Nis elements br imaging software

Manufactured by Nikon

Sourced in Japan, United States

NIS-Elements BR is an imaging software by Nikon. It provides tools for acquisition, processing, and analysis of digital images from Nikon microscopes and cameras.

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Lab products found in correlation

E400 microscope, by Nikon (2 mentions) Ds qi2 monochrome cmos camera, by Nikon (2 mentions) Zen blue 2, by Zeiss (1 mentions) Aperio imagescope, by Leica (1 mentions) Mitotracker red, by Thermo Fisher Scientific (1 mentions) Sc 25806, by Santa Cruz Biotechnology (1 mentions) Anti orp2 14751 1 ap, by Proteintech (1 mentions) Alexa fluor conjugated igg, by Thermo Fisher Scientific (1 mentions) Eclipse ti, by Nikon (1 mentions) Fluoromount g, by Southern Biotech (1 mentions) Hemoglobin γ sc 21756, by Santa Cruz Biotechnology (1 mentions) Eclipse ci, by Nikon (1 mentions) Eclipse ti s light microscope, by Nikon (1 mentions) In situ cell death detection kit, by Roche (1 mentions) Quanta 200 esem, by Thermo Fisher Scientific (1 mentions) Eclipse ti u, by Nikon (1 mentions) Fluorescence microscope, by Nikon (1 mentions) Eclipse ni u microscope, by Nikon (1 mentions) Cm1850, by Leica (1 mentions) Aperio imagescope digital slide scanner, by Leica (1 mentions)

15 protocols using nis elements br imaging software

Quantitative Analysis of MHC-II in Colonoids

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All brightfield images were captured with Nikon E400 microscope, DS-Fil U2 camera, and NIS-Elements BR imaging software (Nikon Corporation, Tokyo, Japan) with 20x objective and processed with Fiji (46 (link)). Confocal fluorescence microscopy images were captured with 20x or 63x objective using a Zeiss LSM 880 Fast Airyscan Confocal microscope (Zeiss, Oberkochen, Germany). To minimize photobleaching, laser power typically was 20% under maximum, and the pinhole was set to 0.8–1.5. Images were processed with Zen Blue 2.6 software (Zeiss). Quantitative confocal image analyses of MHC-II staining in colonoids were performed using Fiji (46 (link)). The fluorescence intensity of MHC-II staining was determined by measuring the integrated density. Otsu’s thresholding algorithm was applied to convert images with DAPI staining to binary images, and the nuclei (cell counts) were quantified using the Analyze Measure plugin in ImageJ. The corrected total cell fluorescence (CTCF) was calculated: CTCF = Integrated density-(Area of selection X Mean fluorescence of background readings). The average of CTCF/cell counts for five power fields per condition for each experiment is represented in the graphs. A total of 2000-6000 cells in the colonoids were counted per treatment condition. Quantification results are presented in Supplementary File SF1, sheet no 3.

Gopalakrishnan S., Hansen M.D., Skovdahl H.K., Roseth I.A., van Beelen Granlund A., Østvik A.E., Bakke I., Sandvik A.K, & Bruland T. (2022). Tofacitinib Downregulates TNF and Poly(I:C)-Dependent MHC-II Expression in the Colonic Epithelium. Frontiers in Immunology, 13, 882277.

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Electrochemical Detection of Dopamine Release

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CFMEs with a ~60 μm protruding tip were prepared as described before.^{29 (link)} Preparation is detailed in the Supporting Information. A Waveneuro FSCV potentiostat (5 MΩ headstage, Pine Research Instrument) and a PCIe-6363 multifunctional I/O device (National Instruments) were used to apply the waveform and to collect data. HDCV software (provided by R. M. Wightman, University of North Carolina) was used to collect data and for background subtraction. The dopamine waveform (−0.4 V to 1.3 V and back to −0.4 V versus chloridized Ag wire reference electrode) was applied to the CFME every 100 ms at a scan rate of 400 V/s for conditioning and measurements. Electrodes were pre-calibrated and post-calibrated with 1 μM dopamine in a flow cell injection system. For picospritzing, an empty glass capillary was pulled, trimmed, and filled with acetylcholine (ACh) for stimulation. A Picospritzer III (Parker Hannfin) was used to pressure eject ACh into the brain tissue. Capillaries were calibrated by picospritzing a droplet of ACh in oil and the diameter of the pressure-ejected droplet was measured using DS-Qi2 monochrome CMOS camera and NIS-Elements BR imaging software (Nikon Instruments Inc.). For all experiments, a volume corresponding to 0.2 pmol ACh was ejected using a constant applied pressure of 20 psi.

