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75 protocols using qe65000

1

Characterization of Nanoparticle Microstructures

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The microstructures of the different kinds of nanoparticles were observed by a transmission electron microscope (JEOL, JEM-2100). The microstructures of the derived SCPs were observed by a scanning electron microscope (Hitachi S–300 N). The optical images of the generated SCPs were captured by a stereomicroscope (NOVEL NTB-3A, Ningbo Yongxin Optics Co., Ltd., China) equipped with a color CCD camera (Media Cybernetics Evolution MP 5.0 RTV). The reflection spectra of the generated SCPs were obtained through an optical microscope (Olympus BX51) equipped with a fiberoptic spectrometer (Ocean Optics QE65000). The fluorescent intensity curves were obtained through a fluorescent microscope (Olympus, CKX41) equipped with a fiberoptic spectrometer (Ocean Optics QE65000). The fluorescent images were captured by a stereoscopic microscope (Olympus, SZX16) equipped with the camera under a mercury lamp (Olympus, U-RFL-T) and a halogen lamp (Olympus, LG-PS2).
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2

Hyperspectral Imaging with Linear Unmixing

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Hyperspectral image data were analyzed using non-negatively constrained linear unmixing, as described previously23 (link) (algorithms available at https://www.southalabama.edu/centers/bioimaging/resources.html). Briefly, pure samples of each spectral component were imaged: Cal-590, Tiny Beads, Big Beands, and unlabeled cells for autofluorescence. Images were corrected to a flat spectral response using measurements of excitation illumination intensity at the microscope stage as recorded by a fiber-coupled spectrometer (QE65000, Ocean Optics) and integrating sphere (FOIS-1, Ocean Optics), calibrated to a NIST-traceable illumination source (LS-1-CAL-INT, QE65000, Ocean Optics). Corrected hyperspectral images of single-label samples were then processed to build a spectral library by selecting a region within each image of high signal level and extracting the pixel-averaged spectrum. Spectra were normalized to a peak value of unity and stored in a spectral library. Timelapse hyperspectral image data were then analyzed utilizing a least-squares non-negatively constrained regression algorithm and the spectral library. Unmixed images were utilized for further analysis.
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3

Hyperspectral Image Analysis Using Linear Unmixing

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Hyperspectral image data were analyzed using non-negatively constrained linear unmixing, as described previously 23 (algorithms available at https://www.southalabama.edu/centers/bioimaging/resources.html). Briefly, pure samples of each spectral component were imaged: Cal-590, Tiny Beads, Big Beands, and unlabeled cells for autofluorescence. Images were corrected to a flat spectral response using measurements of excitation illumination intensity at the microscope stage as recorded by a fiber-coupled spectrometer (QE65000, Ocean Optics) and integrating sphere (FOIS-1, Ocean Optics), calibrated to a NIST-traceable illumination source (LS-1-CAL-INT, QE65000, Ocean Optics). Corrected hyperspectral images of single-label samples were then processed to build a spectral library by selecting a region within each image of high signal level and extracting the pixel-averaged spectrum. Spectra were normalized to a peak value of unity and stored in a spectral library. Timelapse hyperspectral image data were then analyzed utilizing a least-squares non-negatively constrained regression algorithm and the spectral library. Unmixed images were utilized for further analysis.
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4

Second Harmonic Generation in MF-LNOI

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The schematic of our experimental setup is shown in Fig. 4(a). A tapered MF was fixed at and precisely positioned by two xyz-stages. An optical microscope with a CCD camera was used to monitor MF and LNOI waveguide. At one end of the MF, a tunable laser (Santec TSL210) launched light into the sample through an in-line polarization controller. At the other end, a highly-sensitive visible spectrometer (Ocean Optics QE65000) and a power meter were used to measure the SH wavelength and power. Since the spectrometer only responds in the visible, we had not used filter to remove the pump light. Before measurement, the spectrometer was carefully calibrated with the power meter. The normalized SHG efficiencies inside the MF-LNOI structures were calculated by taking into account the in/out-coupling losses, as illustrated in Supplementary Fig. S2.
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5

