An apparatus comprising: an assay chip supported in a chip holder frame that allows a specimen to be placed in contact with a surface of the assay chip, the assay chip comprising a plurality of pixels, each of the plurality of pixels comprising: a sample well configured to receive a sample, which, when excited, emits emission energy; and at least one element for directing the emission energy from the sample well in a particular direction, wherein the at least one element is selected from the group consisting of a refractive element, a diffractive element, a plasmonic element, and a resonator; and an instrument configured to interface with the assay chip, the instrument comprising: an assay chip interface configured to receive the chip holder frame; at least one excitation light source configured to excite the sample; a plurality of sensors, a sensor of the plurality of sensors corresponding to a respective sample well and configured to detect the emission energy from the respective sample well; and at least one optical element configured to direct the emission energy, when the chip frame is received in the assay chip interface, from a sample well towards a respective sensor of the plurality of sensors. an assay chip supported in a chip holder frame that allows a specimen to be placed in contact with a surface of the assay chip, the assay chip comprising a plurality of pixels, each of the plurality of pixels comprising: a sample well configured to receive a sample, which, when excited, emits emission energy; and at least one element for directing the emission energy from the sample well in a particular direction, wherein the at least one element is selected from the group consisting of a refractive element, a diffractive element, a plasmonic element, and a resonator; and a sample well configured to receive a sample, which, when excited, emits emission energy; and at least one element for directing the emission energy from the sample well in a particular direction, wherein the at least one element is selected from the group consisting of a refractive element, a diffractive element, a plasmonic element, and a resonator; and an instrument configured to interface with the assay chip, the instrument comprising: an assay chip interface configured to receive the chip holder frame; at least one excitation light source configured to excite the sample; a plurality of sensors, a sensor of the plurality of sensors corresponding to a respective sample well and configured to detect the emission energy from the respective sample well; and at least one optical element configured to direct the emission energy, when the chip frame is received in the assay chip interface, from a sample well towards a respective sensor of the plurality of sensors. an assay chip interface configured to receive the chip holder frame; at least one excitation light source configured to excite the sample; a plurality of sensors, a sensor of the plurality of sensors corresponding to a respective sample well and configured to detect the emission energy from the respective sample well; and at least one optical element configured to direct the emission energy, when the chip frame is received in the assay chip interface, from a sample well towards a respective sensor of the plurality of sensors.