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Nis elements ar 4

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NIS-Elements AR 4.2 is a software package designed for the operation and analysis of microscope imaging data. It provides a comprehensive suite of tools for image acquisition, processing, and analysis, catering to the needs of researchers and scientists working in various fields of microscopy.

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Lab products found in correlation

Eclipse ti, by Nikon (13 mentions) Eclipse ti microscope, by Nikon (9 mentions) Eclipse ti e, by Nikon (9 mentions) A1r confocal microscope, by Nikon (8 mentions) Triton x 100, by Merck Group (5 mentions) Hoechst, by Thermo Fisher Scientific (4 mentions) Optimal cutting temperature compound, by Sakura Finetek (4 mentions) A1 confocal microscope, by Nikon (4 mentions) Eclipse ni microscope, by Nikon (3 mentions) Fluo 4 am, by Thermo Fisher Scientific (3 mentions) Gelvatol medium, by Merck Group (3 mentions) 2 methylbutane, by Merck Group (3 mentions) Eclipse ni u microscope, by Nikon (3 mentions) N sim, by Nikon (3 mentions) Mitotracker red, by Thermo Fisher Scientific (3 mentions) Af942, by R&D Systems (2 mentions) Imagepro 6.0 plus, by Media Cybernetics (2 mentions) Dxm1200c, by Nikon (2 mentions) Mca341r, by Bio-Rad (2 mentions) Ds qi1mc, by Nikon (2 mentions)

Close spelling variants of this product

NIS-Elements (1183 citations) NIS-Elements AR (215 citations) NIS-Elements 4.0 (93 citations) NIS Elements AR Analysis 4.10.00 (8 citations) NIS-Elements AR version 4.51 (7 citations) Nikon Elements AR 4.30.01 software (5 citations) NIS-Element AR 4.3 Software (5 citations) NIS-Elements AR (V. 4.0) (5 citations) NIS Elements AR Imaging Software 4.10 (3 citations) NIS-Element AR Analysis 4.20.02 64-bit software (2 citations)

145 protocols using nis elements ar 4

1

Quantifying Microglial Density in Grafts

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The density of Iba-1-positive cells was quantified using NIS Elements AR 4.00.08 software (Nikon) in a blinded manner. Briefly, graft pictures were obtained on a Nikon Eclipse Ni-U microscope (Nikon); images were captured with a color Retiga Exi digital CCD camera (QImaging) using NIS Elements AR 4.00.08 software (Nikon) and 20x magnification (air immersion, 0.75 N.A., n = 3/animal/hemisphere), and a border of the graft and striatum was outlined. All the Iba-1-positive cells in the field of view that were within the border were counted using the NIS Elements AR 4.00.08 software (Nikon) using the count feature.
George S., Rey N.L., Tyson T., Esquibel C., Meyerdirk L., Schulz E., Pierce S., Burmeister A.R., Madaj Z., Steiner J.A., Escobar Galvis M.L., Brundin L, & Brundin P. (2019). Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson’s disease. Molecular Neurodegeneration, 14, 34.
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2

Quantification of Iba1-Positive Cells

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The density of Iba1-positive cells was quantified using NIS Elements AR 4.00.08 software (Nikon) in a blinded manner as reported [46 (link)]. Briefly, multiple fields of Iba1-positive cells were captured on a Nikon Eclipse Ni–U microscope; images were obtained with a color Retiga Exidigital CCD camera (QImaging) using NIS Elements AR 4.00.08 software (Nikon) and 20x magnification (air immersion, 0.75 N.A., n = 3/animal/hemisphere), and the region of interest was outlined. All the Iba1-positive cells in the field of view that were within the border were counted using the count feature of the NIS Elements AR 4.00.08 software.
Zhang H., D'Agostino C., Tulisiak C., Thorwald M.A., Bergkvist L., Lindquist A., Meyerdirk L., Schulz E., Becker K., Steiner J.A., Cacciottolo M., Kwatra M., Rey N.L., Escobar Galvis M.L., Ma J., Sioutas C., Morgan T.E., Finch C.E, & Brundin P. (2023). Air pollution nanoparticle and alpha-synuclein fibrils synergistically decrease glutamate receptor A1, depending upon nPM batch activity. Heliyon, 9(4), e15622.
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3

