They use diffuse reflection, on the equatorial region of the egg (to avoid the air sack).
"The NIR spectra were collected in the reflectance mode by using an Antaris II near-infrared spectrophotometer (Thermo Electron Co., USA) with a fiber optic sampling probe. A fiber bundle was used to illuminate the sample and collect the diffusely scattered light. The fiber probe was placed directly to contact with equatorial region of the eggshell, because the internal composition changes are more easily explored in the equatorial region rather than the two sides. Particularly, the air cell contained in the blunt end will greatly effect the spectra collection. In order to avoid possible effects due to differences in the internal composition, the diffuse reflectance spectrum was obtained by averaging three measurements carried out round the equatorial region of eggshell. Each spectrum was the average of 32 scanning spectra. The range of spectra was from 10,000 to 4000 cm−1, and the data were measured in 3.856 cm−1 interval, which resulted in 1557 variables. The temperature was kept around 25 °C and the humidity was kept at a steady level in the laboratory."
Rest of the article focuses on the use of support vector machines as a solution for the problem of having many examples of a single target class (fresh eggs) and only a few examples of an outlier class (unfresh eggs). Their method of spoiling eggs resulted in 66 fresh eggs and only 5 unfresh eggs.