In one aspect, one or more computing devices receive a set of image frames. Each image frame includes pixels. The computing devices align image frames in order to identify flows of the pixels in the set of image frames. Regions of bokeh effect are identified in each image frame by measuring the sizes of areas of expansion across image frames using a set of assumptions and the identified flows. The computing devices adjust the alignment of the set of image frames based at least in part on the identified regions of bokeh effect. For each image frame, the computing devices generates an index map of focus values for each of the pixels that image frame using the improved alignment. A depth map is generated by the computing devices based at least in part on the index maps.