We present CoralCT, a software application for analysis of annual extension, density, and calcification in coral skeletal cores. CoralCT can be used to analyze computed tomography (CT) scans or X-ray images of skeletal cores through a process in which observers interact with images of a core to define the locations of annual density bands. The application streamlines this process by organizing the observer-defined banding patterns and automatically measuring growth parameters. Analyses can be conducted in 2- or 3-dimensions, and observers have the option to utilize an automatic band detection feature. CoralCT is linked to a server that stores the raw CT and X-ray image data, as well as output growth rate data for hundreds of cores. Overall, this server-based system enables broad collaborations on coral core analysis with standardized methods and—crucially—creates a pathway for implementing multi-observer analysis. We assess the method by comparing multiple techniques for measuring annual extension and density, including a corallite-tracing approach, medical imaging software, 2-dimensional versus 3-dimensional analyses, and between multiple observers. We recommend that CoralCT be used not only as a measurement tool but also as a platform for data archiving and conducting open, collaborative science.