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Total Variation-Based Reduction of Streak Artifacts, Ring Artifacts and Noise in 3D Reconstruction from Optical Projection Tomography

Published online by Cambridge University Press:  13 October 2015

Jan Michálek
Jan Michálek*
Affiliation:
Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
*
*Corresponding author.michalek@biomed.cas.cz
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Abstract

Optical projection tomography (OPT) is a computed tomography technique at optical frequencies for samples of 0.5–15 mm in size, which fills an important “imaging gap” between confocal microscopy (for smaller samples) and large-sample methods such as fluorescence molecular tomography or micro magnetic resonance imaging. OPT operates in either fluorescence or transmission mode. Two-dimensional (2D) projections are taken over 360° with a fixed rotational increment around the vertical axis. Standard 3D reconstruction from 2D OPT uses the filtered backprojection (FBP) algorithm based on the Radon transform. FBP approximates the inverse Radon transform using a ramp filter that spreads reconstructed pixels to neighbor pixels thus producing streak and other types of artifacts, as well as noise. Artifacts increase the variation of grayscale values in the reconstructed images. We present an algorithm that improves the quality of reconstruction even for a low number of projections by simultaneously minimizing the sum of absolute brightness changes in the reconstructed volume (the total variation) and the error between measured and reconstructed data. We demonstrate the efficiency of the method on real biological data acquired on a dedicated OPT device.

Keywords

optical projection tomographymicroscopyartifactstotal variationdata mismatch
Type
Equipment and Techniques Development
Information
Microscopy and Microanalysis , Volume 21 , Issue 6 , December 2015 , pp. 1602 - 1615
Copyright
© Microscopy Society of America 2015 

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