Nis element ar software

Manufactured by Nikon

Sourced in Japan, United States

NIS-Element AR software is a comprehensive imaging and analysis solution designed for microscopy applications. It provides a user-friendly interface and a wide range of tools for image acquisition, processing, and analysis. The software is compatible with various Nikon microscope systems and enables researchers to capture, organize, and analyze their microscopic data effectively.

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Lab products found in correlation

Eclipse ti microscope, by Nikon (3 mentions) Orca r2 camera, by Hamamatsu Photonics (2 mentions) Eclipse ti e microscope, by Nikon (2 mentions) Perfect focus system, by Nikon (2 mentions) No 1.5 glass coverslip, by Avantor (2 mentions) Emccd camera, by Oxford Instruments (2 mentions) Eclipse ti2 microscope, by Nikon (2 mentions) Mc ds qi2 mono digital camera, by Nikon (2 mentions) Ds qi2 monochrome microscope camera, by Nikon (2 mentions) Eclipse 80i microscope, by Nikon (2 mentions) Eclipse ti e inverted microscope, by Nikon (2 mentions) Lipofectamine 2000 reagent, by Thermo Fisher Scientific (2 mentions) Orca 2 er, by Hamamatsu Photonics (1 mentions) Plan apochromat 100 1.45 na, by Nikon (1 mentions) Metamorph software, by Molecular Devices (1 mentions) μ slide 8 well, by Ibidi (1 mentions) Allegra 21r centrifuge, by Beckman Coulter (1 mentions) A1 scanning confocal microscope, by Nikon (1 mentions) Ht7700, by Hitachi (1 mentions) Ds ri1 camera, by Nikon (1 mentions)

43 protocols using nis element ar software

Quantifying Droplet Formation and Saturation

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In order to quantify droplet formation, we used the intensity-based cell counting macro from NIS-Element AR software provided by Nikon, extracting the number and size distribution of the droplets at each time point. Then, the data were plotted using Origin Pro 8.5.
For measuring the C saturation, the total area covered by the droplets were measured as a function of FUS concentration using NIS-Element AR software. The C_sat was defined as the intersection between the fit of the linearly growing region of the graph and the x-axis. In other words, the concentration of the protein in which the droplets start to form.

Niaki A.G., Sarkar J., Cai X., Rhine K., Vidaurre V., Guy B., Hurst M., Lee J.C., Koh H.R., Guo L., Fare C.M., Shorter J, & Myong S. (2019). Loss of dynamic RNA interaction and aberrant phase separation induced by two distinct types of ALS/FTD-linked FUS mutations. Molecular cell, 77(1), 82-94.e4.

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Microscopy Imaging of Bacterial Cells

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C. crescentus cells were grown up to exponential phase (OD_660nm < 0.3) and spotted on 0.3% agarose pads containing M2G medium, unless specified otherwise. Microscopy was performed on an Eclipse 80i microscope (Nikon, Tokyo, Japan) equipped with a phase-contrast objective Plan Apochromat 100×/1.40 NA (Nikon, Tokyo, Japan), an Orca-II-ER (Hamamatsu Photonics, Hamamatsu City, Japan) and an Andor iXon DU-897E camera (Andor Technology Ltd., Belfast, UK) with 2× optivar. Images were acquired every 2.5 min using MetaMorph software (Molecular Devices, Sunnyvale, CA, USA). For still images of E. coli strains, cells were grown at 30°C up to exponential phase (OD_600nm<0.3) and spotted on 1% agarose pads. For microfluidic experiments, E. coli cells were loaded and grown for at least 5 generations in the microfluidic device prior to imaging. Microscopy was performed on an Eclipse Ti-E microscope (Nikon, Tokyo, Japan) equipped with Perfect Focus System (Nikon, Tokyo, Japan) and an Orca-R2 camera (Hamamatsu Photonics, Hamamatsu City, Japan) and a phase-contrast objective Plan Apochromat 100×/1.45 NA (Nikon, Tokyo, Japan). Time-lapse images were acquired every 5 sec using NIS-Element Ar software (Nikon Instruments INC., Melville, NY USA).

Campos M., Surovtsev I.V., Kato S., Paintdakhi A., Beltran B., Ebmeier S.E, & Jacobs-Wagner C. (2014). A constant size extension drives bacterial cell size homeostasis. Cell, 159(6), 1433-1446.

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Quantifying Liposomal Particle Extravasation

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The average number of liposomal particles localized in the interstitial space were enumerated from video stills acquired using Nikon NIS element AR software as described previously. In the selected FOVs, a green vessel tracer was used to delineate the vascular region from the interstitial space which was devoid of green (FITC) tracer. The extent of particle extravasation from the vessel walls was determined using an automated intensity profile function (Nikon Elements). For instance, particles located in the interstitial space with minimal vessel tracer were profiled by lowest FITC intensity signal while particles trapped around the vessel walls showed highest intensity of both FITC and rodhamine signals. Cross-sectional intensity profiles of particles were enumerated and plotted as function of distance from nearest vessel wall which was defined by areas with highest FITC signal. Fluorescent settings of FITC and rhodhamine channels were kept same across experimental groups.

