Fraser GM, Milkovich S, Goldman D, Ellis CG. Mapping 3-D functional capillary geometry in rat skeletal muscle in vivo. Am J Physiol Heart Circ Physiol 302: H654 -H664, 2012. First published December 2, 2011; doi:10.1152/ajpheart.01185.2010.-We have developed a novel mapping software package to reconstruct microvascular networks in three dimensions (3-D) from in vivo video images for use in blood flow and O2 transport modeling. An intravital optical imaging system was used to collect video sequences of blood flow in microvessels at different depths in the tissue. Functional images of vessels were produced from the video sequences and were processed using automated edge tracking software to yield location and geometry data for construction of the 3-D network. The same video sequences were analyzed for hemodynamic and O 2 saturation data from individual capillaries in the network. Simple user-driven commands allowed the connection of vessel segments at bifurcations, and semiautomated registration enabled the tracking of vessels across multiple focal planes and fields of view. The reconstructed networks can be rotated and manipulated in 3-D to verify vessel connections and continuity. Hemodynamic and O2 saturation measurements made in vivo can be indexed to corresponding vessels and visualized using colorized maps of the vascular geometry. Vessels in each reconstruction are saved as text-based files that can be easily imported into flow or O2 transport models with complete geometry, hemodynamic, and O2 transport conditions. The results of digital morphometric analysis of seven microvascular networks showed mean capillary diameters and overall capillary density consistent with previous findings using histology and corrosion cast techniques. The described mapping software is a valuable tool for the quantification of in vivo microvascular geometry, hemodynamics, and oxygenation, thus providing rich data sets for experiment-based computational models. microcirculation; oxygen transport; microvascular network geometry; functional capillary density; computer-assisted vascular mapping SINCE AUGUST KROGH first developed a simple model of O 2 diffusion from an idealized capillary into the surrounding tissue (15), researchers have worked to more accurately characterize the microvasculature to develop more realistic models of tissue oxygenation and to provide data for testing these models. To provide a clear picture of the microcirculation as a whole, a variety of tools have been developed to quantify network morphology and flow hemodynamics and to measure conditions within the blood itself. These tools include stereology, microscopy, histology, spectrophotometry, and a variety of mathematical constructs (9,11,16,20,22,27). Drawing on several of these tools, integrated approaches have been made to represent blood flow and O 2 delivery using computer modeling (8,23,25). The majority of modeling efforts have been concentrated on the simplification of complex network geometry using predominantly parallel arrays of microvessels co...