If one cite properly, can start up firm use cell profiler at their commercial lab?
The source code at least has a BSD 3-Clause license. This appears to allow commercial use without much restriction.
Yes, CellProfiler can be used in commercial labs.
There are examples and tutorials available on the website:
https://cellprofiler.org/examples/ and https://cellprofiler.org/tutorials/
We also provide custom support: https://cellprofiler.org/supportplan/