Kirui D.K., Celia C., Molinaro R., Bansal S.S., Cosco D., Fresta M., Shen H, & Ferrari M. (2015). Mild Hyperthermia Enhances Transport of Liposomal Gemcitabine and Improves in vivo Therapeutic Response. Advanced healthcare materials, 4(7), 1092-1103.

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Fluorescence Imaging of E. coli Cells

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A total of 1 ml culture of the E. coli strain to be imaged was grown from an overnight culture till OD₆₀₀ = 0.1–0.2. It was then chilled on ice followed by centrifugation at 6000 × g, 4 °C for 1 min to form a cell pellet. Then they were washed with ice-cold 1× PBS twice and resuspended in 100 μl 1× PBS.
In all, 1.5% (w/v) agarose gel was prepared by dissolving agarose in 1× PBS. A few μl cell suspension was sandwiched between a No. 1.5 glass coverslip (VWR) and a thin slab of the agarose gel. The sample was then imaged.
The epifluorescence images were acquired by a Nikon Ti Eclipse microscope (Nikon Instruments, Inc.) using an oil immersion objective (1.46 NA, 100×), which spans an area of ~133 × 133 μm² for DIC (no filter, autofluorescence) and fluorescence imaging (Ex 480–500 nm, Em 509–547 nm, exposure time 200 ms). The images were acquired using an EMCCD camera (Andor). They were processed using the NIS-Element AR software (Nikon Instruments, Inc.).

Poddar A., Azam M.S., Kayikcioglu T., Bobrovskyy M., Zhang J., Ma X., Labhsetwar P., Fei J., Singh D., Luthey-Schulten Z., Vanderpool C.K, & Ha T. (2021). Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nature Communications, 12, 874.

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Visualizing HIV-1 RNA Packaging Efficiency

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Clarified supernatants were mixed with polybrene (50 μg/ml, final concentration), placed on an 8-well μ-Slide (Ibidi), and centrifuged at low speed (1200 × g, S2096 Rotor, Allegra 21R Centrifuge, Beckman) for 15 min before imaging. Images were acquired using an inverted Nikon Eclipse Ti microscope with a 100× 1.40 numerical aperture oil objective, an X-Cite 120 system (EXFO Photonic Solution Inc.), an ANDOR technology iXon camera, and NIS element AR software (Nikon). The excitation and emission filter sets were 427/10 nm and 480/40 nm for CeFP, 504/12 nm and 542/27 nm for YFP. Gag particles were identified by CeFP signals whereas HIV-1 RNA genomes were identified by the YFP signals. Identification and localization of fluorescent protein signals were performed using custom MatLab programs. RNA packaging efficiency was determined by the proportion of CeFP signals that colocalized with YFP signals.

Liu Y., Nikolaitchik O.A., Rahman S.A., Chen J., Pathak V.K, & Hu W.S. (2017). HIV-1 Sequence Necessary and Sufficient to Package Non-viral RNAs into HIV-1 Particles. Journal of molecular biology, 429(16), 2542-2555.

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Quantifying Adult Hippocampal Neurogenesis

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For the assessment of adult DG neurogenesis and active caspase 3-positive cells, stereological cell counting was performed in serial coronal sections (180 μm pitch) covering the complete rostro-caudal extension of the DG, as previously described [8 (link)]. Fluorescence images were captured with a Nikon A1 confocal scanning microscope equipped with a 40x air objective and a motorized stage. For each section, confocal z-stack images (1 μm z-step size) covering the complete DG were acquired and DG reconstructed with the NIS Element AR software (Nikon). Immunopositive cells in the granular cell layer (GCL) and the subgranular zone (SGZ, defined as a 10 μm region below the GCL) were counted on the reconstructed images by an operator blind to the experimental groups according, to the optical dissector principle [57 (link)].

Barbieri R., Contestabile A., Ciardo M.G., Forte N., Marte A., Baldelli P., Benfenati F, & Onofri F. (2018). Synapsin I and Synapsin II regulate neurogenesis in the dentate gyrus of adult mice. Oncotarget, 9(27), 18760-18774.