Quantifying Alzheimer's-Related Protein Aggregates

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We stained coronal free-floating sections with primary antibodies against pser129 (pser129, rabbit, 1:5000; Abcam, Ab51253) and NeuN (mouse, 1:1000, Millipore, Mab377), and secondary antibodies AlexaFluor 488 anti-mouse (goat, 1:500, Jackson Immunoresearch Laboratories, 115-545-146) and AlexaFluor 594 goat anti-rabbit (goat, 1:500, Jackson Immunoresearch Laboratories, 111-585-144). The staining with thioflavin S was performed in accordance with our previous work [59 (link)].
Stained slides were blind coded before analysis and were imaged with an inverted confocal laser microscope Nikon Eclipse Ti-E. Thioflavin S staining was imaged by averaging 4x scans for each z step of the stack to remove noise using NIS Elements AR 4.00.08 software (Nikon). For all other fluorescence staining, we acquired images by single scan per stack-step. We post-treated the confocal stacks with a kernel-3 median filter to remove noise and generated all final images using NIS Elements AR 4.00.08 software (Nikon).
Rey N.L., George S., Steiner J.A., Madaj Z., Luk K.C., Trojanowski J.Q., Lee V.M, & Brundin P. (2017). Spread of aggregates after olfactory bulb injection of α-synuclein fibrils is associated with early neuronal loss and is reduced long term. Acta Neuropathologica, 135(1), 65-83.
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4

Multi-Labeling of Coronal Brain Sections

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We stained coronal free-floating sections with primary antibodies against pser129 (pser129, rabbit, 1:5000; Abcam, Ab51253) and NeuN (mouse, 1:1000, Millipore, Mab377), and secondary antibodies AlexaFluor 488 goat anti-mouse (1:500, Jackson Immunoresearch Laboratories, 115-545-146) and AlexaFluor 594 goat anti-rabbit (1:500, Jackson Immunoresearch Laboratories, 111-585-144). The staining with thioflavin-S was performed in accordance with our previous work [59 (link)].
Stained slides were blind coded before analysis and were imaged with an inverted confocal laser microscope Nikon Eclipse Ti-E. Thioflavin-S staining was imaged by averaging 4× scans for each z step of the stack to remove noise using NIS Elements AR 4.00.08 software (Nikon). For all other fluorescence staining, we acquired images by a single scan per stack step. We post-treated the confocal stacks with a kernel-3 median filter to remove noise and generated all final images using NIS Elements AR 4.00.08 software (Nikon).
Rey N.L., George S., Steiner J.A., Madaj Z., Luk K.C., Trojanowski J.Q., Lee V.M, & Brundin P. (2017). Spread of aggregates after olfactory bulb injection of α-synuclein fibrils is associated with early neuronal loss and is reduced long term. Acta Neuropathologica, 135(1), 65-83.
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5

LIPUS-Induced Calcium Response in Cells

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The cells were incubated with 2.5 μmol/L Fluo-4 AM (Beyotime) at 37 °C for 10 min. After washing with PBS, Opti-α-MEM was added and cells were observed under a laser scanning confocal microscope. The total observation and baseline times were 12 min and 30 s, respectively, whereas the LIPUS exposure period was 0.5–2.5 min; the treatment parameters were the same as those described in the “LIPUS treatment” subsection, and the interval between image captures was 4 s. The calcium response of each frame of image was quantified as ΔF/F0, where F0 is the average baseline fluorescence intensity before LIPUS processing, ΔF = FP − F0, and FP is the real-time fluorescence intensity [34 (link)]. We compared the highest FP values of each group during and after LIPUS treatment. The analysis was carried out using the NIS-Elements AR 4.20 (Nikon), GraphPad Prism 7.0, and Origin 2019 software packages.
Yao H., Zhang L., Yan S., He Y., Zhu H., Li Y., Wang D, & Yang K. (2022). Low-intensity pulsed ultrasound/nanomechanical force generators enhance osteogenesis of BMSCs through microfilaments and TRPM7. Journal of Nanobiotechnology, 20, 378.
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6

Motility Analysis of Bacterial Cells

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All strains were cultured overnight in MM liquid media and collected by centrifugation at 6000 rpm for 2 min at room temperature. After washing and resuspending in PBS, an aliquot was inserted into a tunnel chamber with 2-mm width, 40-mm length and <1 mm thickness fabricated as described in McBride (2014) . The tunnel chamber was constructed with a coverslip and a glass slide, assembled with double-sided tape and filled with MM liquid media. We also mounted cells directly from MM agar plates into agar pads (2 g of agarose to 100 ml of a 20% vol./vol. PBS and 10% vol./vol. MM broth solution), following a previously published protocol (Heering et al., 2017 (link)). In both experimental setups, motile cells were observed using a Nikon Eclipse Ti-E inverted microscope equipped with Perfect Focus System and differential interface contrast. The microscope was controlled with Nikon NIS-Elements AR 4.20. Time-lapse movies were acquired at 6 fps using a 9v DIA-lamp intensity with exposure of 100–200 ms. Trajectories were visualized in Matlab from spatial coordinates obtained by tracking individual cells using bespoke scripts implemented in ImageJ (http://rsb.info.nih.gov/ij/).
Vences-Guzmán M.Á., Peña-Miller R., Hidalgo-Aguilar N.A., Vences-Guzmán M.L., Guan Z, & Sohlenkamp C. (2021). Identification of the Flavobacterium johnsoniae cysteate-fatty acyl transferase required for capnine synthesis and for efficient gliding motility. Environmental microbiology, 23(5), 2448-2460.
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7

