A rolling shutter digital camera. Each photographic image of a given exposure duration is captured as a multi-frame burst of frames each having a shorter exposure duration to minimize motion blur and to reduce sensor noise by averaging. Each frame is quantized into swaths, captured sequentially by the rolling shutter. Swaths of the first frames are analyzed to select a set of best motion detection reference regions. Swaths of subsequent frames are analyzed versus only those regions, to reduce required computation, and are re-registered accordingly. Corresponding swaths of each frame are accumulated. The accumulator is normalized to the desired bit depth and written as the final image. Averaging of the multiple frames is improved by re-registering swaths rather than entire frames, because of the time delta caused by the rolling shutter. Computation is further reduced by selecting candidate points only along a key line of each swath of the first frame, and still further by pre-limiting the search by using a thumbnail version of the first frame to cull most candidate points. Thresholds are used to ensure adequate motion detection regions are used for each swath.