Light Penetration in Coastal Microbial Mats

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Light penetration in the coastal microbial mat was measured with a scalar irradiance microsensor (Lassen et al., 1992 (link); Kühl et al., 1997 (link); Kühl, 2005 (link)) connected to a sensitive fiber-optic spectrometer (QE65000, Ocean Optics, USA) that was interfaced to a PC running dedicated spectral acquisition software (Spectrasuite, Ocean Optics, USA). Mat samples were illuminated vertically from above with a fiber-optic halogen lamp equipped with a collimating lens (KL-2500, Schott, Germany), where the downwelling photon irradiance was regulated with a built-in neutral density screen to 500 μmol photons m-2 s-1. A scalar irradiance microsensor was mounted in a manually operated micromanipulator (MM33, Märtzhäuser GmbH, Germany) and inserted into the mat at a 45° angle relative to the vertically incident light. Measurements were corrected for the measuring angle, and depths are given as vertical depth below the mat surface. Data were normalized to the incident downwelling irradiance as measured with the scalar irradiance microsensor positioned in the light path at similar distance as the mat surface but over a black light absorbing well.
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6

Optical Sensing System for Antigen-Antibody Reactions

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Figure 2 shows the optical measurement system comprised a white-light source (DH-2000-BAL, Ocean Optics Inc., Dunedin, FL, USA), reflectance optical probe (QD-400, Ocean Optics, Inc.), antigen-antibody reaction chamber made of Teflon, and a spectrometer (QE65000, Ocean Optics, Inc.). The spectrometer, which could measure absorbance and reflectance, was operated over a wide wavelength (200–1100 nm) with high resolution (0.17 nm). During the sensing process, we measure the reflected light from the fabricated Al sheet that had undergone an antigen-antibody reaction. As shown in Figure 2, the perpendicularly-irradiated light on the AAO chip was reflected from the AAO chip and the reflected light was collected through the same optical probe that had one receiver in the center and six sources surrounding the receiver. The collected light was analyzed with spectrum analysis software (spectrasuit, Ocean Optics, Inc.) in real-time.
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7

LSPR Optical Platform Assembly

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The LSPR optical platform was self-assembled in the laboratory (Fig. S2). The LSPR extinction spectra were obtained using a spectrometer (QE65000, Ocean Optics, USA). Scanning electron microscopy (SEM) images were obtained using aby field emission scanning electron microscope (NanoSEM650, FEI, USA). Fluorescence images were obtained using an optical microscope (Ti-s, Nikon, Japan).
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8

Raman Spectroscopy of Biological Cells

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We have used a continuous wavelength DPSSL laser from laser glow technology (LSR-0671-TFM-00300-10) and (LSR-532-TFM-500-10). The laser is operated with 670nm and 532nm as an excitation light source, in combination with InPhotonics 670 nm (TT265044) and 532 nm (TT237316) Raman fiber optic probe. The probe has 105μm excitation and 200μm collection capability with filtering and steering micro-optics. Ocean Optics QE65000 spectrometers equipped with CCD and spectra suite software is used to process Raman scattering data and analysis. IR radiations are prone to damage biological cells, to avoid this situation we maintained the ultra-low doses (~0.22W/cm2) of 670 nm radiation through the course of experiment. Though GO does not show prominent fluorescence at NIR, IR or FIR, however in order to avoid any residual fluorescence background from the Raman spectra, we used LabRam HR, from Horriba Jobin Yvon confocal Raman setup at confocal hole and slit width ranging from 10 μm – 100 μm to minimize fluorescence background from Raman spectrum.
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9

Spectroscopic Analysis of Oxidized Samples

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Data were acquired using Spectrasuite software and a fibre optic system comprising a cooled CCD (QE65000, 25 μm slit width), a tungsten halogen light source (HL-2000-FHSA-HP), 1000 μm optical fibres (QP1000-2-VIS-BX) and either a standard cuvette holder (CUV) (all from Ocean Optics) or a light-integrating sphere with centre mounted cuvette holder (Labsphere, Prolite). Unless otherwise stated the oxidised spectrum was recorded and stored with subsequent spectra acquired as difference spectra relative to oxidised.
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10

Fabrication and Characterization of Silicon Nanocylinders

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The silicon cylinders were fabricated using an etching mask of ZEP-520 electron beam resist patterned by electron beam lithography and subsequent inductively coupled plasma etching on a Soitec SOI wafer with a 220 nm thick Si layer on 2 μm buried oxide. The fabrication is schematically shown in Fig. 9a.
Scattering spectra of the fabricated Si nanocylinders were measured using optical dark-field spectroscopy. The spectroscopic set-up (Fig 9b) included a BX51 microscope (Olympus) equipped with a halogen light source and a fibre-coupled grating spectrometer QE65000 (Ocean Optics). In these measurements a single Si nanoparticle is irradiated at highly oblique angles around 70 deg. and back scattered light collected from angles up to 64 deg. determined by the numerical aperture (NA) of the x100 microscope objective MPLFLNBDP (Olympus). The microscope images were captured with a XC30 digital color camera (Olympus).
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