The experiment was carried out on a homebuilt setup (fig. S1), which combined optically detected magnetic resonance microscopy (ODMR) with AFM. The ODMR was used for addressing, controlling, and measuring single NV centers in diamond, while the AFM controlled the distance between the cell sample and the diamond nanopillars. In the ODMR part, the CFM enabled the state initialization and readout of the electron spin state via a laser with 532-nm wavelength. The laser light passed twice through an acousto-optic modulator (ISOMET 1250C) and then was focused on an NV center by an objective [Olympus, LUCPLFLN 60×; numerical aperture (NA), 0.7]. The phonon sideband fluorescence with wavelengths of 650 to 775 nm was detected to determine the state of the electron spin. The fluorescence passed through the same objective and was collected by an Avalanche Photodiodes (Perkin Elmer SPCM-AQRH-14). A light-emitting diode (LED) illuminator with a 470-nm wavelength (Thorlabs M470L3-C1) and a charge-coupled device (CCD) camera were used for wide-field and interference fringe views.

The AFM based on a tuning fork was controlled by a commercial controller (Asylum Research MFP3D) and mounted with a homebuilt AFM probe head. A translation stage based on a piezo motor (Physik Instrumente Q-522) was used for the coarse approach. Each AFM probe head and the diamond base plate contained a three-axis tilt platform driven by a stepper motor actuator (Thorlabs ZFS25B), allowing accurate tilting adjustment.

The whole probe head was placed in a temperature-stabilized chamber to minimize the positioning thermal drift. A three-level temperature control system was set to control the temperature: (i) The ambient temperature of the laboratory was controlled by air-conditioning. (ii) A soundproof box was used to isolate noise and stabilize the temperature. (iii) The third level included a temperature controller (PTC10 from Stanford Research System) and a copper chamber with a heating resistor. As the core region of the MI system, the scanning part of the AFM could be stabilized at a temperature fluctuation of ±5 mK and a thermal drift of ±20 nm per day by using these multilevel temperature controls.

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