gEMpicker is a template-based cryo-EM particle picking program. The user may define a template particle in one of several ways, and this is then used to pick other similar particles from the micrographs by using a fast Fourier transform (FFT) to calculate the correlation score at each pixel between the template and the micrograph. Multiple micrographs may be processed in parallel, and the calculation may be accelerated considerably by using one or more attached graphics processors (GPUs).

The image below on the left shows an example micrograph from the KHL dataset. The image on the right shows the array of pixel scores after calculating the correlation with a template particle. The dark blue spots correspond to the centres of the picked particles.