General running speed

Hi all,

I’ve been using CellProfiller for a couple of applications in both immuno cytochemistry and fluorescence microscopy. It works great in every thing I’ve tried it for so far. The slight problem I have is the general running speed, which breaks down into two parts: 1. I’m using 3800x2000 pixel images in a total of 10 modules on a Core2Quad Q8300 PC with a decent graphics card. Each image takes ~10mins to process (EnhanceOrSuppress features taking the longest). Does this sound OK? could it be improved by perhaps running on a faster, but single-core processor? 2. The windows detailing each cycle that are left open at the end of the process are nearly impossible to manipulate. For example if I want to view my “Identify Primary Objects” window, it may take 30-60 seconds to select this from the taskbar. Once active, the window make take 30-60seconds to zoom in on a section, or even a minute to maximize the window.

I’m running v.10415 on Vista64. Thanks in advance for any help.


I have a few suggestions that might be helpful:

  • Use a 64-bit computer:
    64-bit have a higher memory overhead than 32-bit machines.
  • Downsample/crop your large images:
    For large images, consider downsampling the image prior to loading in CellProfiler. Alternately, you might try splitting the image into non-overlapping tiles and processing each separately. Finally, if none of these are an option, you could use the Resize module in CellProfiler.
  • Use module windows sparingly:
    Each module window takes a certain amount of time and memory to produce. A single window which produces multiple panels (such as IdentifyPrimaryObjects), each of which containing a very large image, will probably increase the performance overhead until CellProfiler becomes unmanagable. Use Test mode to preview the results but once you are ready for the full analysis run, select Window > Close all open windows to remove the windows that already exist, and then Window > Hide all windows on run** to prevent window creation.