Conventional transmission radiography is based on beam intensity attenuation. The sensitivity of this method is limited for weakly absorbing objects such as biological samples. Phase imaging visualizes phase shift of photons which passed the sample. Although phase sensitive X-ray imaging offers many advantages it is not routinely used in biological research due to demands of high intensity and highly coherent X-ray beam which is accessible mainly at synchrotron facilities. In-line phase enhanced imaging is possible also with microfocus X-ray tubes but low beam intensity of such systems prolongs exposure time to such an extent that common digital imaging detectors (CCD, Flat panels) are disadvantageous due to low efficiency, dark current and noise. This contribution presents a compact phase enhanced imaging system based on a microfocus X-ray tube and single photon counting pixel detector Medipix2. Each detector pixel is provided with pair of discriminators allowing full noise suppression and selection of energy range of interest. The spectral sensitivity of the detector together with the polychromatic nature of the beam allows to distinguish a absorption image from a phase image. Spatial resolution of the system can be on the submicrometer level and measuring times less than a minute. Several applications of the system for biological samples including 3D reconstructions will be presented. The simplicity of the system allows for routine laboratory work including in-vivo studies.