Velox software

Manufactured by Thermo Fisher Scientific

Sourced in United States

Velox software is a data analysis and visualization tool designed for use with Thermo Fisher Scientific's analytical instruments. The software provides users with tools to process, analyze, and visualize data generated from these instruments.

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28 protocols using velox software

STEM and EDS Tomography Protocol

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To obtain the STEM and EDS spectrum images, FEI Double Cs-corrected Titan Themis transmission electron microscope instrument equipped with Super-X EDX detector with an X-FEG module was operated at 300 kV. Samples were loaded in a Fischione Instrument Model 2050 tomography holder. To acquire the tilt series of the STEM and EDS spectrum images, Velox software (Thermo Fisher Scientific) was used, and each tilt series was collected from − 50° to + 70° in 5° steps. The HAADF-STEM and EDS images were simultaneously acquired under the conditions of a magnification of 543 kX, with 1024 × 1024 pixels (pixel size = 180 pm) and a beam current of 342 pA; for each tilt angle, 30 frames of images were collected at a dwell time of 5 μs. Tilt series alignment was carried out by first applying cross-correlation and then tilt-axis rotation/shift alignment; the 3D reconstruction via the SIRT and TV-M algorithm was performed by using tomviz software (Levin et al. 2018 (link)) (the resolution of input images was adjusted to 512 × 512 pixels). The regularization parameter for TV-M was used as default value in the tomviz software. Avizo software (Thermo Fisher Scientific) was used for post-treatment, visualization, and quantification. The summarized tomographic process is illustrated in Scheme 1.Scheme 1

Schematic illustration of STEM and EDS tomography process

Kim T., Lee Y., Hong Y., Lee K, & Baik H. (2023). Three-dimensional reconstruction of Y-IrNi rhombic dodecahedron nanoframe by STEM/EDS tomography. Applied Microscopy, 53, 9.

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TEM Visualization of Tau-3CLpro Interaction

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Tau samples were prepared as follows, 20 μM tau and 10 μM 3CL^pro were incubated for 72 h at 37°C. To prepare specimens for negative staining TEM, a total volume of 3 μL from the corresponding sample was pipetted onto carbon coated 300 Mesh copper EM grids, which were operated by anti-capillary tweezers and glow discharged in advance for 90 seconds using a PELCO easiGlow^™ (Ted Pella, Inc., Redding, California, USA) at 0.39 mbar and 15 mA. After an incubation time of 1 min excess liquid was blotted away by touching the edge of the grid with filter paper. Subsequently the grids were stained with two 4 μL droplets of a 2% Uranyl acetate solution. While the first droplet’s excess liquid was immediately blotted after application, the second droplet stayed on the grid for an incubation time of 1 min before blotting. Finally, the grids were left to dry at room temperature for approximately 1 min. These negatively stained samples were examined on a Talos L120C G2 transmission electron microscope (Thermo Fisher Scientific, Waltham, Massachusetts, USA) which was operated at 120 kV (LaB6 (Lanthanum hexaboride)/Denka). Micrographs were collected in medium magnification (6700x) and high magnification (73kx) on a 4k x 4k Ceta 16M CEMOS camera using the Velox^™ software (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

Eberle R.J., Coronado M.A., Gering I., Sommerhage S., Korostov K., Stefanski A., Stühler K., Kraemer-Schulien V., Blömeke L., Bannach O, & Willbold D. (2023). Tau protein aggregation associated with SARS-CoV-2 main protease. PLOS ONE, 18(8), e0288138.

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Transmission Electron Microscopy Imaging

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Images were recorded with a 200 kV Talos F200C TEM microscope (Thermo Fisher Scientific, Hillsboro, OR, USA) equipped with a CETA camera. The 4 × 4 or 2 × 2 images were acquired by Velox software (Version 2.11, Thermo Fisher Scientific, Hillsboro, OR, USA) or Tecnai T12 TEM (Thermo Fisher Scientific, Hillsboro, OR, USA) operated at 120 kV and equipped with a Gatan ES500W Erlangshen camera.

Milrot E., Lazar S., Schuster O., Makdasi E., Shmaya S., Yahalom-Ronen Y., Tamir H, & Laskar O. (2022). Insights from the Infection Cycle of VSV-ΔG-Spike Virus. Viruses, 14(12), 2828.

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Characterization of Polymer-Based Nanoparticles

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The size (hydrodynamic diameter) and charge (zeta potential) distributions of PBNPs, PEI-PBNPs and CpG-PBNPs were measured using dynamic light scattering (DLS) on a Zetasizer Nano ZS (Malvern Instruments, Malvern, UK). The visible-NIR (Vis-NIR) absorbance spectra of the nanoparticles were measured on the Genesys 10S spectrophotometer using the VISIONlite software (Thermo Fisher Scientific). Transmission electron microscopy (TEM) images of the PBNPs, PEI-PBNPs, and CpG-PBNPs were prepared by loading 5 μL of the nanoparticle suspensions on to formvar carbon coated copper grids (Ted Pella, Inc., Reading CA) and dried overnight. The samples were imaged in a Talos F200× Transmission Electron Microscope (TEM) (Thermo Fisher) at 200 KV. The Velox software (Thermo Fisher) captured images at 200× magnification with a Ceta 4k × 4k camera. Multiday stability of the nanoparticles in ultrapure water was assessed by measuring their hydrodynamic size distributions, zeta potentials, and Vis-NIR spectra every 24 hours over 7 days.

