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Probe-based confocal laser endomicroscopy is a recent tissue imaging technology that requires placing a probe in contact with the tissue to be imaged and provides real time images with a microscopic resolution. Additionally, generating adequate probe movements to sweep the tissue surface can be used to reconstruct a wide mosaic of the scanned region while increasing the resolution which is appropriate for anatomico-pathological cancer diagnosis. However, properly controlling the motion along the scanning trajectory is a major problem. Indeed, the tissue exhibits deformations under friction forces exerted by the probe leading to deformed mosaics. In this paper we propose a visual servoing approach for controlling the probe movements relative to the tissue while rejecting the tissue deformation disturbance. The probe displacement with respect to the tissue is firstly estimated using the confocal images and an image registration real-time algorithm. Secondly, from this real-time image-based position measurement, the probe motion is controlled thanks to a simple proportional-integral compensator and a feedforward term. Ex vivo experiments using a Stäubli TX40 robot and a Mauna Kea Technologies Cellvizio imaging device demonstrate the effectiveness of the approach on liver and muscle tissue.