Elements software

Manufactured by Nikon

Sourced in United States, Japan

Nikon Elements software is a comprehensive imaging and analysis platform designed for microscopy applications. It provides advanced tools for image acquisition, processing, and analysis to support researchers and scientists in various fields of study.

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Lab products found in correlation

Ti e inverted microscope, by Nikon (9 mentions) Eclipse ti, by Nikon (8 mentions) A1r laser scanning confocal microscope, by Nikon (7 mentions) A1r confocal microscope, by Nikon (6 mentions) Zyla scmos camera, by Nikon (5 mentions) Andor spinning disk confocal microscope, by Oxford Instruments (4 mentions) C2 confocal microscope, by Nikon (4 mentions) Vascular endothelial growth factor (vegf), by R&D Systems (4 mentions) 4 6 diamidino 2 phenylindole (dapi), by Merck Group (3 mentions) Spinning disk confocal microscope, by Nikon (3 mentions) A1 confocal system, by Nikon (3 mentions) Wga alexafluor 555 conjugate, by Thermo Fisher Scientific (3 mentions) Sola se light engine, by Lumencor (3 mentions) Bx51 microscope, by Olympus (3 mentions) Ti e microscope, by Nikon (3 mentions) A1rmp multiphoton confocal microscope, by Nikon (3 mentions) Penicillin streptomycin, by Thermo Fisher Scientific (3 mentions) Alexafluor635 conjugated phalloidin, by Thermo Fisher Scientific (2 mentions) Rat anti laminin α2 4h8 2, by Santa Cruz Biotechnology (2 mentions) Anti rat alexafluor488 conjugated igg, by Thermo Fisher Scientific (2 mentions)

Spelling variants of this product

NIS-Element software (210 citations) NIS-Element D software (9 citations) NIS-Element AR analysis software (6 citations) NIS Element software program (4 citations) NIS element software package (3 citations) NIS-element D software version 4.11 (3 citations) NIS Element Basic Research software (2 citations) Nis Element F Imaging Software (2 citations) Nikon NIS element advanced software (2 citations) NIS-element image processing software (2 citations)

208 protocols using elements software

Imaging Developing Zebrafish Eyes

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Images were acquired using a Nikon Andor spinning disk confocal microscope equipped with a Zyla sCMOS camera and computer running Nikon Elements software. Imaging was performed using 20X (air) objective. For whole eyes, z stacks were obtained at 5 µm intervals. For live imaging, z stacks were obtained at 5 µm intervals. Time-lapse movies were visualized using Nikon Elements software, which was used to adjust brightness and contrast, annotate, then (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint this version posted January 31, 2020. ; https://doi.org/10.1101/2020.01.30.925859 doi: bioRxiv preprint generate .avi files at a playback rate of 3 frames per second. The autofluorescent iridophores on the surface of the developing eye were used to determine the boundary of the retina for analysis and quantifications. Selected frames from timelapse movies were visualized using FIJI (ImageJ) or Nikon Elements software. For imaging of 10 µm thick retinal cryosections, Z stacks were obtained at 2 µm intervals. For imaging of whole eyes, z stacks were obtained at 5 µm intervals. DIC optics were used to determine the boundaries of the eye on whole embryos. Images of retinal cryosections and whole eyes were visualized using FIJI (ImageJ) or Nikon Elements software.

Blume Z.I., Lambert J.M., Lovel A.G., & Mitchell D.M. (2020). Microglia in the developing retina couple phagocytosis with the progression of apoptosis via P2RY12 signaling.

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Live Imaging of Developing Zebrafish Eyes

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Images were acquired using a Nikon Andor spinning disk confocal microscope equipped with a Zyla sCMOS camera and computer running Nikon Elements software. Imaging was performed using 20X (air) objective. For whole eyes, z stacks were obtained at 5 μm intervals. For live imaging, z stacks were obtained at 5 μm intervals. Time-lapse movies were visualized using Nikon Elements software, which was used to adjust brightness and contrast, annotate, then generate .avi files at a playback rate of 3 frames per second. The autofluorescent iridophores on the surface of the developing eye were used to determine the boundary of the retina for analysis and quantifications. Selected frames from timelapse movies were visualized using FIJI (ImageJ) or Nikon Elements software. For imaging of 10 μm thick retinal cryosections, Z stacks were obtained at 2 μm intervals. For imaging of whole eyes, z stacks were obtained at 5 μm intervals. DIC optics were used to determine the boundaries of the eye on whole embryos. Images of retinal cryosections and whole eyes were visualized using FIJI (ImageJ) or Nikon Elements software.