Dumitrescu E., Copeland J.M, & Venton B.J. (2022). Parkin knockdown modulates dopamine release in the central complex, but not the mushroom body heel, of aging Drosophila. ACS chemical neuroscience, 14(2), 198-208.

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Quantitative Collagen Assessment in Liver

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We used a quantitative method to determine the collagen proportionate area (CPA).13 Masson’s trichrome stains were digitally scanned on an Aperio ImageScope Digital slide scanner (Leica Biosystems, Wetzlar, Germany), and low‐power (×1.2) images of the entire surface area of each core was measured in number of pixels using Nikon’s NIS Elements‐BR Imaging Software (Tokyo, Japan). Next, blue‐stained areas from the trichrome stain were identified, and thresholds were set using the software. The fibrotic area was divided by the total biopsy surface area to obtain the percent fibrosis (% fibrosis = [∑fibrotic area in pixels/∑ total area in pixels] × 100). Liver capsules and large portal tracts (identified by presence of nerve bundles) were excluded.

Saldarriaga O.A., Freiberg B., Krishnan S., Rao A., Burks J., Booth A.L., Dye B., Utay N., Ferguson M., Akil A., Yi M., Beretta L, & Stevenson H.L. (2020). Multispectral Imaging Enables Characterization of Intrahepatic Macrophages in Patients With Chronic Liver Disease. Hepatology Communications, 4(5), 708-723.

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Immunostaining and Microscopy Protocol

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Immunostaining and microscopy were performed as described previously (Li et al., 2007 (link)). Briefly, H295R cells were plated on glass cover slips, fixed, permeabilized, blocked with 1% BSA for 1 h, and then incubated with anti-ORP2 (14751-1-AP, Proteintech), anti-ORP2 (SAB2500724, Sigma), anti-ORP10 (GTX108097, GeneTex, Inc, Irvine, CA), or anti StAR (sc-25806, Santa Cruz Biotechnology) antibodies (diluted 1:500 in 1% BSA) overnight, followed by incubation with Alexa Fluor-conjugated IgG (Life Technologies, Grand Island, NY) for 1 h. Cover slips were stained with 4,6’-diamino-2-phenylindole dihydrochloride (DAPI; Life Technologies) or MitoTracker Red (Life Technologies) and then mounted onto slides using Fluoromount G (Southern Biotech, Birmingham, AL). Images were captured using a fluorescence microscope (Nikon Eclipse Ti) and processed using NIS-Elements BR imaging software (Nikon).

Escajadillo T., Wang H., Li L., Li D, & Sewer M.B. (2016). Oxysterol-Related-Binding-Protein Related Protein-2 (ORP2) Regulates Cortisol Biosynthesis and Cholesterol Homeostasis. Molecular and cellular endocrinology, 427, 73-85.

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Immunofluorescence Analysis of Hemoglobin Subunits

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Fixed cells were washed in PBS, blocked in 5% BSA (in PBS) and incubated in primary antibody for 1 hour. Next, cells were washed, blocked in 5% normal goat serum and incubated in secondary fluorescent-labeled antibody for 30 minutes. Finally, cells were washed and covered with mounting medium containing DAPI. Images were taken with the Eclipse Ci (Nikon) microscope with a DS-Qi1Mc-03 mono-type (Nikon) camera, using NIS-Elements Br Imaging software (Nikon). The following antibodies were used: Hemoglobin γ (sc-21756, Santa Cruz), Monoclonal Mouse Anti-human β-globin (a gift from IsoLab), Anti-human alpha globin (Wallac Inc.), and Alexa Fluor-594-conjugated AffiniPure F(ab)₂ Fragment Goat Anti-mouse IgG (H+L) (115-586-062, Jackson ImmunoResearch).

Morrison T.A., Wilcox I., Luo H.Y., Farrell J.J., Kurita R., Nakamura Y., Murphy G.J., Cui S., Steinberg M.H, & Chui D.H. (2017). A Long Noncoding RNA from the HBS1L-MYB Intergenic Region on Chr6q23 Regulates Human Fetal Hemoglobin Expression. Blood cells, molecules & diseases, 69, 1-9.

