The Open Microscopy Environment (OME) provides a standardized, open- source environment in which microscope images can be acquired, analyzed, and visualized. The OME analysis system provides a modular architecture for analyzing these images. Analysis routines are broken down into their logical components, which are coded separately as modules. Modules are linked together into analysis chains by using semantic data types to form data dependencies between the modules. Tools are being developed to allow these chains to be pieced together graphically from a toolbox of analysis modules, and to allow the user to extend the toolbox in a seamless, language-independent manner. The execution of an analysis routine against a set of images is automated, allowing the user to focus on the design of the analysis routine, rather than the details of computation, and allowing the analysis engine to perform various optimizations, such as the reuse of analysis results.