Nis elements software

Manufactured by Nikon

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NIS-Elements software is a comprehensive imaging and analysis platform developed by Nikon for its advanced microscope systems. The software's core function is to provide users with a robust and user-friendly interface for capturing, processing, and analyzing high-quality microscopic images and data.

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2 071 protocols using nis elements software

Confocal Imaging of Moss Protonemal Tissue

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For confocal imaging, moss protonemal tissue was grown in microfluidic imaging device as described in Bascom, Wu, Nelson, Oakey, and Bezanilla (2016). The imaging device is filled with half‐strength Hoagland's medium (4 mM KNO₃, 2 mM KH₂PO₄, 1 mM Ca(NO₃)₂, 89 μM Fe citrate, 300 μM MgSO₄, 9.93 μM H₃BO₃, 220 nM CuSO₄, 1.966 μM MnCl₂, 231 nM CoCl₂, 191 nM ZnSO₄, 169 nM KI, 103 nM Na₂MoO₄) and kept at room temperature on the benchtop with overhead fluorescent lights. Images were acquired on a Nikon A1R confocal microscope system with a 1.49 NA 60x oil immersion objective (Nikon Apo TIRF 60x Oil DIC N₂) at room temperature. 488 nm laser illumination was used for mEGFP excitation. Emission filter was 525/50 nm for mEGFP. Image acquisition was controlled by NIS‐Elements software (Nikon). Images were processed using NIS‐Elements software (Nikon): advanced denoising with regression and other parameters set to default.

Mallett D.R., Chang M., Cheng X, & Bezanilla M. (2019). Efficient and modular CRISPR‐Cas9 vector system for Physcomitrella patens. Plant Direct, 3(9), e00168.

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Confocal Microscopy for Cell Identification

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All images were acquired using a Nikon A1 confocal microscope and NIS elements software. For co-localization studies to assess molecular identities of Sim1:Cre and Wfs1:CreER cells, immunostained tissue was imaged using a 20× air objective with a pinhole diameter set to 1 Airy unit and using the z stack function to acquire an image file that encompasses 15–20 μm tissue depth. The co-localization measurements of fluorescent markers were then carried out manually. Cell body size measurements based on diameter calculations for Figure 1 was made using the NIS elements software (Nikon).

Sürmeli G., Marcu D.C., McClure C., Garden D.L., Pastoll H, & Nolan M.F. (2015). Molecularly Defined Circuitry Reveals Input-Output Segregation in Deep Layers of the Medial Entorhinal Cortex. Neuron, 88(5), 1040-1053.

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Quantitative Live-Cell Imaging Analysis

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For live-cell imaging [53 (link)], cells (1×10⁴) were harvested at 24 h after transfection and allowed to attach for 12 h to fibronectin-pre-coated 35 mm dishes. Time-lapse images using phase-contrast and fluorescence microscopy (A1R-A1 confocal laser microscope system, Nikon) were taken at 2 min intervals and assembled into movies using NIS-Elements software (Nikon, Japan). For quantitative image analysis of the lamellipodial extension after transfection of siDOCK3 or siCtrl, we took measurements of cell area changes by subtracting the areas of the cells at 0 min from those at 2 min using NIS-Elements software (Nikon).

Cui H.Y., Wang S.J., Miao J.Y., Fu Z.G., Feng F., Wu J., Yang X.M., Chen Z.N, & Jiang J.L. (2015). CD147 regulates cancer migration via direct interaction with Annexin A2 and DOCK3-β-catenin-WAVE2 signaling. Oncotarget, 7(5), 5613-5629.

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Measuring Tumor Hypoxia and Vasculature

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To measure tumor hypoxia, 0.2 ml of 10mM EF5 (Merck-Millipore) was injected into the peritoneum of tumor bearing mice and tumors harvested after 1h. Pimonidazole adducts in sections were detected by immunohistochemistry using anti-EF5, clone ELK3-51 Cyanine 3 conjugate and the entire tumor section imaged using a Nikon Eclipse Ti epifluorescence microscope. The proportion of each tumor positive for hypoxia stain was measured from identically thresholded images on NIS elements software (Nikon) and reported as a percentage of total image area.
To examine tumor vessel perfusion and leakage, tumor-bearing mice were injected intravenously with FITC-labelled Lycopersicon esculentum lectin (Vector labs; 10 mg/kg) and low molecular weight fluorescent DNA binding dye Hoechst 33342 (Sigma-Aldrich; 7.5 mg/kg), respectively, followed 3min later by perfusion fixation with 4% paraformaldehyde. Cryosections were labelled with an antibody to endomucin to count endothelialized vessels. The percentage of perfused vessels was calculated as the % of endomucin⁺ vessels which were also lectin⁺. The proportion of each ROI positive for Hoechst was measured from thresholded images on NIS elements software (Nikon), and normalized to lectin area, i.e. perfused vessels.

