Digital micrograph 3

Manufactured by Ametek

Sourced in United States, Germany

Digital Micrograph 3.1 software is a comprehensive data acquisition and analysis platform developed by Ametek. It provides a unified interface for controlling and acquiring data from various microscopy and imaging instruments. The software's core function is to enable users to capture, process, analyze, and visualize high-quality images and data from their research or industrial applications.

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Lab products found in correlation

Em10 electron microscope, by Zeiss (5 mentions) Orius sc1000 ccd camera, by Ametek (5 mentions) Ultrascan 1000, by Ametek (4 mentions) Polybed 812 epoxy resin, by Polysciences (4 mentions) Tecnai g2 f20 s twin microscope, by Thermo Fisher Scientific (3 mentions) Gatan sc1000 orius ccd camera, by Ametek (3 mentions) Tecnai 12 120kv tem, by Thermo Fisher Scientific (3 mentions) Uc6 ultramicrotome, by Leica (3 mentions) Leo em910 transmission electron microscope, by Zeiss (3 mentions) Zetasizer nano z, by Malvern Panalytical (2 mentions) Gimp 2, by Ametek (2 mentions) Jem 2010, by JEOL (2 mentions) Em ac20, by Leica (2 mentions) Hq silver kit, by Nanoprobes (2 mentions) Nanogold conjugated anti rabbit secondary antibody, by Thermo Fisher Scientific (2 mentions) Tecnai 12 tem, by Thermo Fisher Scientific (2 mentions) Orius sc1000b ccd, by Ametek (2 mentions) Jem 1400plus, by JEOL (2 mentions) Orius sc1000 ccd digital camera, by Ametek (2 mentions) Ultracut uct microtome, by Leica (2 mentions)

Spelling variants of this product

Digital Micrograph (158 citations) Digital Micrograph (GMS 3, (5 citations) Gatan digital micrograph software version 3.6.4 (3 citations) Digital Micrograph software (GMS 3, (3 citations) Digital Micrograph®, Version 3.21, GMS 3 (2 citations) Orius SC1000 Digital Camera and Digital Micrograph 3.11.0 (2 citations)

41 protocols using digital micrograph 3

Visualizing calcium-alginate-DNA nanoparticles

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5 μL AlgS-Ca²⁺-pDNA NPs (using gold-labeled AlgS) and Ca²⁺-pDNA were placed on carbon-coated film on copper EM grids hydrophilized by glow discharge. The excess liquid was blotted, and the grids were allowed to dry at RT for 4 h. The samples were imaged at RT using an FEI Tecnai 12G2 TWIN TEM (Gatan model 794 charge coupled device [CCD], bottom mounted) at an acceleration voltage of 120 kV. Specimens were studied in a low-dose imaging mode to minimize beam exposure and electron beam radiation damage. Images were recorded digitally using the Digital Micrograph 3.6 software (Gatan, Munich, Germany).
For cryo-TEM analysis, thin (∼0.25-μm) specimens of NPs were deposited, under controlled humidity and temperature, on perforated carbon films supported on copper grids. The excess liquid was blotted, and the specimen was vitrified by rapid plunging into liquid ethane precooled with liquid nitrogen in a controlled-environment vitrification system. The samples were examined at −178°C using an FEI Tecnai 12 G2TWIN TEM (Gatan model 794 CCD, bottom mounted) equipped with a Gatan 626 cryo-holder. Specimens were studied in a low-dose imaging mode to minimize beam exposure and electron beam radiation damage. Images were recorded digitally using the Digital Micrograph 3.6 software (Gatan). Particle size measurements were performed using Adobe Photoshop CS 5.1 (San Jose, CA, USA).

Goldshtein M., Shamir S., Vinogradov E., Monsonego A, & Cohen S. (2019). Co-assembled Ca2+ Alginate-Sulfate Nanoparticles for Intracellular Plasmid DNA Delivery. Molecular Therapy. Nucleic Acids, 16, 378-390.

