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: 1.78). 02/2011; 50(4):392-8. DOI: 10.1364/AO.50.000392
Source: PubMed


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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Available from: Jorge Ripoll
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    • "shows the OPT setup used to acquire the experimental in vivo data (for details on this setup, see [12], [13], [18], [27]). In general terms, a laser is guided and expanded before impinging on the sample in almost epi-illumination geometry (see Fig. 2). "
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    ABSTRACT: Finding the center of rotation is an essential step for accurate three-dimensional reconstruction in optical projection tomography (OPT). Unfortunately current methods are not convenient since they require either prior scanning of a reference phantom, small structures of high intensity existing in the specimen, or active participation during the centering procedure. To solve these problems this paper proposes a fast and automatic center of rotation search method making use of parallel programming in graphics processing units (GPUs). Our method is based on a two step search approach making use only of those sections of the image with high signal to noise ratio. We have tested this method both in non-scattering ex vivo samples and in in vivo specimens with a considerable contribution of scattering such as Drosophila melanogaster pupae, recovering in all cases the center of rotation with a precision 1/4 pixel or less.
    Full-text · Article · Sep 2012 · IEEE transactions on information technology in biomedicine: a publication of the IEEE Engineering in Medicine and Biology Society
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    • "can be found elsewhere [24]. In short, the specimen is placed in a capillary (C, BRAND, Wertheim, Germany, Blaubrand-intraMARK), and put in a custom-built bath (B) filled with glycerol. "
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    ABSTRACT: The application of optical projection tomography to in-vivo experiments is limited by specimen movement during the acquisition. We present a set of mathematical correction methods applied to the acquired data stacks to correct for movement in both directions of the image plane. These methods have been applied to correct experimental data taken from in-vivo optical projection tomography experiments in Caenorhabditis elegans. Successful reconstructions for both fluorescence and white light (absorption) measurements are shown. Since no difference between movement of the animal and movement of the rotation axis is made, this approach at the same time removes artifacts due to mechanical drifts and errors in the assumed center of rotation.
    Full-text · Article · Aug 2010 · Biomedical Optics Express
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    • "Since the relatively recent introduction of OPT, several optimizations and improvements of the technique have been described. Some of these include computational algorithms for improved resolution and reconstruction (Birk et al., 2011; Walls et al., 2007), determination of post-alignment values for reconstruction (Cheddad et al., 2011), noise filtering (Fumene Feruglio et al., 2010), and live imaging of mouse organ cultures (Boot et al., 2008). It is likely that this rapid development will continue in the coming years. "

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