InstrumentFrom chip to number
The MACS® Matchmaker couples laser light into the chip and images the focus below it. Optical normalization and calibration convert the focal signal into coherent mass density. This lesson explains the optical path. The product documentation covers sample handling and operation.
Objective. See what the reader does with the physics, from the laser to the reported number. In the training: The instrument, quick check.
Recommended first: Coupling.
The source: a 785 nm laser
The reader uses a 785 nm laser. The transverse-electric (TE) mode carries light along the chip, with an evanescent field extending into the sample. The waveguide page explores this field using illustrative layer parameters. Wavelength alone does not establish background rejection in a complex sample.
Finding the coupling angle
Efficient coupling requires phase matching between the laser, grating, and guided mode. Angular alignment locates the coupling resonance. Away from that resonance, less light enters the mode and the focal signal weakens. The coupling lesson illustrates this dependence. Exact angles and alignment procedures depend on the chip and instrument configuration.
The grating period and exact coupling angle are chip design values. The teaching models use illustrative values, not instrument alignment settings.
What the reader does before the first frame
- Coupling power. The reader measures how much light is coupled into the chip and stops if there is too little to work with.
- Position. The chip carries physical reference holograms engraved into the waveguide. Their diffraction pattern on the camera is symmetric only when the chip sits on target, so the reader sweeps the chip along one axis and then the other until the pattern is symmetric.
- Exposure. Exposure time is calibrated on the reference holograms so that the brightest spots stay below camera saturation.
- Focus. A single frame tells how far the camera is from focus but not on which side: a frame taken the same distance above or below best focus looks the same. The reader therefore sweeps, watches which way sharpness goes, and crosses the maximum once more slowly to place it.
Imaging the focus below the chip
The reader collects the substrate-side focus through the glass. The focal distance is a design value of the chip and is quoted in air; it is not the distance inside the glass or an objective travel setting. Collection from below separates the imaging path from the bulk sample, but bubbles and fouling can still disturb illumination or binding. The quantification page explains the focal-spot scale.
The imaging optics must resolve the mologram’s focal plane. Defocus spreads the signal over a larger detector area and reduces peak brightness. The lab illustrates this effect.
Move the imaging plane up and down below the chip. The diffracted light converges at the focal plane, where the spot is smallest and brightest; away from it the same light spreads over a wider, dimmer disc. Because the numerical aperture is small, the depth of focus is long: a small offset costs little. You can see which side of focus you are on; from one frame, the reader cannot.
Geometric model: r/r₀ = √(1 + (Δz/z₀)²), where r₀ is the spot radius at focus and z₀ = r₀/NA is the depth-of-focus scale; brightness ∝ (r₀/r)². Offsets are in units of z₀. Not an instrument focus tolerance.
From spot to a number
The camera records the focal spot. Optical normalization, background treatment, and calibration convert the focal signal into coherent mass density (CMD), expressed in pg/mm². Normalization uses the incident power at each mologram's own position, read from the coupling camera, because guided light loses power along the chip. The square root gives an amplitude magnitude; it does not recover the phase or identify which molecules produced the signal. The spot’s lateral position provides a refractometric mass-density readout (MD): a change in effective index shifts the angle at which the mologram diffracts light, which moves the spot on the camera. It responds to effective-index changes from bulk composition, temperature, or surface accumulation. The quantification and spatial lock-in pages cover how brightness becomes a number and how the patterned readout suppresses common optical disturbances.
Sample handling, fluidics, chip loading, and measurement workflows are covered by the MACS Matchmaker documentation. The training introduces experiment planning and interpretation.
This lesson covers only the optical path from the laser to the reported number.
Worked example. In the streptavidin experiment, the focal signal is converted into CMD over time. The measured trace belongs to a research setup, not the current instrument model illustrated here.
Predict before revealing the explanation. Does moving the imaging plane change how much analyte has bound?
Reveal the explanation
No. It changes how the light is distributed on the detector. Focus and optical normalization help separate readout changes from binding changes.