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Characterization of Biosynthesized Quantum Dots

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The size of biosynthesized QDs was determined by dynamic light scattering (DLS). Purified and concentrated QDs were sonicated for 2 min and then measured in triplicate using a Zetasizer Nano (ZS) (Malvern Instrument Ltd.). High resolution scanning transmission electron microscopy (HR-STEM) was used to confirm nanometric size and chemical composition (FEI Tecnai G2 F20 S-Twin microscope, operated at 200 kV). For these purposes, 2 μL of the purified and concentrated QDs solution was added to a HC300-Cu grid and left to dry. TEM images were processed and analyzed with Digital Micrograph 3.9.0 (Gatan Inc) and The Gimp 2.4.0 software packages. In addition, samples were chemically characterized by Energy-dispersive X-ray spectroscopy (EDS or EDX).
To determine the organic composition of the external layer of QDs, samples werefreeze-dried for 48 h and the powder obtained was mixed with KBr to form a thin pellet. FTIR spectroscopy in a range between 600 and 4000 cm^–1 was performed using a Nicolet^TM iS^TM10 (Thermo Fisher Scientific Inc.).

Órdenes-Aenishanslins N., Anziani-Ostuni G., Quezada C.P., Espinoza-González R., Bravo D, & Pérez-Donoso J.M. (2019). Biological Synthesis of CdS/CdSe Core/Shell Nanoparticles and Its Application in Quantum Dot Sensitized Solar Cells. Frontiers in Microbiology, 10, 1587.

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Nanoparticle Characterization by TEM

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TEM measurements were performed using a FEI Tecnai G2 F20 S-Twin microscope, operated at 200 kV. A drop of the dispersed sample was left to dry out on a commercial carbon coated Cu TEM grid. TEM images were processed and analyzed with Digital Micrograph 3.9.0 (Gatan Inc) and The Gimp 2.4.0 software packages. A statistical study of TEM images was carried out to quantify nanoparticles sizes. This study consists of the size measurement (diameter) of about 200 particles per sample. The counts were then plotted as frequency histograms and the mean particle size was calculated. In addition, samples were chemically characterized by Energy-dispersive X-ray spectroscopy (EDX) and electron diffraction (ED).

Bruna N., Collao B., Tello A., Caravantes P., Díaz-Silva N., Monrás J.P., Órdenes-Aenishanslins N., Flores M., Espinoza-Gonzalez R., Bravo D, & Pérez-Donoso J.M. (2019). Synthesis of salt-stable fluorescent nanoparticles (quantum dots) by polyextremophile halophilic bacteria. Scientific Reports, 9, 1953.

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Transmission Electron Microscopy of Dispersed Samples

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Transmission electron microscopy (TEM) measurements were made using a FEI Tecnai G2 F20 S-Twin microscope, operated at 200 kV. For these studies, a drop of the dispersed sample was left to dry out on a commercial carbon coated Cu TEM grid. TEM images were processed and analyzed with Digital Micrograph 3.9.0 (Gatan Inc) and The Gimp 2.4.0 software packages. In addition, samples were chemically characterized by Energy-dispersive X-ray spectroscopy (EDS or EDX).

Ulloa G., Quezada C.P., Araneda M., Escobar B., Fuentes E., Álvarez S.A., Castro M., Bruna N., Espinoza-González R., Bravo D, & Pérez-Donoso J.M. (2018). Phosphate Favors the Biosynthesis of CdS Quantum Dots in Acidithiobacillus thiooxidans ATCC 19703 by Improving Metal Uptake and Tolerance. Frontiers in Microbiology, 9, 234.