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Quantifying Apoptosis by TUNEL Assay

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The presence of apoptotic cells was measured by in situ labeling of DNA fragmentation using a TUNEL assay. An in situ cell death detection kit (Roche Diagnostics; Indianapolis, IN) was used. Slides were counterstained with 4′, 6-diamidino-2′-phenylindole dihydrochloride (DAPI). Analysis was performed using an Eclipse Ti-S light microscope (Nikon), and the NIS-Elements BR imaging software (Nikon) was used to quantify fluorescent cells.

Cen C., Aziz M., Yang W.L., Nicastro J.M., Coppa G.F, & Wang P. (2017). Osteopontin Blockade Attenuates Renal Injury after Ischemia Reperfusion by Inhibiting NK Cell Infiltration. Shock (Augusta, Ga.), 47(1), 52-60.

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Characterization of XEM Morphology and Stability

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The morphology of XEMs was examined by an inverted optical microscope (Nikon Eclipse Ti-U; Nikon Instruments, Melville, NY) and an environmental scanning electron microscopy (ESEM, FEI Quanta ESEM 200). The average size and size distribution were determined from optical images of randomly selected XEMs using NIS-Elements BR imaging software (version 4.12; Nikon Instruments Inc.). XEMs stability was determined based on size and shape changes after 0, 1, 3, 7 and 10 days in PBS, serum, or 10% serum at 37°C or after 18 months in crosslinking solution at 4°C.

Beh C.W., Fu Y., Weiss C.R., Hu C., Arepally A., Mao H.Q., Wang T.H, & Kraitchman D.L. (2020). Microfluidic-Prepared, Monodisperse, X-ray-Visible, Embolic Microspheres for Non-Oncological Embolization Applications. Lab on a chip, 20(19), 3591-3600.

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Apigetrin Impact on Prostate Cancer Cell Spheroids

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The LNCaP (1 × 10⁵ cells/mL) and PC-3 (1 × 10⁵ cells/mL) cells were seeded on Matrigel in 96-well plates and treated with 0, 25 and 50 μM of apigetrin in 96-well plates at the same time and incubated for 48 h and 72 h. The spheroids formed were photographed at 20× magnification under a microscope 48 h and 72 h. The spheroids were then measured and their growth was evaluated using a fluorescence microscope (Nikon, Tokyo, Japan) and Nikon NIS Elements BR Imaging software.

Lee Y.K., Kim J.E., Xu Y., Han H., Lee J.H, & Lee H.J. (2022). AKT, a Key Transmitter of HIF-1α and AR Signaling Pathways, Has a Critical Role in the Apigetrin-Mediated Anti-Cancer Effects in Prostate Cancer Cells. Biomedicines, 10(6), 1370.

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Histological Analysis of Nerve Grafts

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Eight weeks after the surgery, rats were anesthetized with pentobarbital sodium, and the 5-mm-long proximal segments of the nerve grafts were harvested and fixed in 4% paraformaldehyde in phosphate-buffered saline overnight at 4°C, as described before (Zheng et al., 2017). The segments were then submerged in 30% sucrose for 24 hours and mounted in optimal cutting temperature compound (Tissue-Tek, Sakura, Tokyo, Japan), and cut into 12-μm-thick frozen serial sections on a cryostat (CM1850; Leica, Wetzlar, Germany). The allogeneic acellular nerves were fixed and prepared in the same manner. Hematoxylin and eosin staining was performed for observing histological changes, and images were acquired with an Eclipse Ni-U microscope with NIS-Elements BR Imaging software (Nikon Instruments, Tokyo, Japan).

Zheng M.G., Sui W.Y., He Z.D., Liu Y., Huang Y.L., Mu S.H., Xu X.Z., Zhang J.S., Qu J.L., Zhang J, & Wang D. (2019). TrkA regulates the regenerative capacity of bone marrow stromal stem cells in nerve grafts. Neural Regeneration Research, 14(10), 1765-1771.

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Histological Analysis of Spleen and Liver

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Standard hematoxylin and eosin staining of spleen and liver sections was performed at the Cellular and Molecular Imaging Core Facility (CMIC) at Norwegian University of Science and Technology (NTNU) as described previously (12 (link)). Images were acquired with a Nikon E400 microscope and NIS-Elements BR imaging software (Nikon Instruments, Melville, NY, USA).

Dragset M.S., Ioerger T.R., Loevenich M., Haug M., Sivakumar N., Marstad A., Cardona P.J., Klinkenberg G., Rubin E.J., Steigedal M, & Flo T.H. (2019). Global Assessment of Mycobacterium avium subsp. hominissuis Genetic Requirement for Growth and Virulence. mSystems, 4(6), e00402-19.

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