Embodiments of a system for characterization of an imaging sensor using a moving modulated target with unmodulated position references is generally described herein. A target pattern comprises through-holes in a slide and resolved patches on the slide. The slide and patch have different emission intensities in the sensor' detection band. A modulation is applied to only the emission intensities of the through-holes. The target pattern is moved across the field-of view (FOV) of the imaging sensor to present the target pattern across different frames at different positions. Frames of images of the moving target pattern as seen in the FOV of the imaging sensor are captured to generate modulated image data outputs. The unmodulated position references provided by the resolved patches are measured and used to align the modulated image data outputs, which are processed to generate data products representative of a response of the imaging sensor.