The architecture of biological tubes must be tightly regulated for an organism’s survival. Understanding the mechanisms of tube size control requires the ability to quantify many aspects of tube structure such as tube length and diameter and cell shape. Our objective was to develop computational tools that could robustly measure differences in morphology of the Drosophila trachea, using open source and generally accessible software. Although programs to measure planar epithelia exist, few are able to process the more complex problem of a 3-D tube and measure cells on a highly curved surface. We acquired confocal images of the tracheal dorsal trunk and segmented the apical surface and overlying cells using Ilastik, an open source image analysis tool funded by the HHMI and Heidelberg Collaboratory for Image Processing. The segmentation data were imported to Matlab, where we used a marching cubes algorithm to create a tube skeleton, automatically detected branches, and mapped apical cell outlines on the tube surface. From this data, many features of interest can be calculated. Those that we focused on include tube length, luminal volume, cross-sectional regularity, and cell size and orientation relative to the local trunk axis. We are still optimizing and validating our code, but preliminary analysis of src42A26-1 mutants, which have tube length defects and increased variation in cell orientation, produced results comparable to the previous studies done by Nelson et al. (2012) and Förster and Luschnig (2012). The major cell axes of src42A26-1 mutants tend to be orthogonal to the tube axis, resulting in shorter dorsal trunks.