Micro-CT is becoming an increasingly important tool for non-destructive analysis of rock specimens. One of the major challenges with micro-CT is to extract quantitative information as opposed to qualitative information from the datasets. In this paper, PhaseQuant – a new software tool for processing a micro-CT image stack – is introduced. PhaseQuant is an open source freeware distributed as an ImageJ plugin. PhaseQuant is a simple and easy-to-use software tool that comprises phase segmentation, phase measurement, validation and density calibration modules which together enable the user to follow a repeatable experimentation protocol for quantifying phases and components from a micro-CT image stack of rock specimens. The techniques used in the software tool are outlined in this paper along with some illustrative examples of application of the software to meteorites and rock cores. Detailed instructions on how to use the code are available on the Internet. & 2012 Elsevier Ltd. All rights reserved.