Elements ar

Manufactured by Nikon

Sourced in Japan, Canada

Nikon Elements AR is a high-performance software package designed for advanced image analysis and data processing. It provides a comprehensive suite of tools for researchers, scientists, and professionals working in various fields, including life sciences, materials science, and microscopy. The software offers a user-friendly interface, powerful image processing capabilities, and seamless integration with Nikon's imaging systems.

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Lab products found in correlation

Lsm 710, by Zeiss (2 mentions) Ab15530, by Abcam (1 mentions) Ds ri1, by Nikon (1 mentions) A1r point scanning confocal microscope, by Nikon (1 mentions) Alexa fluor 594 secondary antibody, by Thermo Fisher Scientific (1 mentions) Alexa fluor 488 secondary antibody, by Thermo Fisher Scientific (1 mentions) Vectashield mounting medium, by Vector Laboratories (1 mentions) Orca er camera, by Nikon (1 mentions) Rinzl plastic coverslips, by Electron Microscopy Sciences (1 mentions) Te2000 microscope, by Nikon (1 mentions) P35g 1.5 20 c, by MatTek (1 mentions) T1892, by Merck Group (1 mentions) Vectashield, by Nikon (1 mentions) Ti microscope, by Nikon (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Thermo Fisher Scientific (1 mentions) Vector s 1000, by Vector Laboratories (1 mentions) Cytoseal, by Thermo Fisher Scientific (1 mentions) Ab184674, by Merck Group (1 mentions) Ab152, by Merck Group (1 mentions) Ap124b, by Merck Group (1 mentions)

18 protocols using elements ar

Laminin-α2 Chain Immunofluorescence

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Slides were washed three times with 1 × phosphate-buffered saline (PBS) and permeabilized with 0.03% Triton X-100 in PBS for 20 minutes at RT and subsequently blocked with 5% Normal Goat Serum (Vector S-1000, Vector Laboratories, Burlingame, Ca) diluted in PBS for 60 minutes. Slides were washed three times with 1 × PBS and three times with 0.5% bovine serum albumin (BSA), then incubated with Rat anti-Lamininα2 chainprimary (1:100, Abcam 11576, Cambridge, MA) for 60 minutes at RT. Slides were washed three times with 0.5% BSA and incubated with Goat anti-Rat Alexa Fluor 488 secondary (1:500, Life Technologies A-11006) for 60 minutes at RT. Slides were washed three times with 0.5% BSA, 3 × with 1 × PBS, and incubated with 4′,6-diamidino-2-phenylindole (DAPI) (Life Technologies 1370421, Thermo-Fisher) for 1 minute. Slides were washed six times with 1 × PBS and coverslips were mounted with Cytoseal XYL (Richard-Allen Scientific 8312-4, Thermo-Fisher). Slides were imaged using the Olympus Fluo-view 1000-1 confocal microscope. Myofiber diameter was determined using an automated macro written in Nikon Elements AR (Nikon Elements AR, Nikon, Tokyo, Japan).

Zhang C., Ferrari R., Beezhold K., Stearns-Reider K., D’Amore A., Haschak M., Stolz D., Robbins P.D., Barchowsky A, & Ambrosio F. (2016). Arsenic Promotes NF-Kb-Mediated Fibroblast Dysfunction and Matrix Remodeling to Impair Muscle Stem Cell Function. Stem cells (Dayton, Ohio), 34(3), 732-742.

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Immunohistochemical Analysis of α-Synuclein

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A 1:12 series of sections containing the SNpc was washed 6 × 5 min in TBS (pH 7.6). A subset of sections was treated with 10 µg ml⁻¹ proteinase K (Invitrogen, 25530015) for 30 min at RT. Following proteinase K digestion, sections were washed in TBS-Tx, and were processed for immunohistochemistry as described above. A pan rabbit anti-α-syn primary was used at 1:1,000 (Abcam, AB15530). Sections were mounted, dehydrated, and coverslipped as described above. Representative images were taken with a Nikon Eclipse 90i microscope with a Nikon DS-Ri1 color camera using Nikon Elements AR (Version 4.50.00, Melville, NY) software.