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TEM Analysis of Yeast Cell Wall Structure

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Transmission electron microscopy (TEM) analysis of the S. cerevisiae cell wall was carried out as described by Bzducha-Wrobel et al. [42 (link)]. For microscopic observations, yeast cells in glutaraldehyde prepared in phosphate buffer (pH 7.2) were fixed in osmium solution (OsO₄). After rinse with cold water and dehydration with ethanol, the samples were embedded in Epon resin. Ultrathin sections were prepared by means of an ultramicrotome (Leica UC6, Biberach, Germany). Thereafter, the sections were stained as described by Deryabina et al. [43 (link)] and examined by TEM (Hitachi HT7700, Ibaraki, Japan).
Light microscopic images were obtained using a Nikon Eclipse Ti-E inverted microscope equipped with DS-Ri1 camera and NIS-Element AR software (Nikon, Tokyo, Japan).

Xu S., Zhang G.Y., Zhang H., Kitajima T., Nakanishi H, & Gao X.D. (2016). Effects of Rho1, a small GTPase on the production of recombinant glycoproteins in Saccharomyces cerevisiae. Microbial Cell Factories, 15, 179.

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Quantifying Thoracic Aortic Remodeling

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The well-fixed thoracic aortic ring specimens were subjected to conventional tissue processing and embedded in paraffin wax. Thin sections (5 µm) were produced and stained with hematoxylin and eosin (H&E) to visualize the tissue morphology. Nikon Eclipse Ti2 microscope was used to capture the microscopic images of the thoracic aortic rings (4× and 40×). The thickness of the aorta was measured with Nikon NIS-Element AR software (Version 5.1). The media thickness was determined by measuring the distance from the internal elastic lamina to the external lamina. For each slide, measurements from 4 points (12, 3, 6, and 9 o’clock positions) were averaged. The lumen inner diameter was determined from the average of 12 and 6, and 9 and 3 o’clock positions. The media-to-lumen ratio, an index of aortic vascular remodelling, was calculated based on the measured lumen inner diameter and media data [28 (link)].

Goh B.H., Cheng H.S., Alexandra P.T., Ting K.N., Palanisamy U.D, & Tan J.B. (2023). Geraniin Ameliorates Hypertensive Vascular Remodelling in a Diet-Induced Obese Animal Model through Antioxidant and Anti-Inflammatory Effects. Nutrients, 15(12), 2696.

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Cell Morphology Measurements in BHI Broth

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Cell lengths and widths of strains growing in BHI broth were measured from phase-contrast images by using Nikon NIS-Element AR software as described before (Barendt et al., 2009 (link), Tsui et al., 2014 (link)). For strains that do not show chaining morphology, separated stage 1 cells or daughter cells of stage 4 cells were measured. For strains that form short chains of cells, measurements included cells in chains whose widths at constriction sites were < 50% of cell widths. Fifty or more cells from two independent experiments were measured for each strain. P values were obtained by one-way ANOVA analysis (GraphPad Prism, nonparametric Kruskal-Wallis test).

Tsui H.C., Zheng J.J., Magallon A.N., Ryan J.D., Yunck R., Rued B.E., Bernhardt T.G, & Winkler M.E. (2016). Suppression of a Deletion Mutation in the Gene Encoding Essential PBP2b Reveals a New Lytic Transglycosylase Involved in Peripheral Peptidoglycan Synthesis in Streptococcus pneumoniae D39. Molecular microbiology, 100(6), 1039-1065.

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Immunostaining and Imaging of Cells and Organoids

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The cells were fixed with 4% paraformaldehyde for 15 min, whereas whole‐mount organoid samples were fixed using a mixture of 0.2% glutaraldehyde and 4% paraformaldehyde for 20 min. Samples were then permeabilized using 0.1% Triton X‐100 and blocked in a buffer solution (5% goat serum, 1% BSA, 0.05% Triton X‐100, pH 7.4). The fixed cells were then subjected to overnight incubation with a mouse anti‐Ki67 antibody (1 : 100, #550609; BD Pharmingen™, San Diego, CA, USA), followed by staining with Alexa Fluor 488 Goat anti‐Mouse IgG (1 : 500; Invitrogen, Carlsbad, CA, USA) for 1.5 h. Whole‐mount actin staining of organoids was conducted using Alexa Fluor 568 phalloidin staining (1 : 40, #A12380; Invitrogen). Nuclei were counter‐stained with DAPI (1 μg·mL⁻¹). Ki67 staining was imaged using a Zeiss fluorescent microscope (Carl Zeiss AG, Oberkochen, Germany). Whole‐mount actin staining was imaged using confocal laser scanning microscopy, and a maximum intensity projection (Z‐stacking) was performed with nis‐element ar software (Nikon, Minato, Japan).

Chittavanich P., Saengwimol D., Roytrakul S., Rojanaporn D., Chaitankar V., Srimongkol A., Anurathapan U., Hongeng S, & Kaewkhaw R. (2023). Ceftriaxone exerts antitumor effects in MYCN‐driven retinoblastoma and neuroblastoma by targeting DDX3X for translation repression. Molecular Oncology, 18(4), 918-938.

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