An X-ray micro-radiographic system based on the Medipix2 semiconductor pixel detector for dynamic high spatial resolution and high contrast imaging has been developed. Our system is founded on a micro-focus and nano-focus X-ray tube and the hybrid single photon counting silicon pixel detector Medipix2 (matrix 256 x 256 sq. pixels of 55 µm pitch). This compact table-top system stands promising as a new tool in the field of small animal imaging as well as the in-vivo observation of dynamic processes inside living organisms. The main advantages of these Medipix2 pixel detectors include: high sensitivity to low energy X-ray photons; position sensitive and noiseless single photon detection with preselected photon energies; single-quantum counting in each pixel performed by digital counter (therefore there is no dark current); digital integration (providing unlimited dynamic range and absolute linearity in device response to number of photons, high sensitivity and high contrast); real-time digital information, high speed digital communication and data transfer. We improve the picture quality with the help of statistical data analysis and extended calibration of individual pixels response. Obtained 2D and 3D radiographic images of small insects demonstrate the potential and applicability of our system for precise in-vivo x-ray high resolution dynamic diagnostic and biological studies.