In the case of proton tomography, the "microscope" consists of an intense beam of electrons which strikes a hydrogen target. An electron can scatter from a proton in many ways, but here a single collision is sought, a rather rare event called deeply virtual Compton scattering (DVCS); the incoming electron scatters by sending a virtual photon (a high energy gamma ray) out ahead of it. This scatters not from the proton as a whole, but from one of the elementary quarks that together with the gluons are the building blocks of the proton. The quark re-emits a gamma ray but does not otherwise change its identity. In this way the original target proton retains intact.

Thus the overall reaction is as follows: an electron and proton collide and out comes an electron, proton, and gamma ray; the outgoing electron and gamma are detected, and from this a lot about the status of quarks inside the proton can be gleaned. For example, the spatial position of the quark inside the proton (transverse to the direction of the virtual photon) can be related to the angles and energies of the outgoing gamma ray. It's as if a quark had been removed from one place inside the proton and then returned to another place.

In one important sense the Jefferson Lab experiment is not like medical imaging. In conventional microscopy, decreasing the wavelength of the illumination source allows one to see finer details, and this is great when looking at the interior of tumors or cells. But the structures inside a proton, quarks, are pointlike, beyond the resolving power of any probe. Therefore, the structure of protons can be probed but not that of quarks. In proton tomography, the momentum transferred (actually the square of the transfer momentum, or Q2) from electron to quark in the form of a virtual gamma ray should, up to a point, provide better spatial resolution.

Beyond a certain level, however, a larger Q2 does not get you greater resolving power. What this means is that the gamma is no longer probing the proton as a whole but rather individual quarks. The best one can do is to map out the probabilities for the presence of quarks with a certain momentum to reside at various places inside the proton; this is analogous to the "orbital" clouds used to depict the likely position of electrons in various energy levels inside atoms.

Indeed, perhaps the most important thing achieved in the present experiment is to affirm that the scattering becomes independent of Q2 above a level of about 2 gigaelectronvolt2. This says that true tomography of the proton is proceeding. DVCS events, which have been seen in other experiments before but never with the exactitude employed here, are rare. Nevertheless, the Jefferson physicists were able to muster a million of them. With a requested upgrade in electron beam energy, the researchers hope to carry their map of the proton to quarks which carry a higher share of the proton's momentum. This in turn will allow the JLab physicists to explore the origin of proton mass and spin.

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