We describe a newly developed compact micro-CT scanner with rotating gantry equipped with a Timepix Quad hybrid pixel semiconductor detector and a micro-focus X-ray tube providing spatial resolution down to 30 µm. The resolving power of the device in relation to soft tissue sensitivity is demonstrated using a tissue-equivalent phantom and different types of biological samples. The results demonstrate that the use of noiseless particle counting detectors is a promising way to achieve sufficient soft tissue contrast even without any contrast agents.