  Optical projection tomography (OPT) is a powerful tool for biomedical
studies. It achieves 3D visualization of mesoscopic biological samples with
high spatial resolution using conventional tomographic-reconstruction
algorithms. However, various artifacts degrade the quality of the reconstructed
images due to experimental imperfections in the OPT instruments. While many
efforts have been made to characterize and correct for these artifacts, they
focus on one specific type of artifacts, whereas a comprehensive catalog of all
sorts of mechanical artifacts does not currently exist. In this work, we
systematically document many mechanical artifacts. We rely on a 3D description
of the imaging system that uses a set of angular and translational parameters.
We provide a catalog of artifacts. It lists their cause, resulting effects, and
existing correction methods. Then, we introduce an automatic calibration
algorithm that is able to recover the unknown system parameters fed into the
final 3D iterative reconstruction algorithm for a distortion-free volumetric
image. Simulations with beads data and experimental results on a fluorescent
textile fiber confirm that our algorithm successfully removes miscalibration
artifacts in the reconstruction.