Cano-Mejia J., Bookstaver M.L., Sweeney E.E., Jewell C.M, & Fernandes R. (2019). Prussian blue nanoparticles-based antigenicity and adjuvanticity trigger robust antitumor immune responses against neuroblastoma. Biomaterials science, 7(5), 1875-1887.

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Transmission Electron Microscopy of LISO Particles

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TEM samples of o-LISO and ns-LISO were prepared by dispersing the particles onto TEM lacey carbon grids inside an argon-filled glovebox. Diffraction contrast imaging and energy-dispersive X-ray spectroscopy (EDS) were conducted using a monochromated aberration-corrected Titan 80-300 scanning transmission electron microscope operated at 300 kV. To obtain the dark-field diffraction contrast images, the objective aperture was inserted in the back focal plane to select the electrons scattered only from (

2 \bar{2} 0

)_s planes. EDS data were collected using a Super-X detector inside a Themis Z scanning transmission electron microscope operated at 300 kV. The EDS data analysis was performed using Velox software (ThermoFisher Scientific), where the overlapped peaks were deconvoluted using the stored standard reference spectra and using a Filtered Least Squares method to fit the peaks and remove the background.

Chen Y., Lun Z., Zhao X., Koirala K.P., Li L., Sun Y., O’Keefe C.A., Yang X., Cai Z., Wang C., Ji H., Grey C.P., Ouyang B, & Ceder G. (2024). Unlocking Li superionic conductivity in face-centred cubic oxides via face-sharing configurations. Nature Materials, 23(4), 535-542.

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Microscopic Characterization of PbS Nanostructures

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Transmission electron microscopy (TEM) images, high-resolution TEM (HR-TEM) images, and diffraction patterns were obtained using a Thermo Fisher/FEI Tecnai G² T20 S-Twin LaB₆ TEM operated at 200 keV and equipped with a 1K × 1K Gatan 694 slow-scan CCD. Energy-dispersive X-ray spectra (EDS) and high-angle annular dark-field (HAADF) imaging in a scanning transmission electron microscopy (STEM) mode with 200 kV acceleration voltage were registered by the Thermo Fisher/FEI Titan Cubed Themis G² 60-300 FEG double-Cs-corrected S/TEM equipped with Dual Bruker XFlash6|100 EDS detector with an effective solid angle of 1.76 sr for fast and precise local (atomic) chemical analysis. Thermo Fisher Scientific Velox software was used during data registration and for further data analysis. The samples for TEM and STEM measurements were prepared by dropping the PbS several dispersions at room temperature; on copper TEM grids with ultrathin carbon film on lacey carbon (Ted Pella, Inc. ultrathin carbon film on lacey carbon support film, 400 mesh, copper). Samples were purified by plasma cleaning before TEM and STEM investigation.

Abu-Hariri A., Budniak A.K., Horani F, & Lifshitz E. (2021). Star-shaped colloidal PbS nanocrystals: structural evolution and growth mechanism. RSC Advances, 11(49), 30560-30568.

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Heating and UV Effects on Au101NC

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Images showing the effect of heating and UV irradiation on the size and distribution of Au₁₀₁NC over AlSrTiO₃ and rGO along with interaction of Au₁₀₁NC, rGO, and AlSrTiO₃ with each other were acquired with a FEI Titan Themis STEM operating at 200 keV. The STEM was equipped with a Super-X EDS detector in conjunction with a low-background sample holder to minimize Cu background peaks and maximize X-ray collection efficiency. EDS data were analysed using the Velox™ software from Thermo Fisher Scientific. Samples were prepared by dropping prepared dispersions of as-prepared materials (sonicated for 1 min) onto a 300-mesh copper grid with a lacey carbon support film. The solvent was then allowed to evaporate before placing it into the sample holder for analysis. Image J was employed to measure the size of Au particles (200 particles).

Mousavi H., Small T.D., Sharma S.K., Golovko V.B., Shearer C.J, & Metha G.F. (2022). Graphene Bridge for Photocatalytic Hydrogen Evolution with Gold Nanocluster Co-Catalysts. Nanomaterials, 12(20), 3638.