O’Connor M.N., Kallenberg D.M., Camilli C., Pilotti C., Dritsoula A., Jackstadt R., Bowers C.E., Watson H.A., Alatsatianos M., Ohme J., Dowsett L., George J., Blackburn J.W., Wang X., Singhal M., Augustin H.G., Ager A., Sansom O.J., Moss S.E, & Greenwood J. (2021). LRG1 destabilizes tumor vessels and restricts immunotherapeutic potency. Med (New York, N.Y.), 2(11), 1231-1252.e10.

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3D Spatial Imaging of Chromosomal Regions

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BAC RP23-201H14 was kindly provided by Dr. Cornelis Murre (University of California at San Diego). Position-specific 10-kb probes were generated by PCR using BAC templates with the primers listed in Supplemental Table 5 or described in Guo et al. (2011a (link)). FISH with 10-kb probes were performed as described in Guo et al. (2011a (link)) using a Nikon T200 microscope equipped with a 100× lens and motorized 100-μm Piezo Z-stage (Applied Scientific Instrumentation). Depending on the size of the nucleus, 30–40 serial optical sections spaced by 0.2 μm were acquired. The data sets were deconvolved using NIS-Elements software (Nikon). Volumes were measured using NIS-Elements software (Nikon). Statistical analyses of spatial distance measurements were carried out using a two-sample Kolmogorov-Smirnov test in R (Massey 1951 ).

Gerasimova T., Guo C., Ghosh A., Qiu X., Montefiori L., Verma-Gaur J., Choi N.M., Feeney A.J, & Sen R. (2015). A structural hierarchy mediated by multiple nuclear factors establishes IgH locus conformation. Genes & Development, 29(16), 1683-1695.

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Multimodal Imaging of Myelination in EAE

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Images for DAB immunohistochemistry of MBP in the spinal cord and optic nerve were acquired using a Leica SCN400 slide scanner at 40 × magnification. Fluorescent images were acquired using a Nikon C2 confocal microscope system (Nikon, Melville, NY) with NIS-Elements software (Nikon, Melville, NY) at 40x (for sectioned retinas, optic nerve, and spinal cord white matter), 20x (for thalamic regions-dorsal lateral geniculate nucleus (dLGN) and ventral posterolateral nucleus (VPL), and spinal cord gray matter), or 10x (for NeuN in the thalamus and spinal cord gray matter) magnification. For retinal whole mounts, confocal z-stacks of Brn3a⁺ cells were captured in the retinal ganglion cell layer at 20 × magnification with 2.50 µm thickness and 0.5 µm step size. For qualitative images of EAE lesions in the spinal cord and optic nerve, 10 µm-thick confocal z stacks were captured at 20 × and 40x, and 3D reconstructions were generated for representative images. For electron microscopy, grids were examined on a Tecnai G2 SpiritBT transmission electron microscope (FEI Company, Hillsboro, OR) operated at 60 kV. NIS-Elements software (Nikon, Melville, NY) and Adobe Photoshop (for contrast, brightness, and color adjustments) were used to create figures and process images.

Mey G.M., Evonuk K.S., Chappell M.K., Wolfe L.M., Singh R., Batoki J.C., Yu M., Peachey N.S., Anand-Apte B., Bermel R., Ontaneda D., Nakamura K., Mahajan K.R, & DeSilva T.M. (2022). Visual imaging as a predictor of neurodegeneration in experimental autoimmune demyelination and multiple sclerosis. Acta Neuropathologica Communications, 10, 87.

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Spinning Disk Confocal Microscopy

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All live-cell fluorescence images were collected by spinning disk confocal microscopy using a Nikon Ti-E microscope equipped with a 1.45 NA 100× CFI Plan Apo objective, piezo electric stage (Physick Instrumente), spinning disk confocal scanner unit (CSU10: Yokogawa), 488 and 561 nm lasers (Agilent Technologies), and an EMCCD camera (iXon Ultra 897, Andor Technology); using NIS Elements software (Nikon). All fixed-cell images and time-lapse DIC images were collected on a Nikon Ti-E wide field microscope equipped with a 1.49 NA 100xCFI160 Apochromat objective and an ORCA-Flash 4.0 LLT sCMOS camera (Hammamatsu Photonics) using NIS Elements software (Nikon). For live cell imaging on both microscopes, stages were incubated at 30°C using an ASI 400 Air Stream Incubator (NEVTEK). Images were processed in FIJI.

Wethekam L.C, & Moore J.K. (2023). Tubulin isotype regulation maintains asymmetric requirement for α-tubulin over β-tubulin. The Journal of Cell Biology, 222(3), e202202102.

