High-resolution high-contrast X-ray radiography of plant seeds combined with images taken by microscopy. The X-ray images were measured using combination of a micro-focus X-ray source and a state-of-the-art hybrid pixel semiconductor detector. The detector enables imaging in so-called single photon counting regime allowing acquiring radiographs with theoretically unlimited dynamic range (in practice limited just by the number of detected photons). In combination with point-like source magnifying geometry, the technique presents a powerful tool allowing non-destructive investigation of mm-sized object of any kind. The results show a novel application of the technique to plant biology, namely the visualization of seeds (typically 3 mm in size). For better interpretation of imaged features, the radiographs are combined with the images taken by microscopy.