A method and system marks a scene and images acquired of the scene with tags. A set of tags is projected into a scene while modulating an intensity of each tag according to a unique temporally varying code. Each tag is projected as an infrared signal at a known location in the scene. Sequences of infrared and color images are acquired of the scene while performing the projecting and the modulating. A subset of the tags is detected in the sequence of infrared images. Then, the sequence of color image is displayed while marking a location of each detected tag in the displayed sequence of color images, in which the marked location of the detected tag corresponds to the known location of the tag in the scene.