CellProfiler very slow with large images

Hi all, I hope the data treats you well.

I wanted to ask how your machines respond to images greater than 1024x1024 in the user interface. I find that large images will be unbelievably laggy on simply resizing the window. I have found this to be the case on multiple high spec workstations that we run, so it’s not the hardware. It’s the case on both Win 7 and Win 10, both 64bit. It appears to almost be independent of PC specs, as the latest huge workstation I built appears just as laggy as the Dell workstation I was running before that.

I tend to setup a crop at the start of my pipeline and then remove that once happy with the settings. I understand that some of the analyses can be slow on large images, but even viewing is painful. The same image opened in Fiji for viewing is without lag.

This is becoming a bigger issue as more and more people come to me with larger images fomr sCMOS cameras.

I’d love for this part to be optimized, and ask if anybody knows of what I can do with my system to optimize the response of CP.


I’m hoping someone has a more technical reply but my first guess would be that the problem might resolve with CellProfiler 3.0. Have you seen the same behavior in one of our recent nightly builds? See “Nightly” midway down the page: http://cellprofiler.org/releases/

@Anne_Carpenter I think we’re still working out the kinks with the Windows nightly, I don’t think it’s available for public download yet. The ‘Nightly’ that’s there is probably still the (quite old) one.

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