The hybrid semiconductor pixel device Timepix consists of a sensor (e.g. silicon 300 µm thick) bump-bonded to a pixelated ASIC readout chip (256 × 256 square pixels with pitch of 55 μm). In the Time-over-Threshold mode (TOT) the detector enables the direct energy measurement in each pixel. The advantage of noiseless position sensitive detection combined with per pixel spectroscopic capability opens many new applications, which were till now, however, restricted to detection of radiation which is basically above the detector threshold (typically 4 keV). This limitation excludes application of the hybrid technology to highly interesting fields such as plasma diagnostics or X-ray microscopy. In this contribution we demonstrate how the Timepix detector working in TOT mode can be operated as a detector for soft X-ray photons with energy typically 0.5 keV (i.e. for particles which are in principle below the detector threshold). The approach is based on the detection of a larger number of photons incoming in the pixel read-out chain in a time significantly shorter than the shaping time of the pixel electronics. The proposed approach enables a CCD-like operation with many advantages of the hybrid counting technology (high sensitivity, dark-current free operation, enhanced signal-to-noise ratio).