The European Scanning System, developed to analyse nuclear emulsions at high speed, has been completed with the development of a high level software infrastructure to automate and support large-scale emulsion scanning. In one year, an average installation is capable of performing data-taking and online analysis on a total surface ranging from few m(2) to tens of m(2), acquiring many billions of tracks, corresponding to several TB. This paper focuses on the procedures that have been implemented and on their impact on physics measurements. The system proved robust, reliable, fault-tolerant and user-friendly, and seldom needs assistance. A dedicated relational Data Base system is the backbone of the whole infrastructure, storing data themselves and not only catalogues of data files, as in common practice, being a unique case in high-energy physics DAQ systems. The logical organisation of the system is described and a summary is given of the physics measurement that are readily available by automated processing. (C) 2012 Elsevier B.V. All rights reserved.