The technical composition of painted artworks is usually very complex and they belong to the most sophisticated cultural heritage artefacts. In the field of their inspection there is a rising demand for the non-destructive imaging and analytical methods which are able to reveal the inner composition of investigated objects. Several non-invasive methods based on the interaction of ionizing radiation with the matter have been successfully utilized during the last decades. These methods can be divided into two main groups. The better known are transmission methods (e.g. classical X-ray radiography) the less-used are emission methods (e.g. X-ray fluorescence imaging). The quality of the obtained image is highly dependent on the imaging characteristics of the used detector. The presently used ones (CCD cameras and CMOS sensors) create the image from analogue signal by the charge integration. This image is usually degraded by the presence of noise. This complication is exceeded by novel pixel detectors of Medipix family based on single particle digital counting. Furthermore these devices offer very high contrast (in principle unlimited) in the obtained image. The image can be acquired with spatial resolution better than one micro meter. Another advantage of these detectors is their ability to directly measure the energy of incident particles. This feature can be used for energy sensitive X-ray radiography (i.e. multi-channel images) and X-ray fluorescence mapping of the surface elemental composition. For the purposes of this work the laboratory ALMA in Prague prepared several multilayer samples of paints using different pigments. The results of mentioned methods applied on the test samples are summarized in this article. The first goal of these measurements is to build a comprehensive methodology for the application of these procedures in the laboratory. The second goal is to use obtained knowledge for the construction of the mobile measuring system for the analysis of painted artworks in situ without any transportation.