The pipeline from Rodeheffer Lab is not recent, it's actually aimed for specific input.
And if you're new to CellProfiler, I would recommend to try build some simple modules on your own to understand each module better.
- If in NamesAndTypes, you load the image as color image, you first need to convert it to gray, for example adding a module called ColorToGray. If this is a single channel image, in NamesAndTypes, you can load the image as gray image
- You then need to invert the image by ImageMath, because you now have the droplet-membrane brighter than the droplets. You'd want to have the droplets brighter than the droplet-membrane.
- Then add IdentifyPrimaryObjects, and experiment different algorithms to see which works best for you. I think Global > Otsu and Declumping by using intensity,
Good luck and have fun.