Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from wholemount centromere Q-FISH of the Arabidopsis thaliana primary root, Ploidy- QuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.