I have been trying for a while to install from source CellProfiler 2.0 on a MAC with OS X 10.8. (I am trying to process some large images, and the compiled version and pipeline seem to be working perfectly on smaller images, but not on the larger ones).
Thanks to the various wiki, I got somehow pass few initial problems, but right now I a REALLY stuck on the wxPython module. It seems incompatible with the 64 bit version. I may be doing something else wrong, but I would really appreciate any suggestion on this.
Thanks a lot,
You are not alone in this. wx for Mac in 64-bit mode is not compatible, which is frustrating. If you can get it to work, please tell us!
However, our workaround is this – use headless. In the 2.1 (very beta) version of CP’s master branch, you can fire up the GUI and in Analysis Mode (i.e. non-Test Mode) the multiprocessing workers run headless, without importing wx. Unfortunately, we don’t have a way to utilize Test Mode on Mac in 64-bit which uses wx of course, so it may be hard for you to do image assay development. Our only suggestion is for you to find a 64-bit Windows machine to do image assay development on, but at least you ought to be able to run your large-image analysis on Mac in 2.1.
Hope that helps,
After some additional pain, I just switch to a Linux Virtual Machine on the Mac, using VirtualBox and Ubuntu 13.04.
It was a breeze to setup and it is working with no appreciable loss of performance, probably faster than the native 32 bit…
You may consider uploading a Virtual Machine on the Web site for everybody that may like such a shortcut…
Thanks for the explanations,
Interesting solution/workaround! I hadn’t thought to go that far (we have Windows VMs here, so I can fall back to those). I will test this myself when I get some spare time. Thanks for the suggestion!