This section provides an overview of the typical measurement workflow when using the MACS Matchmaker system. It covers the key steps involved in setting up and executing measurements, as well as best practices for ensuring accurate and reliable results.

The measurement workflow generally consists of the following steps:

1. Set up an experimental plan according to the assay requirements. More insight can be found in the experiment design guidelines.
2. Assemble the chip into the chip holder and place it on the MACS Matchmaker. Guidelines for this can be found in the chip assembly section.
3. Prepare the samples according to the planned plate layout. Place the buffer in the buffer position in the fluidic module. Refer to the well plate reference for supported formats and placement rules. Place the samples in the autosampler. Make sure that the waste bottles are empty.
4. Select the flow channel, prime the pump, prime the MACS Sampler and prime the chip. If the selected flow chamber differs from the saved experiment plan, the Prepare page shows a warning. Association flow rates are not recalculated there; update and save the experiment plan to use chamber-specific defaults for a different flow chamber.
5. Prepare reader. When the chip can be successfully prepared in the Matchmaker, all status indicators show “Success”
   If the chip cannot be successfully prepared, the failed steps can be repeated with the button “reoptimize x”. The following parts can further be checked manually:
   • Coupling verification: the coupling should be symmetrical and all 8 channels on the chip should be lit up.
   • Fourier Aperture check: Ensure that the molographic focus lies within the optical aperture and shows symmetric intensity distribution.
   • Manual chip coupling and XY-stage adjustment are described in Manual Chip Preparation. For the Fourier Aperture, use the visual check above during reader preparation; this page does not document a separate manual Fourier-adjustment procedure.

   For a step-by-step checklist of these diagnostics, see the instrument setup workflow guide.

6. Check bubbles. In this setting, the surface image and the molographic image can be seen. If there are air bubbles present, try removing them by priming the chip once or twice. If this does not work, take the chip out and re-assemble it in the fluidic system.

   Refer to the instrument setup workflow for camera references and troubleshooting tips before proceeding.

7. Check mologram recognition: here the recognition of the molographic foci can be tested. If the foci cannot be recognized, try checking the mologram recognition again. If this does not work again, try preparing the reader again.
8. Start measurement.
9. When another measurement should run immediately afterwards, schedule it while the current measurement is running. Before adding it to the schedule, use Review and Edit Injections to adjust its injections and vial assignments. After removing injections that have already run, use Remove Unused Vials to clear their vials from the scheduled setup. These changes do not modify the saved experiment plan.