Patterson J.R., Duffy M.F., Kemp C.J., Howe J.W., Collier T.J., Stoll A.C., Miller K.M., Patel P., Levine N., Moore D.J., Luk K.C., Fleming S.M., Kanaan N.M., Paumier K.L., El-Agnaf O.M, & Sortwell C.E. (2019). Time course and magnitude of alpha-synuclein inclusion formation and nigrostriatal degeneration in the rat model of synucleinopathy triggered by intrastriatal α-synuclein preformed fibrils. Neurobiology of disease, 130, 104525.

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Quantifying Retinal Brn3a-Positive Cells

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At 12, 24, and 48 h after treating the eyes with NMDA or PBS, whole retinas were isolated (three cohorts of six, n = 18) and immunostained with antibody against Brn3a (1:100 dilution) according to the methods published from this laboratory [25 (link)]. Digitized images of the whole retina was obtained by using a Zeiss Imager.Z2 microscope and compiled by using Adobe Photoshop Software 7.0 (Adobe Systems Incorporated, CA). The number of Brn3a-positive cells in each retina was quantitated in four areas of equal size from the optic disc (Boxed areas, 900 x 800 um size, 20x magnification) by using Nikon Elements AR software (Nikon Instruments Inc., Melville, NY). Statistical significance was determined by ANOVA, followed by a post hoc-Tukey’s test (GB-Stat Software, Dynamic Microsystems, Silver Spring, MD) and the results were expressed as the mean ± SEM.

Chintala S., Cheng M, & Zhang X. (2015). Decreased Expression of DREAM Promotes the Degeneration of Retinal Neurons. PLoS ONE, 10(5), e0127776.

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Nikon Eclipse 90i Microscope Imaging

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Imaging was performed with a Nikon Eclipse 90i microscope with a QICAM camera (QImaging, Surrey, British Columbia, Canada), using Nikon Elements AR software (Version 4.500.00, Melville, NY). Stippled images were created from stitched micrographs Adobe Photoshop CS2.

Howe J.W., Sortwell C.E., Duffy M.F., Kemp C.J., Russell C.P., Kubik M., Patel P., Luk K.C., El-Agnaf O.M, & Patterson J.R. (2021). Preformed fibrils generated from mouse alpha-synuclein produce more inclusion pathology in rats than fibrils generated from rat alpha-synuclein. Parkinsonism & related disorders, 89, 41-47.

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Immunofluorescence Staining of Zebrafish Skeletal Myofibers

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Immunofluorescence staining of zebrafish skeletal myofibers was performed by adapting a protocol previously described⁸⁴ (Supplementary Note). Myofibers were incubated in primary antibody overnight at 4 °C, washed in 1x Phosphate-Buffered Saline with 0.1% Tween 20 (PBST), then incubated with goat anti-mouse Alexa Fluor 488 secondary antibody (Thermo Fisher Scientific, A11001; 1:500) and goat anti-rabbit Alexa Fluor 594 secondary antibodies (Thermo Fisher Scientific, A11037; 1:250) for 1 h at room temperature. Further washing in PBST was performed before mounting with Vectashield Mounting Medium (Vector Laboratories). Primary antibodies used were rabbit polyclonal anti-sarcomeric α-actinin (Cell Signaling Technologies, 3134; 1:25) and mouse monoclonal anti-titin (Merck, T9030; 1:200). Digital images were captured with Newcastle University Bioimaging Unit’s Nikon A1R point scanning confocal microscope (Nikon) using Nikon Elements AR (v5.21.03).

