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. 2018 Oct 10;9(11):5330-5339.
doi: 10.1364/BOE.9.005330. eCollection 2018 Nov 1.

Propagation-based phase-contrast tomography of a guinea pig inner ear with cochlear implant using a model-based iterative reconstruction algorithm

Lorenz Hehn  1   2 , Regine Gradl  1   3 , Andrej Voss  4 , Benedikt Günther  1   5 , Martin Dierolf  1 , Christoph Jud  1 , Konstantin Willer  1   2 , Sebastian Allner  1 , Jörg U Hammel  6   7 , Roland Hessler  8 , Kaye S Morgan  1   3   9 , Julia Herzen  1 , Werner Hemmert  4 , Franz Pfeiffer  1   2   3
Affiliations

Propagation-based phase-contrast tomography of a guinea pig inner ear with cochlear implant using a model-based iterative reconstruction algorithm

Lorenz Hehn et al. Biomed Opt Express. .

Abstract

Propagation-based phase-contrast computed tomography has become a valuable tool for visualization of three-dimensional biological samples, due to its high contrast between materials with similar attenuation properties. However, one of the most-widely used phase-retrieval algorithms imposes a homogeneity assumption onto the sample, which leads to artifacts for numerous applications where this assumption is violated. Prominent examples are biological samples with highly-absorbing implants. Using synchrotron radiation, we demonstrate by the example of a guinea pig inner ear with a cochlear implant electrode, how a recently developed model-based iterative algorithm for propagation-based phase-contrast computed tomography yields distinct benefits for such a task. We find that the model-based approach improves the overall image quality, removes the detrimental influence of the implant and accurately visualizes the cochlea.

Keywords: (100.5070) Phase retrieval; (170.6960) Tomography.

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Conflict of interest statement

The authors declare that there are no conflicts of interest related to this article.

Figures

Fig. 1
Fig. 1
In (a) a photograph of the guinea pig cochlea is depicted. A flat-field corrected intensity measurement is shown in (b). The homogeneous character of the cochlea can be seen as well as the position of the strongly absorbing implant. The trace recovered by the single-material phase-retrieval algorithm applied to the corrected intensity measurement in (b) is depicted in (c).
Fig. 2
Fig. 2
Illustration of the two reconstruction approaches using the example of a simulated cylinder. Conventionally, for every projection the trace is recovered by means of the single-material phase-retrieval algorithm of Paganin et al. (PAG) [8]. The volume is then reconstructed using the filtered back-projection (FBP) algorithm. In comparison, we use a model-based iterative reconstruction algorithm (MBIR) [15], which recovers the volume directly from the measured intensities. Thereby, the whole image formation is modeled, including the statistical properties of the x-rays, attenuation, phase-shifts, propagation and prior knowledge about the sample.
Fig. 3
Fig. 3
Comparison of the two reconstruction approaches for a zoomed region of a tomographic slice. The positions of these views are depicted by the red rectangles in the small previews of the whole slices in the upper right corner. The density values - not quantitative on an absolute scale - are displayed using a linear grayscale. The result of the conventional approach is depicted in (a), whereas the iterative approach yields the result depicted in (b).
Fig. 4
Fig. 4
Rendering of the cochlea for the two reconstruction approaches. The position of the implant is segmented from a conventional FBP reconstruction on the measured intensities and depicted in red. In (a) the rendering of the cochlea is performed for the conventional reconstruction and (b) uses the model-based iterative approach. The inserts show zoomed excerpts detailing the degradation caused by the artifacts arising from the phase-retrieval step of the conventional approach.
See this image and copyright information in PMC

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