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34 protocols using crossbeam 550

1

FIB-SEM Analysis of 3D Gold Microstructures

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FIB-SEM (Zeiss Crossbeam 550, Carl Zeiss, Germany)
was used to create and examine the cross sections of the conductive
3D gold microstructures and measure the thickness of the coated gold
layer. In the microscope, the sample was tilted at an angle of 54°.
The Ga+ beam was used to dig a rectangle (20 μm ×
5 μm) at 30 nA, and this was improved by lower current milling
at 1.5 nA to give a smoother finish at the cut face. During SEM imaging,
the in-lens, SESI, and backscattered detectors were operated at 2
kV to acquire images of cross sections.
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2

FIB-SEM and TEM imaging of dividing cells

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FIB-SEM imaging was done largely as previously described [105 (link)]. Briefly, the specimen was cut to approximately 2 mm height and mounted on an SEM stub using silver. The specimen was introduced into a Zeiss CrossBeam 550 (Zeiss), ROI located by SEM imaging, and protected by a patterned platinum and carbon pad. A trench was FIB milled until the profiles of both dividing cells were revealed but stopped before the cleavage furrow was milled away. Images were acquired at 3 nm or 5 nm pixel sampling in XY and step size of 9 or 15 nm in Z, respectively, in an automated FIB-mill-SEM-image cycle with SEM operated at 1.5 kV, 1.2 nA; FIB milling at 30 kV, 1.5 nA, and back-scatter detector grid voltage at 900 V. The image stack was registered, contrast inverted, and binned by 3 in the imaging plane to produce an isotropic 9 nm3 or 15 nm3 image volume reconstruction. For TEM imaging, the cysts were exposed using the same approach, but here, 60-nm serial sections were cut and collected onto TEM grids. STEM imaging was executed at a Zeiss Gemini II SEM 450 at 30 kV landing energy, and the TEM imaging was done on a Hitachi 1050 operated at 80 kV. In both cases, the grids were not post stained; however, approximately 4-nm carbon coat was applied using a sputter coater (Leica) before imaging.
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3

Scanning Electron Microscopy of Cochlear Specimens

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FEI Quanta 250 Field Emission Gun Scanning Electron Microscope (FEI) with Everhardt Thornley secondary electron detector was used to acquire SEM images of cochlear whole mount specimens. Images were captured under high vacuum with a 3–5 kV beam and with a spot size of 2.6–3.0 depending on magnification and sample orientation. For the inter-stereociliary link analysis in P9 whole mount specimens, ZEISS Crossbeam 550 (Zeiss) was used with an accelerating voltage of 1.2 kV and probe current ranging from 80 to 300 pA.
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4

SEM-EDS Analysis of Pyrite Minerals

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SEM is a high-resolution petrographic microscope highly suitable
for mineral surface and shape analysis. Combined with the EDS technique,
it allows both qualitative and quantitative in situ chemical analyses to be conducted. Using a high-resolution version
of FE-SEM (Zeiss Crossbeam 550) by Carl Zeiss Microscopy, the T1–T5
samples (Figure 1c)
were observed for their pyrite (Py) contents, fractures, Py alteration, and relationship to ambient fractures.
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5

Scanning Electron Microscopy of Engineered Macrotissue

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Scanning electron microscopic imaging was performed on dAR8 fused spheroid macrotissue (i.e., day 25 from the initial seeding date) cultured in mineralization media and compared with approximately similar-aged spheroid in growth media (day 28). They were fixed with 4% paraformaldehyde and stored in PBS 1× at 4°C until SEM sample preparation. In brief, the samples were fixed in a solution of 3% glutaraldehyde in 0.1 M of sodium cacodylate buffer (pH 7.3) for 2 h. They were then washed in 3 × 10-min changes of 0.1 M sodium cacodylate buffer. Samples were then postfixed in 1% osmium tetroxide in 0.1 M of sodium cacodylate buffer for 45 min. A further 3 × 10-min washes were performed in 0.1 M of sodium cacodylate buffer. Dehydration in graded concentrations of acetone (50%, 70%, 90%, and 3 × 100%) for 10 min each was followed by critical point drying using liquid carbon dioxide. After mounting on aluminum stubs with carbon tabs attached, the specimens were coated with 9 nm palladium using a Safematic CCU-010 HV sputter coater. The samples were imaged using a Zeiss Crossbeam 550 at 2 and 7 kV using a probe current of 100 pA. An In-lens detector was used to image surface topography.
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6