Blume Z.I., Lambert J.M., Lovel A.G, & Mitchell D.M. (2020). Microglia in the developing retina couple phagocytosis with the progression of apoptosis via P2RY12 signaling. Developmental dynamics : an official publication of the American Association of Anatomists, 249(6), 723-740.

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Live Imaging of Thyroid Hormone Signaling in Zebrafish Larvae

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Five days postfertiliation lws:PAC(H) larvae were immersed in 100 nM T3 at 8:00 AM. Before imaging, larvae were immobilized in a 2% agarose pad in a 35-mm glass-bottom dish and overlaid with 28 °C system water containing 100 nM T3, 0.02% MS-222, and 0.003% PTU. Imaging was performed with a 40× water-immersion lens using a Nikon Andor spinning-disk confocal microscope equipped with a Zyla sCMOS camera running Nikon Elements software. Time course began at 4:00 PM and lasted for 9 h total. Images were captured at 30-min intervals. A 3-μm step z-series covering the area of interest was converted into volume view using the Nikon Elements software. The Director feature in Nikon Elements software was used to create the time-lapse movie (Movie S1).

Mackin R.D., Frey R.A., Gutierrez C., Farre A.A., Kawamura S., Mitchell D.M, & Stenkamp D.L. (2019). Endocrine regulation of multichromatic color vision. Proceedings of the National Academy of Sciences of the United States of America, 116(34), 16882-16891.

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Laser Confocal Microscopy Imaging Protocol

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All microscopy was performed on a laser-scanning confocal microscope (A1R; Nikon) using a 20 × water objective lens (live imaging) or a 60 × oil Plan-Apochromat objective lens with a 1.4 NA (fixed imaging). Nikon Elements Software was used for all acquisition and image processing. For all fixed images, multiple z planes were visualized in 0.4 μm steps (4–10 μm total depth). For live imaging, a 20 μm range was imaged with 0.5 μm steps. Images were acquired every 10 minutes for the duration of the time lapse. Images are maximum intensity projections of z stacks. Images were processed in Nikon Elements Software.

Collins C., Kim S.K., Ventrella R., Carruzzo H.M., Wortman J.C., Han H., Suva E.E., Mitchell J.W., Yu C.C, & Mitchell B.J. (2021). Tubulin acetylation promotes penetrative capacity of cells undergoing radial intercalation. Cell reports, 36(7), 109556.

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Laser Scanning Confocal Microscopy Protocol

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All microscopy was performed on a laser-scanning confocal microscope (A1R; Nikon) using a 60× oil Plan-Apochromat objective lens with a 1.4 NA. Nikon Elements Software was used for all acquisition and image processing. For all images, multiple z planes were visualized every 0.2–0.4 μm. Images are maximum intensity projections of z stacks. Images were processed in Nikon Elements Software.

Collins C., Majekodunmi A, & Mitchell B. (2020). Centriole number and the accumulation of microtubules modulate the timing of apical insertion during radial intercalation. Current biology : CB, 30(10), 1958-1964.e3.

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Whole Retina Imaging by Confocal Microscopy

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Whole, fixed lws:PAC(H) adult retinas, cryosections of lws:PAC(H) eyecups, and HCR-processed, adult (0.5–1.5 years) WT retinas were mounted in glycerol and imaged with a 20× dry lens using a Nikon–Andor spinning disk confocal microscope and Zyla sCMOS camera running Nikon Elements software (RRID:SCR_014329), and 3 µm-step sizes were used for Z-series images. Z-stacks were flattened by max projection, and brightness/contrast adjusted in FIJI (ImageJ) (RRID:SCR_002285). Multiple images encompassing the entirety of whole retinas or whole cryosections were stitched together using the “large stitched image” feature in Nikon Elements software.

Farre A.A., Thomas P., Huang J., Poulsen R.A., Owusu Poku E, & Stenkamp D.L. (2023). Plasticity of cone photoreceptors in adult zebrafish revealed by thyroid hormone exposure. Scientific Reports, 13, 15697.

