A functional microcirculation is vital to the survival of mammalian tissues. In vivo videomicroscopy (IVVM) is often used in animal models to assess microvascular function, providing real-time observation of blood flow in normal and diseased tissues. To extend the capabilities of IVVM, we have developed a contrast enhanced system, with post-processing video analysis tools that permit quantitative assessment of microvascular geometry and function in vital organs and tissues. Fluorescein Isothiocyanate labeled Dextran (250kDa) was injected i.v. into anesthetized mice to provide intravascular fluorescence contrast with darker red blood cell (RBC) motion. Digitized video images of the microcirculation in a variety of internal organs (e.g. lung, liver, ovary, kidney) were processed using computer based motion correction to remove background respiratory and cardiac movement. Stabilized videos were analyzed, to generate a series of functional images revealing microhemodynamic parameters, such as plasma perfusion, RBC perfusion and RBC supply rate. Fluorescence contrast revealed characteristic microvascular arrangements within different organs, and images generated from video sequences of liver metastases showed a marked reduction in the proportion of tumor vessels that were functional. Analysis of processed video sequences showed large reductions in vessel volume, length and branchpoint density, with a near doubling in vessel segment length. This study demonstrates that post-processing of fluorescence contrast video sequences of the microcirculation can provide quantitative images useful for studies in a wide range of model systems.