Data is encoded on an image sensor that has a plurality of pixels including one or more bio-sensing pixels and one or more data encoding pixels. The method includes applying a covering material selectively to the data encoding pixels depending on the data to be encoded, the covering material having a detectable difference in opacity relative to having no covering material present. The method includes reading the data encoding pixels, in the presence of light, and decoding data according to a pre-determined scheme depending on the presence of the covering material on the data encoding pixel. As bio-reagents are typically applied after manufacture of the image sensor, the image sensor can have information encoded for electronic detection subsequent to manufacture.