We present a video analysis and content-based video query and retrieval system for research videos arising from biological microscopy (a) that uses image processing procedures to identify objects and events automatically within the digitized videos, thus leading to the generation of content information (specific intrinsic metadata) of high information value by automated analysis of their visual content, and (b) that permits subsequent queries to be performed on the specific intrinsic metadata thus generated, allowing important factual and analytical information to be obtained and selected video sequences matching the query criteria to be retrieved. Such a system requires the novel use of image and video processing techniques, and new approaches to the organization, accessing and querying of video metadata databases.