CP utilisation of multi-core CPUs



Hi all,

Firstly I want to say a BIGGGGGGGGGGGGGGG thank you to anne carpenter and all those who are involved in the development of this software. And to those who respond to forum topics with really good advice.

The advice I have read through the forum, plus the help file, plus the tutorials has really given me the grounding I need in using CP. And I’ve only been using CP for less than 1 month.
I have since had many colleagues throughout the institute I’m working at, to take up the challenge of CP for their cell analysis.

I’m using HCS with the BD Pathway 855 for my project and hence I have a great amount of data to analyse. It was only through the lack of software claiming to be able to do auto-ROI, and failing that prompted me to find alternative. Hence, thanks to google as well.

Anyway, I’m currently using a dual-G5 mac which is ok, runs my pipeline 3.5times slower than a 4-core intel mac.

I’m just curious to know if CP takes advantage of multi-core CPU’s? …whether CP can run even quicker?

Kind regards,


Glad to hear that you have found CellProfiler to be useful for your experiments! Currently, CellProfiler does not utilize multiple cores, but you can run multiple instances of CellProfiler on your computer (in essence, running multiple pipelines at the same time). We are always trying to speed up the code, so incremental speed changes have been implemented. One way to run your pipelines a bit faster is to turn off the figure windows; they use a lot of memory.



Hi Martha!

Yes I have been running multiple pipelines… which is super handy!

If I turn off the figure windows, will the error messages still appear?



Yes, error messages will appear (if there is an error). By turning off the figure windows, you won’t see the windows for each individual module.


A little extra note, for those reading the thread who don’t already know - you can turn off figure windows in the main CellProfiler window: go to File > Set Preferences, and you will see Display Mode options. One of the options is to turn all windows off, but another option is for CellProfiler ask you, every time you use the Analyze images button, which modules’ figure windows you want to display (“Specify which windows to display” option).