CellProfiler runs faster on Mac


I was processing large images with the most recent version of CP (r11710) on my computer, which is Windows7, and it was very slow, almost crashing. A friend of mine had a Mac and we just wanted to try it on his computer. We found that the program runs much faster on Mac than PC. Since then I tried very powerful PCs (Win7 and Windows server 2008), kind of supercomputers, and they still do weaker than an ordinary Mac! I was wondering whether anybody has noticed this difference, and wanted to let the developers know this, maybe there is a way to make it faster on PCs.

Hi Amir,

I’m not certain of the difference, but here are some thoughts:
(1) Antivirus scanners can slow down CP markedly. Of course, Windows machines always have AV running (right?!), but many Macs don’t. Try adding an exception in your Windows AntiVirus scanner for the whole CP installation directory in Windows.
(2) I don’t think it’s useful spending time to debug this, since we have been developing for 1.5 years past version 11710! If you want to try a beta version that has a lot of bug fixes which might have slowed you down, try the 2.0 version here:
And if you are really bold, you can try the 2.1 version on the same page which should run significantly faster than 11710, since it takes advantage of multiple cores on your CPU. Though the interface has changed and do please read all the caveats before you start using it for real image analysis.

Let us know how it goes.