A single pipeline in CellProfiler with UnmixColors or ColorsToGray may be possible, but as I tried myself, it may involve quite complex image filtering and morph.
So I would suggest you to try Ilastik with at least 4 classes of pixels:
- The bright green dots
- The blue dots
- The black holes
- The giant syncytium (dimmer green) near the black hole peripheral.
Then export the probability maps for each of these classes from ilastik and use them as inputs for CellProfiler (please do a search “ilastik” in the forum, there’re many examples)
The bright green dots will be the easiest targets, because they will stand out clearly.
You can then do a quick segmentation on green dots and blue dots in CellProfiler and count them, i.e. unfused cells over total numbers of cells.
You can also measure the areas of giant syncytium , and compare it with whole image area and black hole area to have an idea of how aggressive was the cell-fusion process.