Immunohistochemical Staining of Tissue Sections

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Adjacent serial sections were routinely stained with H&E, immunohistochemically stained for SPARC (1:200 for 45 min; AF942, R&D Systems), the cell proliferation marker Ki-67 (1:250 for 40 min; M7249, Dako), and the macrophage/histiocyte marker CD68 (1:200 for 30 min; MCA341R, Serotec) as previously reported (36 (link)). Additional adjacent sections were subjected to the periodic acid Schiff (PAS) reaction with or without diastase (liver tissue was positive control) as previously described (43 (link)) to demonstrate phagocytic activity (histiocytes). Images of stained sections were captured on either a Nikon Eclipse E800 microscope with a Nikon DXM1200C digital camera using ImagePro 6.0 Plus (Media Cybernetics) software or a Nikon Eclipse Ni microscope with a Digital Sight DS-U3 digital camera using NIS-Elements AR 4.20 (Nikon) software. Composite figures were prepared using Adobe Photoshop CS6 software.
Thomas S.L., Schultz C.R., Mouzon E., Golembieski W.A., Naili R.E., Radakrishnan A., Lemke N., Poisson L.M., Gutiérrez J.A., Cottingham S, & Rempel S.A. (2015). Loss of Sparc in p 53‐null Astrocytes Promotes Macrophage Activation and Phagocytosis Resulting in Decreased Tumor Size and Tumor Cell Survival. Brain Pathology, 25(4), 391-400.
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8

Time-lapse Imaging of hiPCS-CMs

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Morphology of control and doxorubicin exposed hiPCS-CMs was followed by a time-lapse imaging system BioStation IM (Nikon, Prague, Czech Republic) which recorded multiple cells at varying magnification and time-lapse modes (small as well as high for both global and detailed view of changes in behavior of treated cell populations). Recorded sequences were subsequently semi-automatically analyzed with the software NIS Elements AR 4.20 (Nikon, Prague, Czech Republic) and individual representative frames chosen for demonstration of detected trends.
Adamcova M., Skarkova V., Seifertova J, & Rudolf E. (2019). Cardiac Troponins are Among Targets of Doxorubicin-Induced Cardiotoxicity in hiPCS-CMs. International Journal of Molecular Sciences, 20(11), 2638.
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9

Histological and Immunohistochemical Tissue Analyses

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Adjacent serial sections were routinely stained with hematoxylin and eosin (H&E), immunohistochemically stained for SPARC (1:200 for 45 minutes; AF942, R&D Systems), cell proliferation marker Ki‐67 (1:250 for 40 minutes; M7249, Agilent Technologies) and macrophage/histiocyte marker CD68 (1:200 for 30 minutes; MCA341R, BioRad, Los Angeles, CA, USA) as previously reported 36. Additional adjacent sections were subjected to the periodic acid Schiff (PAS) reaction with or without diastase (liver tissue was positive control) as previously described 43 to demonstrate phagocytic activity (histiocytes). Images of stained sections were captured on either a Nikon Eclipse E800 microscope with a Nikon DXM1200C digital camera using ImagePro 6.0 Plus (Media Cybernetics, Rockville, MD, USA) software or a Nikon Eclipse Ni microscope with a Digital Sight DS‐U3 digital camera using NIS‐Elements AR 4.20 (Nikon, New York, NY, USA) software. Composite figures were prepared using Adobe Photoshop CS6 software.
Thomas S.L., Schultz C.R., Mouzon E., Golembieski W.A., Naili R.E., Radakrishnan A., Lemke N., Poisson L.M., Gutiérrez J.A., Cottingham S, & Rempel S.A. (2015). Loss of Sparc in p 53‐null Astrocytes Promotes Macrophage Activation and Phagocytosis Resulting in Decreased Tumor Size and Tumor Cell Survival. Brain Pathology, 25(4), 391-400.
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10

Quantifying Medulla Immunohistochemistry

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Images were obtained using a Nikon Eclipse 90i microscope, ×10, ×20, and ×40 objectives, a Nikon DS-Qi1Mc camera, and NIS-Elements AR 4.20 (Nikon) software. ImageJ (Rasband WS, ImageJ, US NIH, Bethesda, MD, USA, http://imagej.nih.gov/ij/, 1997-2016) was used for most analysis. To quantify staining in slices, a region of interest was drawn around the medulla (minus any cell-free areas) and the integrated pixel intensity was calculated and compared across the experimental groups. In most experiments >3 sections from each animal (two animals per group) were used to calculate the mean. All slides were blinded until the analysis was complete.
Giri P., Hu F., La Gamma E.F, & Nankova B.B. (2019). Absence of gut microbial colonization attenuates the sympathoadrenal response to hypoglycemic stress in mice: implications for human neonates. Pediatric research, 85(4).
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