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Characterizing Nanoparticle Sizes via HR-TEM

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High-resolution transmission electron microscopy (HR-TEM) measurements were made using a JEOL JEM 2010, operated at 200 kV. For these studies, a drop of the dispersed sample was left to dry out on a commercial coal formvar Cu TEM grid 300 mesh copper grid hole with a size of 63 µm. HRTEM images were processed and analyzed with Digital Micrograph 3.9.0 (Gatan Inc.) and the Gimp 2.4.0 software packages. A statistical study of HRTEM images was carried out in order to quantify the particle size by measuring the diameter of 150 particles for each sample. Counts were then plotted as frequency histograms and the mean particle size was calculated. Chemical characterization of the samples was performed by Energy-dispersive X-ray spectroscopy (EDS o EDX) and ED (electron diffraction).

Órdenes-Aenishanslins N., Anziani-Ostuni G., Monrás J.P., Tello A., Bravo D., Toro-Ascuy D., Soto-Rifo R., Prasad P.N, & Pérez-Donoso J.M. (2020). Bacterial Synthesis of Ternary CdSAg Quantum Dots through Cation Exchange: Tuning the Composition and Properties of Biological Nanoparticles for Bioimaging and Photovoltaic Applications. Microorganisms, 8(5), 631.

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Structural Characterization of Materials by TEM

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TEM, electron diffraction, and HRTEM was performed on an FEI Tecnai T20 S-twin TEM operating at 200keV with a LaB6 filament. The FIB prepared sample was loaded in an FEI double tilt TEM holder and aligned to the desired zone axes using the diffraction pattern. TEM images and diffraction patterns were collected using a Gatan Rio 16 camera using the drift correction feature, which collects images at 20FPS, calculates the drift between subsequent images, removes the drift, and sums the images. Diffraction contrast images were collected with a 30 μm objective aperture and HRTEM images were collected without an objective aperture. Image analysis was done in Gatan Digital Micrograph 3.0 (GMS 3.0). For all FFTs displayed and analyzed care was taken to avoid streaking artefacts that result from image edges. Briefly in GMS 3.0, a 2ⁿ by 2ⁿ pixel area of interest was cropped from the image and was subsequently multiplied by a 2D Hanning window followed by computing the FT. For visualization, the log of the modulus of the FT was saved and visualized in ImageJ using the fire lookup table to facilitate viewing. For electron diffraction patterns, the log of the intensity was calculated to allow weaker peaks to be visible. Electron diffraction patterns were simulated using the CryTBox software.⁸¹

Mukhina M.V., Tresback J., Ondry J.C., Akey A., Alivisatos A.P, & Kleckner N. (2021). Single Particle Studies Reveal a Nanoscale Mechanism for Elastic, Bright, and Repeatable ZnS:Mn Mechanoluminescence in a Low Pressure Regime. ACS nano, 15(3), 4115-4133.

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Characterization of Calcified Bacterial Particles

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A FE Tecnai G2 F20 field emission transmission electron microscopy (FE-TEM) equipped with an Oxford energy dispersive X-ray (EDX) spectrometer was used. For isolation and EDX mapping analysis of calcified bacterial, samples of calcified bacterial particles were prepared by dispersing sample powders in ethanol using ultrasound for 10 minutes, then a Cu grid was used to dip part of the suspension which contained the tiny particles, and then air-dried before observation. A copper TEM half grid hold FIB sample was observed by TEM. TEM and HAADF images were collected before the EDX mapping and SAED operation was performed on samples we prepared. The TEM analytical work was carried out at 200 kV, and the diameter of selected area for SAED analysis was about 180 nm. The SAED data were analyzed by Gatan DigitalMicrograph 3.0.

Lyu J., Li F., Long H., Zhu X., Fu N., Guo Z, & Zhang W. (2024). Bacterial templated carbonate mineralization: insights from concave-type crystals induced by Curvibacter lanceolatus strain HJ-1. RSC Advances, 14(1), 353-363.

