CellProfiler is a modular software in which you can quite easily set up your own pipeline. However, there are many examples online available which you can take as a starting point. Just go here and check which one does the closest to what you are trying to do: https://cellprofiler.org/examples
Thank you..I have already checked that site but the pipeline that I want is not in the list. So,I tried another software for myotube assessment. Myotube Analyzer app looks quite useful and I will try it out.