New version of cellprofiler does not open

Hi – On startup today I had a message that a new version of cellprofiler 2.0 was available so I downloaded the new version of cellprofiler 2.0 (32-bit windows version) and now the program does not open – I only get the black window, which has no message in it. I tried uninstalling and re-downloading, and had the same problem.

Hi ditag,
Which operating system are you using? (Windows XP / Vista / 7, 32-bit or 64-bit) Also, could you open a command prompt (from start, select “Run” and type “cmd”) and, in the command window do the following:

> c:
> cd "\Program Files\CellProfiler"
> CellProfiler --help

CellProfiler should print a help message and exit. Could you tell us if it does that? Also any error message if it doesn’t?


Thank you for your swift reply. Something must have been happening in the background – the first time the program finally opened after ~30 minutes, the next time after ~5 min, and now it opens straight away. (the system is windows 7 32-bit) thanks! Dita

Thank goodness,
And thanks for getting back to us. I have noticed that it can take a while for CellProfiler to start the first time. It’s worth some time for us to investigate this. Please don’t hesitate to contact us if you have any further difficulties.


Hi ditag,
I’ve found a machine here that’s having similar problems to yours. The anti-virus software is taking an inordinate amount of time to investigate the libraries that CellProfiler uses and this makes CellProfiler take a long time to open - the anti-virus vendor is Sophos, but it’s possible others have similar problems. Is it possible for you to turn off your anti-virus checking, restart CellProfiler and check the load time?

The problem we’re having is related to the Windows installation tools and is documented here: … tid=115583


I had the exact same problem with sophos antivirus. Easiest solution for me was to uninstall sophos and replace with another antivirus product. It fixed the whole slow load time at application startup bug for me.