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Characterization of CuO Nanoparticle Conjugates

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The morphologies of CuO‐NP, CuO‐NP‐GramAb⁺ and CuO‐NP‐AbGram⁻ were analyzed by transmission electron microscope (TEM, JEOL JEM‐2010) operated at 200 kV, and the images were analyzed using the Digital Micrograph 3 (Gatan, Inc. Pleasanton, CA). The crystal phase was analyzed by X‐ray diffraction (XRD, X BRUKER D2 PHASER) using Cu Kα (λ=1.5418 Å) in the range of 10° to 80°. Absorption spectra of CuO‐NP were recorded by UV‐Vis spectrophotometry (Perkin Elmer Lambda 25 UV/Vis) in the wavelength range 200–700 nm. The hydrodynamic diameter size of CuO‐NP, CuO‐NP‐NH₂, CuO‐NP‐AbGram⁺ and CuO‐NP‐Ab⁻ and surface charge were measured with dynamic light scattering (DLS) and Zeta potential was determined using a Zetasizer Nano ZS (Malvern Panalytical).

Ontiveros‐Robles J.A., Villanueva‐Flores F., Juarez‐Moreno K., Simakov A, & Vazquez‐Duhalt R. (2023). Antibody‐Functionalized Copper Oxide Nanoparticles with Targeted Antibacterial Activity. ChemistryOpen, 12(5), e202200241.

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TEM Sample Preparation and Imaging

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For transmission electron microscopy, samples were prepared on 400-mesh carbon-Formvar-coated copper grids (Ted Pella, Redding, CA, USA). Grids were placed, carbon-Formvar down, on a 5 μL droplet of culture supernatant for 2 min. Culture supernatants were generated by centrifugation at 3000× g for 5 min. Samples were removed from the grid by wicking. Grids were then stained for 15–60 s on 5 μL of either 2% uranyl acetate stain (pH 3) or 2% sodium phosphotungstate tribasic hydrate stain (pH 6). Phosphotungstate stain was made freshly every week to ensure that the solution did not disassociate. Grids were allowed to dry in air overnight and were examined within 48 h of staining. Images were obtained at 8500 to 34,000 magnification on an FEI Tecnai F20 transmission electron microscope (TEM) (FEI Inc. Hillsboro, OR, USA). Grids were analyzed by examining randomly selected grid squares. Images were obtained with a BM UltraScan camera and stored in digital micrograph 3 (Gatan, Pleasanton, CA, USA) and TIFF formats.

Iverson E.A., Goodman D.A., Gorchels M.E, & Stedman K.M. (2017). Genetic Analysis of the Major Capsid Protein of the Archaeal Fusellovirus SSV1: Mutational Flexibility and Conformational Change. Genes, 8(12), 373.

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Electron Microscopy Sample Preparation Protocol

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For electron microscopy (EM), cells were cultured on lumox cell culture dishes (Sarstedt AG & Co., Nümbrecht, Germany) and fixed in 4% PFA, 2.5% glutaraldehyde, and 0.1 M cacodylate buffer (pH 7.4) for 15 min at 37 °C. After PBS wash, cells were fixed with 1% OsO4 in cacodylate buffer for 1 h at RT followed by a second wash with 0.1 M cacodylate buffer. Cells were dehydrated using an acetone series and mounted in Epon resin (Fluka, Buchs, Switzerland). Blocks with embedded cells were sectioned with a vibratome VT 1000 S (Leica, Wetzlar, Germany) and ultrathin sections were stained with uranyl acetate and lead citrate. The sections were examined and photographed with a Zeiss EM10 electron microscope (Zeiss) and a Gatan SC1000 OriusTM CCD camera (GATAN, Munich, Germany) in combination with the DigitalMicrograph™ 3.1 software (GATAN, Pleasanton, CA, USA).

Pieger K., Schmitt V., Gauer C., Gießl N., Prots I., Winner B., Winkler J., Brandstätter J.H, & Xiang W. (2022). Translocation of Distinct Alpha Synuclein Species from the Nucleus to Neuronal Processes during Neuronal Differentiation. Biomolecules, 12(8), 1108.

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