Cannot load large images, java heap space error?

Hi, I have enjoyed using cellprofiler in the past to generate some quite useful data however now I would like to process relatively much larger images. I’m currently using a ‘tiling’ microscope to stitch together images of whole microarrays, so the images I am dealing with are tiffs between 200mb and 1.5gb (and potentially even bigger in the future). Currently, I am using windows 64bit and have downloaded cellprofiler 2.0, but i am not able to open images that are even 40mb in size, without the program crashing or freezing or taking forever to respond. I am also given the ‘java heap space error’ message on startup of the images, my computer has 16gb of available RAM, and i think this is available to the program since i’ve seen it max that out (even when dealing with a 200mb image) and then refusing to open the images.
Please tell me if it is possible to use cellprofiler to process large images such as these. Perhaps you can email me directly as well at

Many, many thanks!
Michael Nastasie

Having a lot of RAM does not mean that CellProfiler (or rather the Java Virtual Machine under which CP2 is running) uses all of it. You should try to assign more RAM to the JVM.

I haven’t tried it myself, but I think this can be done with the –jvm-heap-size switch to CP2. Try starting CP2 like this:

to give it 4 GB of RAM.