A spectroscopy system for auto-aligning a biopsy collecting device is presented. The spectroscopy system includes an illumination subsystem configured to emit an illumination light towards the biopsy collecting device, whereas the biopsy collecting device includes an activator unit and a needle unit and wherein the needle unit includes a cannula and a stylet having a biopsy specimen. Also, the spectroscopy system includes a fixation subsystem capable of holding the biopsy collecting device and configured to place the needle unit comprising the biopsy specimen across the illumination light. Further, the spectroscopy system includes a detection subsystem configured to receive a light comprising at least one of an attenuated illumination light and a re-emitted light from the needle unit. In addition, the detection subsystem is configured to send a control signal to align the needle unit at a predetermined position in the spectroscopy system based on the received light.