SEM Sample Preparation Protocol

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In preparation for SEM, cells were fixated and dried by exposure to paraformaldehyde in HBSS (4%) for 20 min at 37 °C. Substrates were rinsed three times with purified water and successively submerged in 10%, 25%, 50%, 75% and 99.5% v/v ethanol absolute (VWR Chemicals) solution for 10 min each. Subsequently, the substrates were either air dried or critically point dried for optimal preservation (Autosamdri-815 Series A, Tousimis). Substrates were stored under vacuum in a desiccator until further use. All substrates were coated with approx. 30 nm Au by sputter coating (K550 Emitech Sputter Coater) before SEM imaging (Zeiss Crossbeam 550).
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7

Cryoimmobilization and Cryo-SEM Analysis

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Dual vehicle and single vehicle (only high molecular weight HA) were cryoimmobilized by plunge freezing into a liquid nitrogen bath at −196°C. Frozen samples were fractured and coated with a platinum. After transfer to the SEM chamber, samples were examined at 1.5 kV under high vacuum on the cryo-SEM stage (Crossbeam 550, Carl Zeiss, Oberkochen, Germany).
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8

FIB-SEM Imaging of Planktonic Cells

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The block was cut parallelly to its surface in order to be 2–3 mm high, and mounted on an SEM stub (Agar Scientific) using a 1:1 mix of superglue (Loctite precision max, Henkel Corp., Rocky Hill, CT, USA) and silver paint (EM-Tec AG44, Micro to Nano, Haarlem, the Netherlands). Silver paint was further added around the block surface. The sample underwent gold sputtering for 180 s at 30 mA (Q150RS, Quorum, Laughton, UK) before insertion in the FIB-SEM chamber. FIB-SEM imaging was performed using a Zeiss Crossbeam 550, following the Atlas 3D nanotomography workflow. FIB milling was performed at 1.5 nA. SEM imaging was done with an acceleration voltage of 1.5 kV and a current of 750 pA using an energy-selective backscattered (ESB) detector (ESB grid 1100 V). Imaging of the planktonic cell was done using an 8 nm isotropic voxel size with a dwell time of 9 µs. Post-acquisition dataset alignment was performed using the automated Alignment to Median Smoothed Template (AMST) procedure from Hennies et al. (2020) (link).
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9

Comprehensive Characterization of Material Samples

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Thermogravimetric analysis (TGA) was carried out using a TA instrument (HR-1) from room temperature to 1000 °C at a heating rate of 10 °C min−1 under nitrogen protection. X-ray diffraction (XRD) data were collected on a Rigaku SmartLab diffractometer (D/MAX-γA, λ = 1.54 Å). The scanning electron microscopic (SEM) images were obtained on a Zeiss Crossbeam 550, and the transmission electron microscopic (TEM) images, scanning transmission electron microscopic (STEM) images, and the corresponding elemental mapping results on a JEM-F200. Raman spectra were collected using a Renishaw InVia Reflex confocal microscope with an excitation light source of 532 nm. The laser power used was 0.15 mW to minimize burning the samples. X-ray photoelectron spectroscopy (XPS) spectra were collected on an ESCALAB 250Xi and calibrated by setting the C 1s photoemission peak for sp2-hybridized carbons to 284.8 eV. N2 adsorption/desorption isotherms were acquired using a Quadrasorb Instrument (Quantachrome, Autosorb IQ-MP-MP) at 77 K, where the surface area and pore size distributions were calculated by the quenched solid density functional theory (QSDFT) method.
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10

Morphological Analysis of Pyrite in Shale

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Based on
the results of mineralogy from XRD analysis, shale samples having
different mineralogical constituents were carefully chosen for FE-SEM
observation to study different morphological features of various forms
of pyrite and the distribution of OM along with pyrite in the shale
samples. For FE-SEM analysis, 17 representative shale samples were
selected and polished with argon ions and then coated with gold to
increase the smoothness and conductivity, respectively. The FE-SEM
analysis was performed using a “Zeiss Crossbeam-550 (Gemini-2)”
scanning electron microscope. Additionally, an EDS system (Bruker
Nano GmbH, model: Flash Detector 6|100) was also used to specify the
elemental constituents in detected minerals. The concentration of
various oxides in the different forms of pyrite is calculated using
EPMA analysis, and elemental mapping has been done by BSE-elemental
mapping. Four representative samples were selected for EPMA for elements
identification and mapping. An electron probe micro-analyzer (EPMA-1720
H Series electron probe of the Shimadzu Corporation, Kyoto, Japan)
was used to investigate the elemental composition of the different
forms of the pyrite in the studied shale. 10 nA electric current with
15 kV of accelerating voltage is used as a standard for EPMA analysis.
The diameter of the beam during EPMA analysis was 5 μm.
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