Abstract: Infrared thermography is applied to measure the spiral vortices in the boundary layer over a rotating cone under axial inflow. The data sets are analysed using proper orthogonal decomposition (POD). A criterion based on the signal-to-noise ratio is defined for the selection of relevant POD modes, such that a low-order reconstruction with reduced measurement noise is obtained without affecting the thermal footprint of the spiral vortices. The resulting reconstruction still includes the large-scale modulations in the local vortex strength, relating to low-frequency phenomena like amplification, changing vortex states, disturbances in outer flow, etc. The effect of coherent vortical structures is further separated from such phenomena by selective reconstruction of the POD modes based on the number of observed vortices (n) along the circumference. The counter-rotating nature of these vortices is confirmed by PIV measurements. The number of spiral vortices shows good agreement with previously reported methods in the literature. The spiral vortex angle is in good agreement with the previous methods at low rotation ratio (S) , but deviates towards the direction of the local wall shear for high values of S. Graphic abstract: [Figure not available: see fulltext.].