That's what I was thinking if their bones have to be at least partially empty then some of those stem cells must be somewhere else. That makes a lot of sense.

That's cool it seems way more complex and diverse than I thought. I thought all bones were calcium like matrices with small differences but turns out birds have some other composite

Then downstream, depending on its properties it may be difficult to separate it from contaminants from the upstream processes mentioned above. Attachment to some resin based on charge or a binding site can be used in a chromatography setup. Solubility or inertness in some chemical can help. Finally regular filtration or some sort of hollow fibre tff setup.