Artifacts in optical projection tomography due to refractive-index mismatch: model and correction

Optical projection tomography (OPT) is a powerful tool for three-dimensional (3D) imaging of mesoscopic samples. While it is able to achieve resolution of a few tens of microns over a sample volume of several cubic centimeters, the reconstructed images often suffer from artifacts caused by inaccurate calibration. In this work, we focus on the refractive-index mismatch between the sample and the surrounding medium. We derive a 3D cone-beam forward model of OPT that approximates the effect of refractive-index mismatch. We then implement a fast and efficient reconstruction method to correct for the induced seagull-shaped artifacts on experimental images of fluorescent beads.