Mr. Ashish H. Poddar Profile

Ashish H. Poddar

at Syracuse Univ

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Proceedings Article | 26 March 2007 Paper

Large volume reconstruction from laser scanning microscopy using micro-CT as a template for deformation compensation

A. Subramanian, A. Krol, A. Poddar, R. Price, R. Swarnkar, D. Feiglin

Proceedings Volume 6512, 651221 (2007) https://doi.org/10.1117/12.709855

KEYWORDS: Image segmentation, Tissues, Heart, Microscopy, Image registration, Binary data, RGB color model, Spatial resolution, Fourier transforms, Laser scanners

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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.

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