I can highly recommend the screeningBee workflow manager “BeeWM”. Its not published yet, but working very well and has been used to process thousands of plates. It currently supports DRMAA clusters, SGE, UGE, and LSF. Adding support for other clusters is not super hard, and I could probably help.
BeeWM supports not only CellProfiler, it can execute any kind of executable. It works very well with CellProfiler though, and that is one of our core use cases.
It can fully batch CellProfiler jobs on the cluster, i.e. you can start from a pipeline and images only, and it will process all images. You can also automatically split into batches of image sets, like 200 images per job or whatever. Furthermore you can create more complex workflows, with multiple (possibly chained) jobs. As an example, we execute shading correction on all images first, then we execute CellProfiler on the shading-corrected images. If a job in the queue fails (multiple times), subsequent jobs are aborted. Of course it supports email notification to admins and users, depending on success or error. It also supports automatic re-tries in case of errors. It understands the concept of multiple cluster queues with different runtimes (i.e. for shorter and longer jobs). And it has many other helpful goodies. For example it can copy your data to a cluster scratch before execution, and copy results back afterwards. Its programmable via a REST API. And its fully open source.
Let me know if you’re interested and/or need help. Download from https://www.screeningbee.org/
Disclaimer: I’m one of the main authors of BeeWM