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Cardiomyocyte Size Analysis Protocol

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Unfixed slides with the transversally cross-sectioned heart were incubated for 1h with blocking buffer (PBS with 2% BSA and 0.1% Triton X-100) prior to overnight immunostaining at 4°C with rat anti-laminin α2 (4H8–2; Santa Cruz, cat. no. sc-59854) and AlexaFluor635-conjugated phalloidin (Invitrogen, cat. no. A22284). The slides were washed and incubated with anti-rat AlexaFluor488-conjugated IgG (Invitrogen, cat. no. A48262). DAPI (Sigma Aldrich, cat. no. 10-236-276-001) was used to identify nuclei.
For the analysis of cardiomyocyte size, the left ventricle of the heart was identified and imaged on the Nikon C2 confocal microscope with a 20X objective. Phalloidin was used to classify the individual cardiomyocytes (red), while the inverse threshold of laminin α2 was used to determine cardiomyocyte boundaries. Cardiomyocyte size was determined with the Nikon Elements software by using the intersection of inverse laminin and the phalloidin staining. Cardiomyocytes with an area of <100 and >1000 μm² were excluded. The Feret’s minimal diameter was used to measure cardiomyocyte size and this analysis was performed by using the Nikon Elements software and the “Object Count” function.

Graca F.A., Stephan A., Wang Y.D., Shirinifard A., Jiao J., Vogel P., Labelle M, & Demontis F. (2022). Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice. Cell reports, 42(1), 111934.

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Laser Confocal Microscopy Imaging Protocol

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3D Invasion Assay for Cancer Cells

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This specialized invasion assay was performed according to previously published protocols (24 (link), 25 ). Assays were performed in 96-well plates (Black wells, clear bottom, PerkinElmer). Briefly, ice-cold serum-free liquid bovine collagen (PureCol) was prepared at 1 mg/ml concentration. After trypsinization, the cells were added to the collagen suspension at a final concentration of 5×10⁴cells/ml, and 100 µl aliquots were dispensed into five replicate wells. The cells were subsequently spun down, then incubated in a 37°C/5% CO2 tissue-culture incubator to allow the collagen to solidify. Finally, the collagen plug was covered by 30 µl of a mixture of the appropriate culture medium diluted 1:1 with PBS. After 48 hours, the cells were fixed with 4% PFA (final concentration) and stained with 10 µg/ml Hoechst-33342. Images of nuclei staining were obtained on an inverted microscope operated by Nikon Elements Software using a 20× air objective. Twenty-five adjacent images covering ~85% of the well area were taken from 0 µm (bottom of the plate) to 150 µm up in the collagen plug, at 25 µm steps. Quantification of nuclei/well was obtained using the “object count” feature of Nikon Elements Software. Invasion ratio was calculated as the sum of cell counts at 50, 75, 100, 125 and 150 µm over cell counts at 0 µm.

Pagano P.C., Tran L.M., Bendris N., O’Byrne S., Tse H.T., Sharma S., Hoech J.W., Park S.J., Liclican E.L., Jing Z., Li R., Krysan K., Paul M.K., Fontebasso Y., Larsen J.E., Hakimi S., Seki A., Fishbein M.C., Gimzewski J.K., Di Carlo D., Minna J.D., Walser T.C, & Dubinett S.M. (2017). Identification of a human airway epithelial cell subpopulation with altered biophysical, molecular, and metastatic properties. Cancer prevention research (Philadelphia, Pa.), 10(9), 514-524.

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Stereological Quantification of Dopaminergic Neurons

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Stereology was initially performed on serial sections from the midbrain following a protocol adapted from Tapias et al. 2014^{67 (link)}. Briefly, tissue was immunolabeled for TH, MAP2, and DAPI and imaged at ×20 on a Nikon90i fluorescent microscope in the Center for Biologic Imaging at the University of Pittsburgh. Images were analyzed in Nikon Elements software counting the number of dopaminergic neurons determined by overlap between DAPI, MAP2, and TH within a region of interest defining the substantia nigra pars compacta as previously described^{67 (link)}. Subsequent experiments were performed with a modified method of stereology utilizing overlap between TH and fluorescent Nissl (NeuroTrace 647, Life Technologies) within the substantia nigra pars compacta as previously described^{68 (link),69}. These images were obtained on an Olympus BX61VS slide scanning microscope, and analysis was performed utilizing Nikon Elements software.

Bucher M.L., Barrett C.W., Moon C.J., Mortimer A.D., Burton E.A., Timothy Greenamyre J, & Hastings T.G. (2020). Acquired dysregulation of dopamine homeostasis reproduces features of Parkinson’s disease. NPJ Parkinson's Disease, 6, 34.

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