Extended Data Fig. 2: Experimental setup.
488 nm and 912 nm diode lasers are gated using acousto-optic modulators (AOMs) and coupled into single-mode fibres. The fibres deliver laser light to a movable optical assembly for scanning over the sample. Dichroic mirrors overlap the excitation beams such that they are focused to the same spot by the microscope objective (60x magnification, 0.7 numerical aperture). The optical powers at the back of the objective for the 488 nm and 912 nm lasers are about 0.4 mW and 65 mW, respectively. Light collected from the sample passes through the dichroic mirrors and filters for removing the laser light, and is focused onto a single-mode fibre. The fibre acts as a pinhole, filtering out-of-focus light such that the signal is primarily from proteins illuminated with the highest laser intensities. After being gated by an AOM, the collected light is detected by a single-photon counting module or, in Extended Data Fig. 3a, a spectrometer. The sample is mounted in a custom imaging cell that holds 5 μl. It encapsulates the sample between two 500 μm thick sapphire windows, sealed by an o-ring. The sapphire substrate nearer to the cryostat window is photolithographically patterned with microwave loop structures using a lift-off process. The cryostat is evacuated to < 1 Torr and subsequently cooled following a temperature profile similar to Extended Data Fig. 4b. An external DC magnetic field is applied using a permanent magnet attached to a motorized translation stage outside of the cryostat. The microwave output of the RFSoC is fed into a series of amplifiers before being delivered to the loop structures. The microwave power before entering the cryostat was approximately 1 W.
