With the increasing maturity of optical biopsy techniques,
routine clinical use has become more widespread. This wider adoption of
the technique demands effective tracking and retargeting of the biopsy
sites, as no visible markers are left following examination. This study
presents a high-speed framework for intra-procedural retargeting of probebased
optical biopsies in gastrointestinal endoscopy. A probe tip localisation
method using active shape models and geometric heuristics, which
eliminates the traditional dependency on shaft visibility, is proposed for
automated initialisation. Partial occlusion and tissue deformation are addressed
by exploiting the benefits of indirect and direct tracking through
a novel combination of geometric association and online learning. Robustness
to rapid endoscope motion and improvements in computational
efficiency are achieved by restricting processing to the automatically
detected video content area and through a feature-based rejection of
non-informative frames. Performance evaluation in phantom and in-vivo
environments demonstrates accurate biopsy site initialisation, robust retargeting
and significant improvements over the state-of-the-art in processing
time and memory usage.