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13 protocols using mplanfl n

1

Optical Characterization of Reflected Samples

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Reflection color images of the sample were characterized using an objective lens (MPlanFL N, ×50×/0.8, Olympus Co.). A CCD camera (Olympus, BX53, Olympus Co) was used to acquire the images from the sample. The spectra were characterized with a home built confocal microscope coupled to a spectrometer (Andori500). The sample was illuminated using a halogen white light source using an objective lens (MPlanFL N, ×20×/0.45, Olympus Co.). The reflected light was collected through the same objective lens and recorded using a spectrometer. The reflected intensity was normalized by the spectrum of the lamp obtained by reflection measurements with a silver mirror.
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2

Optical Characterization of Nanostructures

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An optical microscope (Carl-Zeiss Axio-10) equipped with ×5 (0.13 NA), ×10 (0.25 NA), ×20 (0.4 NA), ×50 (0.75 NA), and ×100 (0.85 NA) objective lens is used to obtain the reflection and transmission optical micrographs with different magnifications. The transmittance spectra under normal incidence were collected by an Olympus microscope (BX-51) with a spectrometer through a ×100 objective (MPlan-FLN, 0.9 NA). The extinction spectra were measured in transmission mode using a 2030 PV ultraviolet–visible–near-infrared range microspectrophotometer (CRAIC Technology Inc.) equipped with a xenon light source (80 W) and an optical objective (ZEISS Ultrafluar, ×10, 0.2 NA). Both the incident and collected light were normal to the quartz substrate, thus providing linearly polarized light excitation in plane with the surface of the nanostructures.
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3

SERS Imaging of Plasmonic Nanostructures

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SERS imaging was performed with a confocal Raman microscope (WITec alpha300) equipped with an upright optical microscope. For excitation a 532 nm laser was used that was coupled into a single-mode optical fiber and focused through a 100× objective (Olympus MPlanFL N, NA = 0.9) to a diffraction-limited spot (1.3 μm2) on the Si sample. Due to the size of the laser spot only NP structures without any other potential SERS active NPs in the vicinity of 0.65 μm radius have been analyzed. The laser power and the integration time were set to 900–1000 μW and 2 s for dye-covered AuNPs (structures 1, 2) or to 400–500 μW and 10 s in the case of single-molecule measurements (structures 4a, 4b). The grating of the spectrograph was set to 600 g mm–1. For better visualization SERS spectra are vertically shifted in all diagrams presenting more than one spectrum.
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4

Dark-Field Scattering Mapping and Spectroscopy

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The dark-field scattering mapping and spectra were measured with a commercial hyperspectral imaging system (Cytoviva, HISV3). The white light was focused by a 100× objective with a high NA (Olympus, MPlanFLN, NA = 0.9). The mapping of the scattering signal was realized with a precise motorized translation stage, and spectral profiles of all pixels could be obtained. Scattering signals were recorded by a spectrometer (Horiba, iHR550) cooled to −60 °C. Scattering spectra of samples were corrected with the substrate using build-in software (Cytoviva, ENVI 4.8).
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5

Confocal Raman Microscopy Protocol

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For Raman measurements a drop of the corresponding was applied to a freshly cleaned glass slide. Raman measurements have been performed using a confocal Raman microscope (WITec 300α) equipped with an upright optical microscope. The excitation laser light at 532 nm was coupled into a single-mode optical fiber and focused through a 100x objective (Olympus MPlanFL N, NA = 0.9) to a diffraction-limited spot of about 1.3 μm2. The laser power was set to 13 mW and the integration time was 10 s for all measurements. Each spectrum has been obtained by an average of three accumulations. The spectra that cover a broad range of wavenumbers have been recorded using a grating with 600 g/mm whereas for the more detailed measurement a grating with 1800 g/mm has been used.
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6

SERS Spectra Acquisition Protocol

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SERS spectra
have been recorded using a confocal Raman microscope (WITec 300α)
equipped with an upright optical microscope. For Raman excitation,
laser light at λ = 633 nm was used that was coupled into a single-mode
optical fiber and focused through a 50× objective (Olympus MPlanFL
N, NA = 0.75) to a spot size of about 1000 nm. The laser power was
varied (100, 200, 500, and 1000 μW) at the focal plane, and
the integration time was 1 s. The kinetics were followed between 5
to 15 min for each sample, i.e., each curve is based on 300–900
different spectra. Each sample was measured at least 3 times, and
the results shown here are the average of all the different Raman
measurements, i.e., all the spectra collected were averaged over time,
and the time traces are extracted directly from the average data.
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7

Optical Microscopy of GT Resonators

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The completed GT resonator with NPs was mounted onto the stage of optical microscopy system (BX53M, Olympus, Tokyo, Japan). Optical bright-field micrographs were captured using a 100× objectives lens (MPlanFLN, Olympus, Japan) and a computer-connected CMOS camera (STC-MCCM200U3V, Omron Sentech, Ebina, Japan) under a white LED lamp as a continuous light source.
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8

Optical Imaging and Spectroscopy of Samples

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Optical BF/DF images and spectra of samples were obtained using a CCD camera (Infinity 2) and spectrometer (Ocean Optics QE65000) with 100 × objectives (Olympus MPlanFLN) in a customized microscope (Olympus BX51). A halogen lamp (Philip 7023) was used as the white light source. Reflection and transmission measurements were conducted in BF configuration, and scattering measurements were conducted in DF configuration.
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9

High-resolution Optogenetic Mapping of Neural Circuits

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Optical stimulation was implemented using a digital micromirror device (DMD) coupled to a 463 nm CW laser (Polygon 400, Mightex Systems). The stimulus consisted of a 1000 x 500 µm grid divided into 24 x 12 spots of light (41.7 µm x 41.7 µm square) delivered through a 5x/0.15 NA objective (Olympus MPlanFL N). The grid was centered on the soma and aligned to the pia orthogonal to the apical dendrite. The laser output associated with each spot was measured (PM100D and S121C, Thorlabs) and adjusted to obtain a measured power of approximately 300 µW (173 mW/mm2). Optical stimuli were delivered for 1 ms at 10 Hz in a pseudo-random sequence designed to maximize the distance between consecutive spots and the time between stimulation of neighboring spots. Each recording trial consisted of a single repetition of all 288 stimuli followed by a full-field stimulus, in which all stimulation spots were illuminated simultaneously for 1 ms. 5-20 trials were recorded, with 30s pauses between trials, making the interval between consecutive stimulation of the same spot 60s. An image of the recorded cell (filled with Alexa Fluor 488) relative to the stimulation grid was used during analysis to align the recorded sCRACM heatmap with the location of the pia or soma.
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10

Optical Characterization of Microscale Materials

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The transmittance spectra under normal incidence were acquired by Olympus microscope (BX-51) equipped with a spectrometer through a 100 × objective (MPlan-FLN, NA = 0.9). An optical microscope (Carl-Zeiss AXIO-10) with ×5 (0.13 NA), ×10 (0.25 NA), ×20 (0.4 NA), ×50 (0.75 NA), and ×100 (0.85 NA) objective lens is used to obtain the transmission optical micrographs with different magnifications.
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