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Burning of clinker is the most influencing step of cement quality during the production process. Appropriate characterisation for quality control and decision‐making is therefore the critical point to maintain a stable production but also for the development of alternative cements. Scanning electron microscopy (SEM) in combination with energy dispersive X‐ray spectroscopy (EDX) delivers spatially resolved phase and chemical information for cement clinker. This data can be used to quantify phase fractions and chemical composition of identified phases. The contribution aims to provide an overview of phase fraction quantification by semi‐automatic phase segmentation using high‐resolution backscattered electron (BSE) images and lower‐resolved EDX element maps. Therefore, a tool for image analysis was developed that uses state‐of‐the‐art algorithms for pixel‐wise image segmentation and labelling in combination with a decision tree that allows searching for specific clinker phases. Results show that this tool can be applied to segment sub‐micron scale clinker phases and to get a quantification of all phase fractions. In addition, statistical evaluation of the data is implemented within the tool to reveal whether the imaged area is representative for all clinker phases. [ABSTRACT FROM AUTHOR]