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.




Hi Peter,

Are you using a Macintosh system? I am assuming you are using MatLab. We saw many Java errors using Max OS X 10.3.x and MatLab 7 R14 SP2. Upgrading to SP3 solved this problem and we no longer see Java errors. Does the MatLab prompt spit out many of these java errors before closing? If so, I think this upgrade would solve the issue.



Hi Mike,

No I am using Windows2000 Professional v5.0 build 2195 with service pack 4 installed. These machines have 0.5GB RAM and >25GB free local hard disk space. Any other suggestions? Thanks



Whoops! Sorry I missed that last sentence!

Are you using the MatLab version of CellProfiler or the Windows compiled version? If you are using MatLab I would still try to upgrade to the latest version. Another issue might be upgrading Java to its newest version. I have honestly never run into this error on a PC (although we are using XP professional) and have only witnessed it on the Macintosh.

One other possibility is the lack of RAM. We typically do large batches of images on machines with > 1GB of RAM. If you cannot try on a system with more memory, you can try closing all of the display windows during the run. You do not need to have any of the displays showing for the analysis to run. This can reduce the amount of memory needed by the system. Although this sounds more like an issue with MatLab/Java, I would still give this a shot and let me know how it works out.



Hi Mike,

I obtain the NullPointerException with the following software:

Windows PC binary version 1.0.3215 of CellProfiler
Java version 1.5.0_06

I believe these are the latest versions for both items.

I followed your suggestion of shutting all display windows after initiating the run. This solved the problem. I could process 960 cycles without generating any errors. Thanks for your help.