Electronic devices may include super-resolution imaging systems for capturing multiple relatively low-resolution images and combining the captured images to form a high-resolution image. The imaging system may include image sensors configured to capture information above the Nyquist frequency of the image sensor by providing each image sensor pixel in an array of image sensor pixels with structures for reducing the size of the clear pixel aperture below the size of the image sensor pixel. The structures may be configured to pass light that is incident on a central region of the image sensor pixel to a photo-sensitive element through a color filter element and to reject light that is incident on a surrounding edge region. The structures may include a microlens configured to reject light that is incident on the edge region or a combination of a microlens and masking structures. Masking structures may be absorbing, reflecting, or interfering structures.