The InputExternal and OutputExternal modules are placeholders if CellProfiler is run programatically. For example, another program, e.g., a plugin to ImageJ, is provided with a CellProfiler pipeline. This program should then replace the input modules with InputExternal modules and prompt the user what inputs should be supplied to the pipeline through InputExternal. The program should also specify which inputs are to be sent back to the source program via OutputExternal. The calling program would insert the images into the image set before running the pipeline and remove the images from the image set at the end.
See also RunImageJ