I have a simple pipeline which works nicely with the MeasureObjectIntensity only. As soon as I add afterwards the MeasureObjectAreaShape module to the pipeline, cellprofiler returns a lot of error messages through the console like (java… source unknown etc). The measurement should be performed on the same objects as with MeasureObjectIntensity module. I noticed that the MeasureObjectAreaShape module does not offer any option to define a source image, as opposed to the MeaureObjectIntensity module. Might this be the reason? If you like, I can send you the pipeline.