A pathogen reduction tool implementing a method of processing eggs at a poultry hatchery is provided. Such a method includes setting a production quantity of avian eggs in a setter incubator, the eggs being maintained in a plurality of egg flats. The avian eggs are removed from the setter incubator on a predetermined day of incubation, such predetermined day being during about day nine to day twelve of incubation. Subsequent to removal of the avian eggs from the setter incubator, the avian eggs are subjected to an egg detection system on the predetermined day to determine which of the avian eggs are viable and non-viable. The non-viable avian eggs are removed from the egg flats on the predetermined day. The viable avian eggs remaining in the egg flats post-inspection by the egg detection system are incubated through hatch.
