Background: Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment. Results: Here, we describe CellProfiler Analyst, open-source software for the interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments. Conclusion: The system enables interactive data exploration for image-based screens and automated scoring of complex phenotypes that require combinations of multiple measured features per cell.