I am using CellProfiler for a translocation assay. A test of my pipeline works fine with 5 cycles ( 2 images per cycle). If I load 960 cycles worth of images, I get a Java NullPointerException in the console window around cycle 50-55. Windows keep popping up but the application makes no further progress and has to be killed with task manager. I am using the SpeedUpCellProfiler module, saying yes to clear the memory. I successfully restart but again after 50-55 more cycles, same problem. This happens on two different Win2000 Professional machines. I am open to suggestions.