Quantitative analysis of mosaic tissues is a powerful method for following developmental lineages; however, analytical techniques are often subjective and repetitious. Here a flexible, semi-automated image analysis method for mosaic patterns is described. ClonalTools is a free customizable tool-set designed for the open-source image analysis package ImageJ. Circular, polygonal or linear one-dimensional mosaic arrays can be interrogated to provide measurements of the total number and width of positive and negative patches in a region of interest. These results are adjusted for the effects of random clumping using a previously described method to correct for differences in the contribution of the positive and negative cell type. The applicability of ClonalTools to different systems is discussed with reference to the analysis of mosaic patterns in the mouse corneal epithelium and adrenal cortex and in the outgrowth of neurites from explant cultures of mouse retina as example systems. To validate ClonalTools quantitatively, a recently published manual clonal analysis of the corneal epithelium of X-inactivation beta-Gal-mosaic mice was re-analysed. The semi-automated results did not differ significantly from the published data. Rapid quantification of such patterns to produce biologically relevant results represents a welcome improvement in terms of ease and speed of use over previous methods.