Methods and apparatus for capturing and rendering images with focused plenoptic cameras employing different filtering at different microlenses. In a focused plenoptic camera, the main lens creates an image at the focal plane. That image is re-imaged on the sensor multiple times by an array of microlenses. Different filters that provide different levels and/or types of filtering may be combined with different ones of the microlenses. A flat captured with the camera includes multiple microimages captured according to the different filters. Multiple images may be assembled from the microimages, with each image assembled from microimages captured using a different filter. A final image may be generated by appropriately combining the images assembled from the microimages. Alternatively, a final image, or multiple images, may be assembled from the microimages by first combining the microimages and then assembling the combined microimages to produce one or more output images.