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6 protocols using spcm aqrh

1

Confocal Fluorescence Microscopy Measurements

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CFM measurements were
acquired with an inverted confocal scanning microscope (MicroTime
200, PicoQuant, Germany) with a 100× air objective (UPLFLN, numerical
aperture (NA) 0.9, Olympus, Japan). For excitation, a picosecond pulsed
TM-polarized laser diode source (LDH-D-C-405, PicoQuant, Germany)
with a center wavelength of 405 nm and a pulse width of 110 ps, driven
at a repetition rate of 0.5 MHz, was used. For fluorescence collection,
a dichroic mirror (ZT405-442/510rpc-UF3, Chroma, USA), a long-pass
filter with a cutoff below 425 nm (FF01–519/LP, Shamrock, USA),
and a single photon counting module (SPCM-AQRH, Excelitas, USA) were
used. For evaluation, SymphoTime 64 2.3 was used. The fluorescence
image scans were recorded at 1 μW excitation power (before the
objective) and a dwell time of 2 ms per pixel. The average contrast
was calculated as the average deviation of all points of the contrast
profile from a mean line over the evaluation length, similarly to
the average surface roughness.94
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2

STED-Anisotropy Measurement System Setup

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A home-built setup was used for STED-anisotropy measurements. CW laser at 488 nm, generated by an OBIS LX 120 mW CW laser (Coherent), was passed through Glan–Taylor polarizer (Thorlabs) to obtain highly pure (100,000:1) linearly polarized excitation beam. CW laser at 592 nm (VFL-P-1000 592; MPB Communications Inc.) was passed through a vortex phase plate (VPP-1a; RPC Photonics) to generate a depletion with a doughnut profile. The excitation and depletion beams were focused on the sample using a 100×, 1.49 NA oil immersion objective (Nikon). Excitation modulation and synchronous detection were carried out according to SI Appendix, section 3.
The emitted fluorescence was collected by the same objective lens. The parallel and orthogonal components of the emitted fluorescence were separated by a polarizing cube (CCM1-PBS251; Thorlabs) and steered to 2 single-photon counters (SPCM-AQRH; EXCELITAS) for anisotropy measurements. The TTL signal from SPC was acquired with a DAQ card (PCIe-6353; National Instruments). Data acquisition and analysis was automated by custom LabVIEW software (National Instruments).
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3

Single-Molecule Fluorescence Detection Setup

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The ARROW-based fluorescence single-molecule detection setup is depicted in (Fig. 1a). Two lasers running at 738 nm (Ti:Sapphire, Del Mar Photonics) and 556 nm (SSD Nd:YAG, Shanghai Dream Laser Technology Co.) are coupled into a single-mode optical fiber (F-SA, Newport) using a 60× microscope objective (Newport). A pair of modified PC cooling fans are used as mechanical shutters (MS1, MS2) to close/open optical paths for each color. The optofluidic chip is mounted on a 3D printed custom stage using double-sided tape, and the two brass cylindrical fluid reservoirs are glued to the liquid channel ends with wax. The vacuum line is connected to the outlet reservoir to provide negative pressure for sample flow inside the ARROW chip. The fluorescence signal from the labeled targets is guided through the collection waveguide and gathered from the side-facet by a 60× objective (Newport). The excitation light is then removed by a penta-bandpass optical filter (FF01-440/521/607/694/809-25, Semrock) before coupling the collected light with a multi-mode fiber optic patch cable with an FC connector. A single-photon counting module (SPCM-AQRH, Excelitas Technologies) converts fluorescence photons into electrical pulses, and a time-correlated single-photon counting (TCSPC) board (TimeHarp 260 nano, PicoQuant) records time-tagged photon events onto the computer storage disk.
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4

Optimized Confocal and STED Imaging

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Confocal and STED imaging was performed using the following microscopes: Abberior Expert Line STED 775 QUAD Scan, inverted setup, NA 1.4 oil immersion objective lens (UPlanSApo 100x, Olympus), pulsed excitation lasers at wavelengths 640/591/485 nm, pulsed STED laser at wavelength 775 nm, detection by avalanche photodiodes (SPCM-AQRH, Excelitas Technologies Corp.). STEDYCON upright setup, NA 1.1 water immersion objective lens (LUMFLN60X-W, Olympus), pulsed excitation lasers at wavelengths 646/561/488 nm, pulsed STED laser at wavelength 775 nm.
Acquisition parameters were optimized, balancing spatial resolution, temporal resolution, and sensitivity. Settings for Abberior Expert Line (inverted setup): 30% excitation laser power at 640 nm, 12% STED laser power, pixel size 30 nm (live-cell)/25 nm (SPMBs), pixel dwell time 36 µs (live-cell)/64 µs (SPMBs), time gating window 0.5–6 ns. Settings for STEDYCON (upright setup): 10% excitation laser power at 488 nm, 3/10% excitation laser power at 488 nm (SPMB/close-up), 100% excitation laser power at 640 nm, 70/99% STED laser at 775 nm (SPMB/close-up), pixel size 30 nm, pixel dwell time 30 µs/250 µs (SPMB/close-up), time gating window 1–7 ns, 1×/25× line accumulation (SPMB/close-up).
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5

Relaxometry Probing of Intracellular Radicals

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To perform relaxometry, we utilized a home-made magnetometry setup. The setup is in principle a confocal microscope with a few changes as described below. First, we implemented an acousto-optical modulator (Gooch & Housego, model 3350-199) to conduct the pulsing sequence shown in Fig. 1. For focusing and light collection we used a 100x magnification oil-immersion objective (Olympus, UPLSAPO 100XO). 50 μW laser power measured on top of the objective lens was the optimal laser power for avoiding damage to the cells while being high enough to polarize the NV centers. The photons emitted by an FND are detected using an avalanche photodiode (Excelitas, SPCM-AQRH) after passing through a 600 nm long-pass filter.

Schematic representation of probing general intracellular free radical response (a), and free radical response near viral particles (b) of BHK-21 upon SFV infection using relaxometry.

Fig. 1
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6

Super-Resolution STED Microscopy Setup

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Experiments were performed on a custom-built super-resolution stimulated emission depletion (STED) microscope (Abberior Instruments, Gottingen, Germany) combined with a tuneable two-photon excitation laser system (Chameleon Discovery, Coherent, Santa Clara, CA, USA). Briefly, imaging was done with Olympus 60× water immersion objective (NA = 1.2) using two pulsed lasers simultaneously with a fast gating system controlled by the FPGA unit. For detecting fluorescence of endogenous tissue fluorophores, a pulsed diode laser was used (λ = 561 nm, pulse length 120 ps and repetition rate 80 MHz). For experiments with reflected and scattered near-IR light, a tuneable pulsed near-IR laser was used (λ = 760–780 nm, pulse length 100 fs and repetition rate 80 MHz). Both fluorescence and reflected/scattered light were detected using avalanche photodiodes (APD, SPCM-AQRH, Excelitas, Mississauga, ON, Canada) with photon detection efficiency (PDE) above 50% at the whole detected visible spectrum. Fluorescence was detected within spectral window λ = 580–625 nm using dichroic and bandpass filter (both Semrock). For a detailed optical setup, see the schematics on Figure S1 in the Supplementary Materials.
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