Systems and methods are provided for capture control of video data from a capsule camera system having an on-board storage or wireless transmission. The capsule camera system moves through the GI tract under the action of peristalsis and records images of the intestinal walls. For some periods of time, the capsule camera system may move very slowly and there are little differences in the image data between different frames. These frames can be designated for discard to conserve storage space or conserve power. A capsule control processing unit is incorporated to evaluate motion metric based on image data associated with a current frame and a previous frame. A decision is made based on a profile of the motion metric to select an operation mode from a group comprising Capture Mode and Conservation Mode. The capsule camera system is then operated according to the selected operation mode.