In vivo imaging technologies such as optical coherence tomography (OCT) and rodent models enable longitudinal studies of different ophthalmic pathologies and their underlying physiological changes. In this work a custom-made high resolution polarization sensitive OCT system is used to image the posterior eye of small rodents like mice and rats. En-face projections at certain depths/levels in the three-dimensional (3D) reflectivity images enable to visualize different vascular structures in the retina as well as in the choroid. Further, phase resolved motion contrast based OCT angiography allows to create vascular maps with a high contrast to distinguish between static tissue and dynamic scatterers such as red blood cells. The levels of the vascular maps are determined by a semi-automatic approach in which layers of the retina are segmented in a first step. In a second step the projection level can be adjusted by the operator to restrict the volume in which the en-face projection is carried out. To demonstrate the functionality of this approach rats and mice of different strains were imaged. The anesthetized rodents were scanned with an angle of up to 28° × 28°. Respiration induced motion artefacts were compensated by post-processing. The vascular maps based on the OCT reflectivity information as well as on the phase variance showed that the resolution of the custom-made systems is suitable to resolve small retinal capillaries in the outer plexiform layer. Further, larger vessels within the nerve fiber layer and the inner nuclear layer as well as in the choroid were visualized by the proposed approach.
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