Acquisition, analysis and output for a digital image analysis system. Acquisition and analysis of immunohistochemical staining of CD3+ T lymphocytes in synovial tissue using a digital image analysis system . Three different areas from each biopsy sample, which are representative of the whole tissue section are selected. During analysis, staining thresholds are set for primary staining (i.e. CD3+ T lymphocytes), nuclear staining and background staining. The output is generated in a spreadsheet as the total number of positive cells per square millimetre of synovial tissue.