So, in light of the issues I mentioned here, I am continuing with CellProfiler 3.0 for now.
However, I have encountered an issue on Windows 7 while refurbing some of the workstations in our facility. We are trying to maintain a clean separation between user data and system files on the drives in our workstations, so all applications are installed on the system drive (let’s call it ‘C’), while a separate drive (D) holds all user profiles.
Under these circumstances (CellProfiler installed on C, user profile on D), CellProfiler does not launch - it would appear that it is searching for something in the user’s AppData folder, which it expects to find on the same drive it is installed on.
As a workaround, I have reinstalled CellProfiler on the D drive, which has resolved the issue, but is not an ideal solution for us.