have constructed a three-dimensional (3D) whole body mouse atlas from coregistered x-ray CT and cryosection data of a normal nude male mouse. High quality PET, x-ray CT and cryosection images were acquired post mortem from a single mouse placed in a stereotactic frame with fiducial markers visible in all three modalities. The image data were coregistered to a common coordinate system using the fiducials and resampled to an isotropic 0.1 mm voxel size. Using interactive editing tools we segmented and labelled whole brain, cerebrum, cerebellum, olfactory bulbs, striatum, medulla, masseter muscles, eyes, lachrymal glands, heart, lungs, liver, stomach, spleen, pancreas, adrenal glands, kidneys, testes, bladder, skeleton and skin surface. The final atlas consists of the 3D volume, in which the voxels are labelled to define the anatomical structures listed above, with coregistered PET, x-ray CT and cryosection images. To illustrate use of the atlas we include simulations of 3D bioluminescence and PET image reconstruction. Optical scatter and absorption values are assigned to each organ to simulate realistic photon transport within the animal for bioluminescence imaging. Similarly, 511 keV photon attenuation values are assigned to each structure in the atlas to simulate realistic photon attenuation in PET. The Digimouse atlas and data are available at http://neuroimage.usc.edu/Digimouse.html.

Figure 1

The sequence of processing of the mouse for acquiring the PET, x-ray CT and cryosection image data.

Figure 2

Representative slices from the image data for (a) PET (b) x-ray CT and (c) cryosection (voxel and matrix sizes are given in the sagittal, axial and coronal directions, respectively).

Figure 3

Surface rendering of atlas structures: whole brain, external cerebrum, cerebellum, olfactory bulbs, striatum, medulla, masseter muscles, eyes, lachrymal glands, heart, lungs, liver, stomach, spleen, pancreas, adrenal glands, kidneys, testes, bladder, skeleton and skin in Digimouse.

Figure 4

Coronal and transaxial sections through the coregistered PET, x-ray CT and cryosection datasets and atlas.

Figure 5

(a) Tetrahedral mesh representation of the mouse atlas using 3D constrained Delaunay method; (b) assignment of optical absorption coefficients to the FEM mesh at 700 nm; (c) assignment of optical diffusion coefficients also at 700 nm.

Figure 6

Comparison of PET and 3D bioluminescence reconstructions in coronal (top row) and transaxial (bottom row) views: (a) PET; (b) bioluminescence; (c) fusion of bioluminescence and PET reconstructions; (d) fusion of bioluminescence and ground truth tumour image.