  Endomicroscopy is an emerging imaging modality, that facilitates the
acquisition of in vivo, in situ optical biopsies, assisting diagnostic and
potentially therapeutic interventions. While there is a diverse and constantly
expanding range of commercial and experimental optical biopsy platforms
available, fibre-bundle endomicroscopy is currently the most widely used
platform and is approved for clinical use in a range of clinical indications.
Miniaturised, flexible fibre-bundles, guided through the working channel of
endoscopes, needles and catheters, enable high-resolution imaging across a
variety of organ systems. Yet, the nature of image acquisition though a
fibre-bundle gives rise to several inherent characteristics and limitations
necessitating novel and effective image pre- and post-processing algorithms,
ranging from image formation, enhancement and mosaicing to pathology detection
and quantification. This paper introduces the underlying technology and most
prevalent clinical applications of fibre-bundle endomicroscopy, and provides a
comprehensive, up-to-date, review of relevant image reconstruction, analysis
and understanding/inference methodologies. Furthermore, current limitations as
well as future challenges and opportunities in fibre-bundle endomicroscopy
computing are identified and discussed.
