A device, comprising: a reaction structure that forms a plurality of reaction recesses for containing a reaction solution with a pH of less than or equal to about 5 or a pH greater than or equal to about 8 and at least one reaction site that generates light emissions in response to incident excitation light after treatment with the reaction solution; and a device base positioned beneath the reaction structure, comprising: a sensor base; a plurality of light sensors included in the sensor base; dielectric material layers stacked on the sensor base; device circuitry electrically coupled to the light sensors to transmit data signals based on photons detected by the light sensors, wherein the device circuitry is provided within the dielectric material layers; a plurality of light guides with input regions arranged to receive the excitation light and the light emissions from at least one corresponding reaction recess, the light guides extending into the device base through the dielectric material layers from the input regions toward at least one corresponding light sensor and comprising at least one filter material arranged to filter the excitation light and to permit the light emissions to pass to the at least one corresponding light sensor; a liner layer extending over the device base and about the side surfaces of each light guide and positioned between each light guide and the device circuitry; a protection layer extending about each light guide and positioned between the filter material of each light guide and the liner layer, wherein the protection layer is arranged to prevent reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry, wherein the protection layer is chemically inert with respect to the reaction solution with a pH of less than or equal to about 5 or a pH greater than or equal to about 8. a reaction structure that forms a plurality of reaction recesses for containing a reaction solution with a pH of less than or equal to about 5 or a pH greater than or equal to about 8 and at least one reaction site that generates light emissions in response to incident excitation light after treatment with the reaction solution; and a device base positioned beneath the reaction structure, comprising: a sensor base; a plurality of light sensors included in the sensor base; dielectric material layers stacked on the sensor base; device circuitry electrically coupled to the light sensors to transmit data signals based on photons detected by the light sensors, wherein the device circuitry is provided within the dielectric material layers; a plurality of light guides with input regions arranged to receive the excitation light and the light emissions from at least one corresponding reaction recess, the light guides extending into the device base through the dielectric material layers from the input regions toward at least one corresponding light sensor and comprising at least one filter material arranged to filter the excitation light and to permit the light emissions to pass to the at least one corresponding light sensor; a liner layer extending over the device base and about the side surfaces of each light guide and positioned between each light guide and the device circuitry; a protection layer extending about each light guide and positioned between the filter material of each light guide and the liner layer, wherein the protection layer is arranged to prevent reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry, wherein the protection layer is chemically inert with respect to the reaction solution with a pH of less than or equal to about 5 or a pH greater than or equal to about 8. a sensor base; a plurality of light sensors included in the sensor base; dielectric material layers stacked on the sensor base; device circuitry electrically coupled to the light sensors to transmit data signals based on photons detected by the light sensors, wherein the device circuitry is provided within the dielectric material layers; a plurality of light guides with input regions arranged to receive the excitation light and the light emissions from at least one corresponding reaction recess, the light guides extending into the device base through the dielectric material layers from the input regions toward at least one corresponding light sensor and comprising at least one filter material arranged to filter the excitation light and to permit the light emissions to pass to the at least one corresponding light sensor; a liner layer extending over the device base and about the side surfaces of each light guide and positioned between each light guide and the device circuitry; a protection layer extending about each light guide and positioned between the filter material of each light guide and the liner layer, wherein the protection layer is arranged to prevent reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry, wherein the protection layer is chemically inert with respect to the reaction solution with a pH of less than or equal to about 5 or a pH greater than or equal to about 8.