Java Exception on pressing Update inside Metadata module

Hi guys,

I just restarted CP (CellProfiler_2.1.2_win64_r20150128120936.exe) and wanted to start the analysis, but when I pressed update (below the divider) inside Metadata I got:

Traceback (most recent call last):
File “cellprofiler\gui\cornerbuttonmixin.pyc”, line 124, in on_corner_left_mouse_up
File “cellprofiler\gui\moduleview.pyc”, line 3908, in on_corner_button_clicked
File “cellprofiler\modules\metadata.pyc”, line 917, in update_table
File “cellprofiler\pipeline.pyc”, line 2699, in get_image_plane_details
File “cellprofiler\pipeline.pyc”, line 2665, in __prepare_run_module
File “cellprofiler\modules\metadata.pyc”, line 738, in prepare_run
File “javabridge\jutil.pyc”, line 830, in call
File “javabridge\jutil.pyc”, line 797, in fn
JavaException: GC overhead limit exceeded

Any ideas?


Hi Sebi,

This occurs when you are essentially running out of memory to run the process smoothly. The amount of memory allocated to Java at the outset defaults to a typical value that works for most cases, but sometimes for larger analyses, it’s not enough. You can increase the amount of memory for this purpose by running CellProfiler from the command line.

  • From the Start menu, type “cmd”
  • In the command window that appears, use ‘cd’ to switch to the folder where you sinstalled CellProfiler.
  • Type “CellProfiler --help” to get the full list of options. One of them will be “—jvm-heap-size” where you can set the memory.
  • If you run CellProfiler with something like CellProfiler --jvm-heap-size=1gyou can overcome this error with a high enough value.