Improved reconstructions and generalized filtered back projection for optical projection tomography

Institute of Electronic Structure & Laser, Foundation for Research and Technology-Hellas, FORTH, Heraklion, Greece. ‐
Applied Optics (Impact Factor: 1.69). 02/2011; 50(4):392-8. DOI: 10.1364/AO.50.000392
Source: PubMed

ABSTRACT Optical projection tomography (OPT) is a noninvasive imaging technique that enables imaging of small specimens (<1 cm), such as organs or animals in early developmental stages. In this paper, we present a set of computational methods that can be applied to the acquired data sets in order to correct for (a) unknown background or illumination intensity distributions over the field of view, (b) intensity spikes in single CCD pixels (so-called "hot pixels"), and (c) refractive index mismatch between the media in which the specimens are embedded and the environment. We have tested these correction methods using a variety of samples and present results obtained from Parhyale hawaiensis embedded in glycerol and in sea water. Successful reconstructions of fluorescence and absorption OPT images have been obtained for weakly scattering specimens embedded in media with nonmatched refractive index, thus advancing OPT toward routine in vivo imaging.

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    ABSTRACT: An Optical Projection Tomography (OPT) system was developed and optimized to image 3D tissue engineered products based in hydrogels. We develop pre-reconstruction algorithms to get the best result from the reconstruction procedure, which include correction of the illumination and determination of sample center of rotation (CoR). Existing methods for CoR determination based on the detection of the maximum variance of reconstructed slices failed, so we develop a new CoR search method based in the detection of the variance sharpest local maximum. We show the capabilities of the system to give quantitative information of different types of hydrogels that may be useful in its characterization. ©2014 Optical Society of America OCIS codes: (100.6890) Three-dimensional image processing; (100.6950) Tomographic image processing; (160.1435) Biomaterials; (170.3010) Image reconstruction techniques., "Optical projection tomography as a tool for 3D microscopy and gene expression studies," Science 296(5567), 541–545 (2002). 2. U., "Improved reconstructions and generalized filtered back projection for optical projection tomography,. Cardinal, "Thinking inside the box: keeping tissue-engineered constructs in vitro for use as preclinical models,, "Automated recovery of the center of rotation in optical projection tomography in the presence of scattering," IEEE J. Biomed. Health Inform. 17(1), 198–204 (2013). 9. J. Sharpe, "Optical projection tomography as a new tool for studying embryo anatomy," J. Anat.
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    ABSTRACT: Advancements in cell biology have made it possible to generate large quantities of human pluripotent stem cells (hPSC) in three-dimensional cultures in bioreactors. Volumetric imaging of hPSC cell aggregates with Scanning Laser Optical Tomography can provide insight into their physiology and growth behavior. Containing cell clusters in a glass capillary for in vitro imaging introduces a non-vanishing refractive index gradient into the field of view that will produce artifact in reconstructed tomographic images. The effects of refraction are studied by means of numerical simulations. Further-more we present a method of correcting for the effects of refraction utilizing a reordering step for the projections before tomographic reconstruction. Removal of artifacts is successfully demonstrated on experimental data of human pluripo-tent stem cell (hPSC) clusters. This will enable long term in vitro studies of hPSC clusters with Scanning Laser Optical Tomography.
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