In biomedical research, there is an increased need for reconstruction of large soft tissue volumes (e.g. whole organs) at
the microscopic scale from images obtained using laser scanning microscopy (LSM) with fluorescent dyes targeting
selected cellular features. However, LSM allows reconstruction of volumes not exceeding a few hundred ìm in size and
most LSM procedures require physical sectioning of soft tissue resulting in tissue deformation. Micro-CT (&mgr;CT) can
provide deformation free tomographic image of the whole tissue volume before sectioning. Even though, the spatial
resolution of &mgr;CT is around 5 &mgr;m and its contrast resolution is poor, it could provide information on external and
internal interfaces of the investigated volume and therefore could be used as a template in the volume reconstruction
from a very large number of LSM images. Here we present a method for accurate 3D reconstruction of the murine heart
from large number of images obtained using confocal LSM. The volume is reconstructed in the following steps: (i)
Montage synthesis of individual LSM images to form a set of aligned optical planes within given physical section; (ii)
Image enhancement and segmentation to correct for non-uniform illumination and noise; (iii) Volume matching of a
synthesized physical section to a corresponding sub-volume of &mgr;CT; (iv) Affine registration of the physical section to
the selected &mgr;CT sub-volume. We observe correct gross alignment of the physical sections. However, many sections
still exhibit local misalignment that could be only corrected via local nonrigid registration to &mgr;CT template and we plan
to do it in the future.
Phase correlation is applied to the mosaicing of confocal scanning laser microscopy data. A large specimen (i.e., a murine heart) is cut into a number of individual sections with appropriate thickness. The sections are scanned horizontally and vertically to produce tiles of a 3D volume. Image processing based on phase correlation is used to rebuild the 3D volume and stitch the tiles together. Specifically, 2D registration of in-plane tiles and 3D alignment of optical slices within a given physical section are performed. The approach and performance are presented in this paper along with examples.