An image sensor integrated circuit may contain image sensor pixels. A channel for receiving a fluid with particles such as fluorescent biological samples may be formed on top of the image sensor. Light-control layers may be interposed between the fluid channel and the top of the image sensor. The light-control layers may include a color filter array, a microlens array over the color filter array, and a plasmonic color filter. The plasmonic color filter may be formed from a patterned metal layer on the color filter array or on the microlens array. The patterned metal layer may include openings that are configured to use plasmonic effects to control the colors of light that pass through the plasmonic color filter. The color filter array and the plasmonic color filter, in combination, may block light from a light source in the system while passing fluorescent light from the sample.