A method of arranging an optical device into a predefined position with respect to a cartridge, using an assembly which comprises, a cartridge comprising a channel along which a sample fluid can flow, one or more elements (3,4) which are configured to manipulate light in a predefined manner, and wherein said one or more elements (3, 4) are located in a predefined position relative to the channel; an optical device which is configured such that it can be selectively operated to emit light which is incident on the cartridge; a means for moving the optical device with respect to the cartridge, or a means for moving said cartridge with respect to the optical device; and a sensor which can receive light from said cartridge, said light having been emitted by said optical device, and which can output a signal which is representative of the light which it receives, the method comprising the steps of, operating the optical device to emit light which is incident on the cartridge; moving the optical device, from a starting position, over the cartridge and over said one or more elements (3,4) on the cartridge; as the optical device is moved from said starting position, over the cartridge and over said one or more elements (3,4) on the cartridge, recording the position of the optical device relative to the starting position; at each position for the optical device, detecting light using said sensor and outputting from the sensor a signal which represents light detected by the sensor, so as to provide an output signal which represents light detected by the sensor at each position of the optical device; determining, from said output signal, the position at which the optical device was aligned over said one or more elements (3,4); characterized in that the method further comprises the steps of, using said determined position and the predefined position of the one or more elements (3,4) relative to the channel, to determine how to move the optical device so that it is aligned above the channel; moving the optical device so that it is aligned above the channel. operating the optical device to emit light which is incident on the cartridge; moving the optical device, from a starting position, over the cartridge and over said one or more elements (3,4) on the cartridge; as the optical device is moved from said starting position, over the cartridge and over said one or more elements (3,4) on the cartridge, recording the position of the optical device relative to the starting position; at each position for the optical device, detecting light using said sensor and outputting from the sensor a signal which represents light detected by the sensor, so as to provide an output signal which represents light detected by the sensor at each position of the optical device; determining, from said output signal, the position at which the optical device was aligned over said one or more elements (3,4); characterized in that the method further comprises the steps of, using said determined position and the predefined position of the one or more elements (3,4) relative to the channel, to determine how to move the optical device so that it is aligned above the channel; moving the optical device so that it is aligned above the channel.