According to embodiments of the technology, an automated thermal desorption system includes a sample tube including a chamber to contain an analyte, visible indicia on the sample tube, a thermal desorption apparatus, and a sample tube monitoring system. The thermal desorption apparatus is configured to receive the sample tube and includes a heating device. The heating device is configured to heat the sample tube in the thermal desorption apparatus and thereby desorb the analyte from the sample tube. The sample tube monitoring system includes: an optical sensor configured to read the visible indicia on the sample tube and to generate an output signal corresponding thereto; and a controller configured to receive the output signal corresponding to the visible indicia from the optical sensor and to determine an orientation of the sample tube with respect to the thermal desorption apparatus based on the output signal.