ARTICLE liu_OPTICA_2022/IDIAP Mechanical Artifacts in Optical Projection Tomography: Classification and Automatic Calibration Liu, Yan Dong, Jonathan Pham, Thanh-An Marelli, François Unser, Michael Image quality Image registration Reconstruction algorithms Spatial resolution Three dimensional imaging X ray computed tomography EXTERNAL http://publications.idiap.ch/attachments/papers/2022/liu_OPTICA_2022.pdf PUBLIC Opt. Continuum 1 12 2577--2589 2022 10.1364/OPTCON.474540 doi 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.