.

I'd be careful about using anything that puts out fumes like a sharpie or oil-based paints to mark them. They're respiratory systems are pretty easily irraitated by things like that.

Maybe find something water-based instead.
 
Do you just want to know these things about the feathers or is it the experimenting for yourself that you want?

I wasn't going to say anything but if your chicks are stressed by the process and it is just the results you want - the info is in at least some of the old poultry textbooks from the 1950s.
 

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