Fluorescent microscope imaging technologies have developed at a rapid pace in recent years. High-throughput 2D fluorescent imaging platforms are now in wide use and are being applied on a proteome wide scale. Multiple fluorophore 3D imaging of live cells is being used to give detailed localization and subcellular structure information. Further, 2D and 3D video microscopy are giving important insights into the dynamics of protein localization and transport. In parallel with these developments, significant research has gone into developing new methodologies for quantifying and extracting meaning from the imaging data. Here we outline and give entry points to the literature on approaches to quantification such as segmentation, tracking, automated classification and data visualization. Particular attention is paid to the distinction between and application of concrete quantification measures such as number of objects in a cell, and abstract measures such as texture.