Töpf A., Cox D., Zaharieva I.T., Di Leo V., Sarparanta J., Jonson P.H., Sealy I.M., Smolnikov A., White R.J., Vihola A., Savarese M., Merteroglu M., Wali N., Laricchia K.M., Venturini C., Vroling B., Stenton S.L., Cummings B.B., Harris E., Marini-Bettolo C., Diaz-Manera J., Henderson M., Barresi R., Duff J., England E.M., Patrick J., Al-Husayni S., Biancalana V., Beggs A.H., Bodi I., Bommireddipalli S., Bönnemann C.G., Cairns A., Chiew M.T., Claeys K.G., Cooper S.T., Davis M.R., Donkervoort S., Erasmus C.E., Fassad M.R., Genetti C.A., Grosmann C., Jungbluth H., Kamsteeg E.J., Lornage X., Löscher W.N., Malfatti E., Manzur A., Martí P., Mongini T.E., Muelas N., Nishikawa A., O’Donnell-Luria A., Ogonuki N., O’Grady G.L., O’Heir E., Paquay S., Phadke R., Pletcher B.A., Romero N.B., Schouten M., Shah S., Smuts I., Sznajer Y., Tasca G., Taylor R.W., Tuite A., Van den Bergh P., VanNoy G., Voermans N.C., Wanschitz J.V., Wraige E., Yoshimura K., Oates E.C., Nakagawa O., Nishino I., Laporte J., Vilchez J.J., MacArthur D.G., Sarkozy A., Cordell H.J., Udd B., Busch-Nentwich E.M., Muntoni F, & Straub V. (2024). Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy. Nature Genetics, 56(3), 395-407.

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Agar Pad Microscopy for Time-Lapse Imaging

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2% LB agar was cut into approximately 10 mm × 10 mm squares and inoculated with 1 µl of liquid culture. The pad was then wedged, in a glass-bottomed dish (P35G-1.5-20-C; MatTek Corp.), between two plastic coverslips (Rinzl Plastic Coverslips, Size 22 × 22 mm; Electron Microscopy Science) manually bent in half at a 90° angle. Thus, half of each plastic coverslip made contact with the bottom of the dish, while the other half made contact with the agar pad. After placing a drop of approximately 50 µl of water on top of each plastic coverslip to maintain humidity in the dish, the MatTek dish was sealed with parafilm (this setup is illustrated in Fig. 1A). Cells (Table 1) were grown for approximately 6 h at room temperature (approximately 23°) during a timelapse acquisition on a Nikon TE 2000 microscope equipped with an Orca ER camera, a 20 × phase contrast objective, and Perfect Focus. A large area of the sample was composited with automatic image stitching by Nikon Elements AR. Areas toward the center of the pad were selected for imaging.

Polka J.K, & Silver P.A. (2014). Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression. PeerJ, 2, e597.

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Thioflavin-S Staining of SNpc

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A 1:12 series of sections containing the SNpc was washed 4 × 5 min in TBS (pH 7.3), mounted on subbed slides, and allowed to dry for at least an hour. Samples were incubated for 25 min in 0.5% potassium permanganate (Sigma-Aldrich, 223468) in TBS to quench autofluorescence. Sections were washed in TBS, destained 3 min in 0.2% potassium disulfite (Sigma-Aldrich, P2522) and 0.2% oxalic acid (Sigma-Aldrich, 75688) in TBS, and stained for 3 min in 0.0125% thioflavin-S in 40% ethanol/60% TBS (Sigma-Aldrich, T1892). Sections were differentiated in 50% ethanol/50% TBS, washed 5 × 5 min in TBS, washed 3 × 5 min in ddH₂O, and coverslipped with Vectashield hard set mounting media (Vector Laboratories, H-1400). Images were taken with a Nikon Eclipse 90i microscope with a QICAM camera (QImaging, Surrey, British Columbia, Canada), using Nikon Elements AR (Version 4.50.00, Melville, NY) software.

