Java error on 64 bit system-GUI problems


I have recently installed CellProfiler (both 32 and 64 bit) on a QuadCore Xeon workstation with Windows XP64bit. It is really amazing how fast it is compared to our old computer, thanks a lot again for CellProfiler, it is a really great tool. I have a somehow nasty problem, however: When trying to use some Data Tools (like show data on image) or even to load a new pipeline sometimes nothing happens, there is just an error message on the console saying that an unexpected Java error had occurred, Array out of range… end ending with “Error while evaluating UICallback”. The window to select the pipeline file or the output file does not even appear. I would like to send you the exact message, but it is quite long and I cannot find the log file. Is there any? This error occurs somehow randomly, sometimes it also works again without any obvious reason, sometimes I have to restart CellProfiler or even the computer, although there is no crash, in order to load a pipeline. In addition to this, with the latest version and the Show data on Image tool, if you get past the first dialogue (choosing the output file), after the last step (choosing the image file the data should be displayed on) there is the following error message: “Error opening image erste10x_A01_s3_w2.TIF in folder D:\StefanF\screencherrypicking\20080505erste10x Stack: ShowDataOnImage in C:\Documents and Settings\user\Desktop\CellProfiler_1.0.5122_XP64\CellProfiler_1.0.5122_XP64\CellProfiler_mcr\DataTools\ShowDataOnImage.m (146)” from CellProfiler (not on the console) and no image is displayed. This is reproducible also on another 32 bit computer.

Any ideas what is going on or how I can find out?

Thanks a lot,



Hi Stefan,

Glad to hear you like the software!
The ShowDataonImage error is a bug which was introduced around version 4957. It has been fixed, but isn’t available to the public until the next release (which may be as soon as next week). Since it looks like you’re using the compiled version, the workaround I would suggest is to download a previous version of CP and run the ShowDataOnImage DataTool on the previous version (v4844 should be fine).

I looked at the 5122 version code, and it looks like this bug should affect the DataTools ShowDataOnImage and TrackingTool, and the module SubtractBackgroundSingle. (For any power users out there, the bug was in CPimread.m, which now has only one input argument and no handles).

Another tip to note, is that you need to select the correct image for ShowDataOnImage to work properly, otherwise it errors. There is a dialog box which pops up that tells you which image to select, but sometimes this window is hidden behind windows.

I don’t know why you would have a trouble loading a pipeline, however, unless you had a previous error in the session. It’s best to restart CellProfiler in this case. Also, there is no error log file per se, though the console window should show all the relevant error output, which you can cut & paste.

Hope this helps!