In this work we present the study of applicability of a desktop size radiographic/tomographic X-ray system for real-time microscopy and micro-tomography in the fields of biology, entomology, botanic and medical imaging. The apparatus is made up of the single photon counting pixel silicon detector, Medipix2 (matrix of 256x256 square pixels of 55 μm pitch) and a microfocus X-ray tube with a minimum spot size of 5 μm and a tungsten anode. The system has been used for observations of time-dependent processes inside living and still biological and organic samples. Excellent contrast and spatial resolution (micrometer scale) were obtained as a combination of a) low photon energy (40 kVp X-ray tube voltage), b) single photon counting operation, witch avoids integration of dark current c) energy discrimination in each pixel, allowing noise rejection and providing high SNR, d) high effective dynamic range for long exposures, which allows for high signal with high SNR, e) implementation of an original procedure for the energy response calibration of each pixel of the detector matrix, f) high speed read-out hardware and software, which opens the possibility to perform real-time studies of biological processes permitting, e.g., observation of morphological changes, mutations or metamorphosis of living animals and plants. Static and dynamic images of a parasite life cycle from the larva stage to pupa stage are presented here, as well as an in vivo computed tomography of the parasite living inside its host.