Advancements in cell biology have made it possible to generate large quantities of human pluripotent stem cells (hPSC) in three-dimensional cultures in bioreactors. Volumetric imaging of hPSC cell aggregates with Scanning Laser Optical Tomography can provide insight into their physiology and growth behavior. Containing cell clusters in a glass capillary for in vitro imaging introduces a non-vanishing refractive index gradient into the field of view that will produce artifact in reconstructed tomographic images. The effects of refraction are studied by means of numerical simulations. Furthermore we present a method of correcting for the effects of refraction utilizing a reordering step for the projections before tomographic reconstruction. Removal of artifacts is successfully demonstrated on experimental data of human pluripotent stem cell (hPSC) clusters. This will enable long term in vitro studies of hPSC clusters with Scanning Laser Optical Tomography.