Microalgae and cyanobacteria are common colonisers of stone of buildings and monuments in different climates throughout the world; reports of their diversity are available from Europe, Asia, and South America. Rindi reviewed the diversity of green algae and cyanobacteria in urban habitats and highlighted how limited our knowledge is in this field. At the invitation of the Museum Conservation Institute, a group of interested researchers from the U.K., Germany, and Italy participated in a workshop and visited the museum during April 2010 to consider the nature and causes of the staining. Samples were removed during the visit and taken back to individual laboratories for analysis. This report is a summary of investigations undertaken at the University of Portsmouth in the Schools of Biological Sciences and Geography. The paper focuses on identifying the biological basis of the discoloration and on analysing the images of surface discoloration. Image analysis is being increasingly used in the identification and quantification of stone decay and this paper adds to this literature by introducing a method for quantifying variations in the spatial patterns of discoloration across a number of scales.