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Zebrafish Model for Tumor Engraftment

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Zebrafish husbandry procedures were performed according to the Directive 2010/63/EU and in compliance with local animal welfare regulations (authorization n. prot. 18311/2016; released by the “Comune di Meldola”, 9 November 2016). Ab and fli1a wild-type strain fertilized eggs were obtained and cultured according to previous works [29 (link),33 (link)]. The embryos were anesthetized with 0.02% tricaine solution before any manipulation. For DF1 engraftment, the embryos were dechorionated at 48 h postfertilization (hpf). Patient-derived tumor cells were red labelled (CellTracker™ CM-DiI, Invitrogen) using a concentration of 2.5 × 10⁵/µL. From 300 to 500 cells were injected in the yolk sack or in perivitelline space of 48 hpf embryos. DF1-grafted embryos were treated with DENO (Amgen Inc., Milan, Italy) LENVA (Eisai Ltd., Milan, Italy) and DENO + LENVA, or not treated. Embryos were exposed to the drugs at 32 °C for 72 h and imaged through a fluorescence stereomicroscope (Nikon SMZ 25 equipped with NIS Elements software) at 2, 24 and 72 hpi. Untreated embryos were also imaged using an A1 laser confocal microscope (Nikon Corporation, Tokyo, Japan), and images were analyzed with the NIS Elements software (Nikon Corporation, Tokyo, Japan).

De Vita A., Vanni S., Miserocchi G., Fausti V., Pieri F., Spadazzi C., Cocchi C., Liverani C., Calabrese C., Casadei R., Recine F., Gurrieri L., Bongiovanni A., Ibrahim T, & Mercatali L. (2022). A Rationale for the Activity of Bone Target Therapy and Tyrosine Kinase Inhibitor Combination in Giant Cell Tumor of Bone and Desmoplastic Fibroma: Translational Evidences. Biomedicines, 10(2), 372.

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Quantification of N-cadherin Trafficking

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Primary cortical neurons were transfected as indicated with pCAG‐PM‐mAG1, pCAG‐HA‐N‐cadherin and Rab21‐sh115 or control vectors. After 2 days of culture in vitro, cells were fixed with 4% PFA in PBS for 20 min and subjected to immunocytochemical analyses for anti‐HA and anti‐APPL1 antibodies. Fluorescence intensities of HA‐tagged N‐cadherin in the PM‐mAG1‐positive region (plasma membrane) and APPL1‐positive region (early endosomes) in each neuron were measured using the NIS elements software (Nikon). The ratio of the fluorescence intensities in the PM‐mAG1‐ or APPL1‐positive regions to that of whole cells was calculated.
For in vivo analyses, frozen sections of E17 cerebral cortices, electroporated with pCAG‐PM‐mAG1, pCAG‐HA‐N‐cadherin and Rab21‐sh115 or control vectors at E14, were examined immunohistochemically with anti‐HA antibody. Fluorescence intensities of HA‐tagged N‐cadherin in the PM‐mAG1‐positive region (plasma membrane) in each neuron were measured using the NIS elements software (Nikon). The ratio of the fluorescence intensities in the PM‐mAG1‐positive regions to that of whole cells was calculated.

Shikanai M., Ito S., Nishimura Y.V., Akagawa R., Fukuda M., Yuzaki M., Nabeshima Y, & Kawauchi T. (2023). Rab21 regulates caveolin‐1‐mediated endocytic trafficking to promote immature neurite pruning. EMBO Reports, 24(3), e54701.

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Imaging Gonadal Stem Cells in C. elegans

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Animals were anaesthetized in 0.04% tetramisole (Sigma) in M9 buffer and transferred to a 3% agarose pad, molded with 20-to 80-mm-wide grooves made by a custom nanofabricated silica plate, onto which a coverslip was placed. The chamber was backfilled with M9 buffer containing 0.04% tetramisole and sealed using VaLaP (1:1:1 Vaseline, lanolin, and paraffin). Imaging of GSPCs expressing the b-tub::GFP transgene alone was carried out on a Nikon A1R point scanning confocal microscope (Nikon Canada) using an Apo 403/ 1.25 numerical aperture (NA) water-immersion objective. A z stack through the entire distal gonad (18-25 0.75-mm sections) was acquired every 30 s for 30 to 60 min using NIS-Elements software (Nikon). These imaging conditions did not appear to affect mitotic progression, as mitotic timing was largely independent of when, relative to the start of image acquisition, a division occurred (data not shown). Two-color time-lapse movies (b-tub::GFP, H2B::mCh and CYB-1::YFP, H2B::mCh) were acquired on a swept field confocal microscope (Nikon Canada and Prairie Technologies) using a Plan-Apo 603/1.4 NA oil-immersion objective and a CoolSnap HQ2 CCD camera (Photometrics). z stacks of 9-13 0.75 mm sections were acquired in NIS Elements software (Nikon) every 30 s for 30 to 60 min using 2 3 2 binning, 400 ms exposure, and the 70 mm confocal slit aperture.

Gerhold A.R., Ryan J., Vallée-Trudeau J.N., Dorn J.F., Labbé J.C, & Maddox P.S. (2015). Investigating the regulation of stem and progenitor cell mitotic progression by in situ imaging. Current biology : CB, 25(9).

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