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Updated: Nov 22, 2025

Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales
Published on: August 21, 2019
Generating large field of view en-face projection images from intra-acquisition motion compensated volumetric optical
Florian Schwarzhans1, Sylvia Desissaire2, Stefan Steiner3
1Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, 1090, Austria.
Abstract:
A technique to generate large field of view projection maps of arbitrary optical coherence tomography (OCT) data is described. The technique is divided into two stages - an image acquisition stage that features a simple to use fast and robust retinal tracker to get motion free retinal OCT volume scans - and a stitching stage where OCT data from different retinal locations is first registered against a reference image using a custom pyramid-based approach and finally stitched together into one seamless large field of view (FOV) image. The method is applied to data recorded with a polarization sensitive OCT instrument in healthy subjects and glaucoma patients. The tracking and stitching accuracies are quantified, and finally, large FOV images of retinal nerve fiber layer retardation that contain the arcuate nerve fiber bundles from the optic nerve head to the raphe are demonstrated.
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