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Kinetoplast Staining and Microscopy Protocol

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For experiments with kinetoplast staining, MitoTracker^® Red was added to the culture at 500 nM and shaken at 27 °C for 30 minutes to allow uptake. Cells were harvested for microscopy at 2–5 × 10⁶cells/mL and washed twice in PBS before suspending in 3.7% formaldehyde/PBS solution and 100 μl of suspension was fixed to glass slides for 10 minutes. Cells were washed three times in PBS, permeabilized with 0.1% Triton X-100 and washed an additional three times in PBS. Blocking was performed for 60 minutes using 5.5% FBS supplemented with 0.05% Tween 20 in PBS. All incubation steps were performed in humid chamber and all antibodies were used at concentrations indicated in text. Cells were stained using 100 uL 1 μg/mL DAPI solution for 1 minute and washed three times with PBS. Cells were air dried and mounted using Vectashield^® before imaging was performed using a Nikon Ti microscope. Image analysis was performed using ImageJ (NIH) and Nikon Elements AR.

Fleming I.M., Paris Z., Gaston K.W., Balakrishnan R., Fredrick K., Rubio M.A, & Alfonzo J.D. (2016). A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Scientific Reports, 6, 21438.

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Primary Hippocampal Neuron Transfection Protocol

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Primary cells were harvested from the hippocampi of E18 Sprague-Dawley rat pups obtained from Charles River Laboratories. Hippocampal tissue was digested using papain and mechanical trituration. Cells were plated onto poly-ornithine/laminin coated 24-well plates with a density of approximately 100,000 per well. Cells were cultured in medium composed of 50/50 DMEM/F12, 0.5× N2 and 0.5× B27 supplements. 1% Penicillin/Streptomycin was added to the medium for the first 36 hours following harvest and subsequently removed 4 hours before transfection to avoid adverse effects on lipid-based delivery vehicles. Transfections were carried out by adding 20 μL of the lipidoid-RNA complex (containing a total of 0.5 μg RNA) to each well and incubating the primary hippocampal cultures at 37°C for 24 hours. After incubation, mCherry expression was observed via fluorescence imaging with 10X magnification, and the images were analyzed using Nikon Elements AR.

Chang T.Y., Shi P., Steinmeyer J.D., Chatnuntawech I., Tillberg P., Love K.T., Eimon P.M., Anderson D.G, & Yanik M.F. (2014). Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery. Integrative biology : quantitative biosciences from nano to macro, 6(10), 926-934.

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Immunohistochemical Analysis of Neurodegeneration

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Fixed brains were frozen on a sliding microtome and sliced at 40 μm. Free-floating sections were stored in cryoprotectant (30% sucrose, 30% ethylene glycol, 0.05M PBS) at −20°C. A 1:4 series was used for staining. Nonspecific staining was blocked with 10% normal goat serum. Sections were then incubated overnight inappropriate primary antibody: pSyn (Abcam, Ab184674, 1:10,000) or TH (Millipore, AB152, 1:4,000). Primary antibodies were prepared in Tris-buffered saline with 1% NGS/0.25% Triton X-100. Sections were incubated with appropriate biotinylated secondary antibodies at 1:500 (anti-mouse, Millipore AP124B or anti-Millipore AP132B), followed by Vector ABC standard detection kit (Vector Laboratories PK-6100). Visualization was performed using 0.5 mg/ml 3,3’ diaminobenzidine (DAB, Sigma-Aldrich) for 30-60 seconds at room temperature and enhanced with nickel. Slides stained for pSyn were counter-stained with Cresyl violet. Slides were dehydrated before cover-slipping with Cytoseal (Richard-Allan Scientific) and imaged on a Nikon Eclipse 90i microscope with a QICAM camera (QImaging) and Nikon Elements AR (version 4.50.00).

Gezer A.O., Kochmanski J., VanOeveren S.E., Cole-Strauss A., Kemp C.J., Patterson J.R., Miller K.M., Kuhn N.C., Herman D.E., McIntire A., Lipton J.W., Luk K.C., Fleming S.M., Sortwell C.E, & Bernstein A.I. (2020). Developmental exposure to the organochlorine pesticide dieldrin causes male-specific exacerbation of α-synuclein-preformed fibril-induced toxicity and motor deficits. Neurobiology of disease, 141, 104947.

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