Quality-based registration and reconstruction of optical tomography volumes.

Ultramicroscopy, a novel optical tomographic imaging modality related to fluorescence microscopy, allows to acquire cross-sectional slices of small specially prepared biological samples with astounding quality and resolution. However, scattering of the fluorescence light causes the quality to decrease proportional to the depth of the currently imaged plane. Scattering and beam thickness of the excitation laser light cause additional image degradation. We perform a physical simulation of the light scattering in order to define a quantitative function of image quality with respect to depth. This allows us to establish 3D-volumes of quality information in addition to the image data. Volumes are acquired at different orientations of the sample, hence providing complementary regions of high quality. We propose an algorithm for rigid 3D-3D registration of these volumes incorporating voxel quality information, based on maximizing an adapted linear correlation term. The quality ratio of the images is then used, along with the registration result, to create improved volumes of the imaged object. The methods are applied on acquisitions of a mouse brain and mouse embryo to create outstanding three-dimensional reconstructions.