As far as I understand all matter is made of atoms so at the atomic level there wouldn't really be matter (wall, ground etc.) for the shadow to be cast on.
The paper the article is based on talks about "absorption imaging". Googling that I found another paper  in ArXiV which describes the method a little bit: "absorption imaging, where the attenuation of a laser beam passing through an atom cloud is measured, is the workhorse of ultracold atom experiments. The shadow cast by the atom cloud onto the CCD allows an estimation of the atomic column density."
And if I understood correctly, a CCD is a "charge-coupled device" , sort of a digital camera. And that's where the shadow falls.