Help with installing CellProfiler on the USC cluster

Hello,

We installed everything in order and when we run “python -v CellProfiler.py” it hangs just after this point:

/auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.pyc matches /auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.py

import cellprofiler.modules.classifypixels # precompiled from /auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.pyc

Can you tell me what error this is diagnostic for?

Hello!

I am still trying to figure out how to get “python -v CellProfiler.py” to stop stalling at import classifypixels.pyc. We are able to get ilastik to run both by using “python CellProfiler.py --ilastik” and “python -m ilastik.ilastikMain”. Please respond with anything that you think may help.

Thanks!

Hello again,

If we start CellProfiler with “python CellProfiler.py --log=10” This is the last entry:

/auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.pyc matches /auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.py

import cellprofiler.modules.classifypixels # precompiled from /auto/rcf-proj/met1/software/CellProfiler/cellprofiler/modules/classifypixels.py

I don’t know why but in the log file, every instance of the word classify is highlighted yellow. Could there be a syntax error?

Hello,

Turns out it was X windows, or something to do with exporting the display. CellProfiler will run ‘headless’. Thanks for looking!

Sorry for the delay in response. Glad you got it figured out!
-Mark