We're aware that some users are having trouble opening CellProfiler on the latest Mac OSX security patch. We're working on resolving this, in the meantime you may want to build from source (see below).
Note 1: On Mac, after downloading, put CellProfiler in your Applications folder and ctrl-click (or right-click) and choose Open. Otherwise, you will receive a warning: “CellProfiler can’t be opened because it is from an unidentified developer”.
Note 2: Ignore the warning “Error loading pipeline file” - just click OK.
Note: On Windows, after downloading and launching CellProfiler, if you get the “Windows protected your PC” message, click “More info” to allow you to hit “Run anyway” to install.
Source code available on Github