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Multimodal Characterization of Materials

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Scanning transmission electron microscopy (STEM) and energy-dispersive X-ray spectroscopy (EDX) were conducted on a FEI Talos F200X microscope. The microscope was operated at an acceleration voltage of 200 kV. STEM-EDX elemental maps were recorded by a SuperX system, including four silicon drift detectors. Background-corrected and fitted intensities were used for image visualization. All samples were prepared on carbon-coated copper grids. Line profile and area-selective EDX analyses were performed in Velox software (Thermo Scientific). Powder X-ray diffraction (XRD) measurements were performed in Bragg–Brentano geometry on a Rigaku SmartLab with a D/teX Ultra 250 detector using Cu Kα_1,2 radiation. Data were acquired in the 2θ range of 10–80° with an angular step size of 0.025° and a counting time of 1.5 s per step. Fourier-transform infrared (FTIR) spectra (4000–400 cm⁻¹) were recorded on a Bruker Invenio-S spectrometer with a DTGS detector. Samples (approx. 10 mg) were diluted with KBr (1:10) and measured as pellets in transmission. The spectra were acquired with a spectral resolution of 4 cm⁻¹ and an accumulation of 32 scans with OPUS software (Bruker).

Preikschas P., Martín A.J., Yeo B.S, & Pérez-Ramírez J. (2023). NMR-based quantification of liquid products in CO2 electroreduction on phosphate-derived nickel catalysts. Communications Chemistry, 6, 147.

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TEM Analysis of Degraded Mg-4Ag Wire

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Electron
microscopy experiments of a Mg-4Ag wire sample degraded in SBF are
performed at the Ernst-Ruska center in Jülich. An approximately
100 nm thin TEM lamella is prepared using the Dual-FIB workstation
FEI Helios NanoLab 400S (Thermo Fisher Scientific Inc., Waltham, Massachusetts).
Carbon is used as a protective layer for the region of interest by
both electron and ion beam deposition. At 30 kV and 5.5 nA cross-sectional
trenches are milled above and below the ROI by an Ion beam (Gallium).
The TEM lamella is further prepared by edge cleaning and undercutting
and transferred to a copper grid by the use of a micromanipulator
needle. Step wise thinning of the TEM lamella is performed until a
thickness of under 100 nm is reached. A final polishing at 2 kV and
47 pA is done. HAADF STEM imaging and EDX analyses shown in Figure 7 are conducted with
the aid of probe-corrected FEI Titan G2 80–200 operated at
200 kV^{36 (link)} and Velox Software (Thermo Fisher
Scientific Inc., Waltham, Massachusetts). Quantification of EDX data
in Table 2 is corrected
for absorption, using a sample thickness of 100 nm and applying the
Brown-Powell model for the ionization cross section.

Reimers J., Trinh H.C., Wiese B., Meyer S., Brehling J., Flenner S., Hagemann J., Kruth M., Kibkalo L., Ćwieka H., Hindenlang B., Lipinska-Chwalek M., Mayer J., Willumeit-Römer R., Greving I, & Zeller-Plumhoff B. (2023). Development of a Bioreactor-Coupled Flow-Cell Setup for 3D In Situ Nanotomography of Mg Alloy Biodegradation. ACS Applied Materials & Interfaces, 15(29), 35600-35610.

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Characterization of Gadodiamide Nanostructures

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For gadodiamide samples, 1 droplet of the suspension of insoluble DCN fraction was deposited on a copper grid covered with a amorphous carbon thin film, and air-dried during 2h under a protective glass cup. The TEM-STEM-EDX was a Talos F200S (Thermo Fischer Scientific, Waltham, MA) working at 200 keV, equipped with a field emission gun. The emission rate was with a C2 aperture of 50 μm (nominal diameter). Bright field and high resolution up to 800 k maximum magnification were used to image the morphology, dimension, and texture of the material. Selected area diffraction was used to resolve the state of the material (amorphous or crystallized) using a microprobe of 4 upon a scale of 10, a camera length of 1 m, and a diffraction diaphragm aperture of 40 μm (nominal diameter). For STEM-EDX mode, the operational parameters were a C2 of 50 μm, a nanoprobe of 4 upon a scale of 10, an aperture with a converge angle of 7.5 mrad, and camera length of 260 mm to optimize the spatial resolution (around 0.5 nm) and X photons rate (between 800 and 1100 counts/s). The X-EDS spectra and maps were drawn using Velox software. The TEM and STEM images were converted to .tiff format after their treatment with Digital Micrograph software (Gatan, Pleasanton, CA). The spectra and elemental maps were transferred to .tiff format using Velox software (Thermo Fisher Scientific, Waltham, MA).

Strzeminska I., Factor C., Jimenez-Lamana J., Lacomme S., Subirana M.A., Le Coustumer P., Schaumlöffel D., Robert P., Szpunar J., Corot C, & Lobinski R. (2022). Comprehensive Speciation Analysis of Residual Gadolinium in Deep Cerebellar Nuclei in Rats Repeatedly Administered With Gadoterate Meglumine or Gadodiamide. Investigative Radiology, 57(5), 283-292.

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