A method of recalibrating to compensate for thermal drift between a micro-imaging system and a sample integrated circuit (IC) under investigation determines a planar drift using a cross-correlation between a reference calibration image and a recalibration image, and further determines a focus drift from a difference between a reference focus setting and a recalibration focus setting. The recalibration is performed on detection of a recalibration trigger event, such as expiry of a recalibration time interval. The recalibration time interval can be adaptively adjusted based on a magnitude of the thermal drift. Tile images captured since a last recalibration are recaptured if the thermal drift is too great for reliable image compensation. The system ensures seamless assembly of tile images into image photo-mosaics and increases image photo mosaic throughput.