Helicobacter pylori is one of the most prevalent bacterial pathogens, inflicting hundreds of thousands of peptic ulcers and gastric cancers to patients every year. Antibacterial treatment of H. pylori is complicated due to the need of combining multiple antibiotics, entailing serious side effects and increasing selection for antibiotic resistance.

We present a technique for correcting image artifacts caused by refractive index distributions in Scanning LaserOptical Tomography (SLOT) and Optical Projection Tomography (OPT). Projection images can be distorted due to the presence of a refractive index distribution around the sample. We consider the special case of a refractive index distribution given by a capillary around a sample. The particular application we are interested in is in vitro imaging of cell spheroids in a glass capillary. Numerical simulations and experimental results are used to illustrate the connection between the Radon transform and the refracted projection. Thereupon we will describe a technique that transforms refracted projections to parallel ray Radon projections and thus allows artifact free reconstruction within the sample volume.

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