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A1r confocal microscope system

Manufactured by Nikon
Sourced in Japan

The Nikon A1R confocal microscope system is a high-performance imaging solution designed for advanced biological research. It features a point-scanning confocal architecture that provides optical sectioning capabilities, enabling the acquisition of high-resolution, three-dimensional images of biological samples. The A1R system is equipped with a range of laser excitation sources and sensitive detectors, allowing for the visualization of a variety of fluorescent probes and labels.

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22 protocols using a1r confocal microscope system

1

Imaging Techniques for 3D Cellular Structures

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Immunostained spheroids in Fig.
6G
were imaged by two-photon microscopy using a Nikon 20×,
0.75 NA objective on a Nikon A1R Confocal Microscope System equipped with a
Ti:sapphire laser (used at 760 nm, 3% or 90 mW) controlled by Nikon
NIS-Elements software. All other immunostained spheroids and salivary glands
were imaged by laser scanning confocal microscopy using Nikon 20×,
0.75 NA or 60×, 1.4 NA Plan Apo objectives on a Nikon A1R Confocal
Microscope System controlled by Nikon NIS-Elements software or a Zeiss
20×, 0.75 NA or 63×, 1.4 NA Plan Apo objective on a Zeiss LSM
880 system controlled by Zeiss ZEN software. Immunostained tissue culture
cells were imaged using a Nikon 40×, 1.25 NA, Plan Apo,
silicone-immersion objective on a Nikon spinning disk confocal system
equipped with a Yokogawa CSU-X1 unit and a Prime 95B sCMOS camera
(Photometrics) controlled by Nikon NIS-Elements software.
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2

Immunofluorescence Imaging of Cells and Bone Slices

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For cell imaging, all cells were fixed by 4% paraformaldehyde for 24 hours. After washing three times with PBS, cells were permeabilized with 0.3% Triton X-100 for 10 min and washed three times again with PBS. After blocking with PBS solution with 1% bovine serum albumin (BSA; B14, Thermo Fisher Scientific) for 1 hour, cells were incubated with indicated primary antibodies in PBS overnight at 4°C. The cells were then washed three times and incubated with accordant secondary antibodies in PBS containing 0.2% BSA for 2 hours at room temperature. After DAPI staining, cells were imaged by an A1R confocal microscope system (Nikon, Shinagawa, Japan). For bone slice imaging, 20-μm cryo-sectioned femur slices were prepared. Slices were permeabilized with 0.3% Triton X-100 for 10 min and washed three times with PBS. After blocking with PBS solution with normal donkey serum (566460, MilliporeSigma) for 1 hour, slices were incubated with indicated primary antibodies in PBS overnight at 4°C. The slices were then washed three times and incubated with accordant secondary antibodies in PBS containing 20% donkey serum for 2 hours at room temperature. After DAPI staining, each slice was imaged by A1R confocal microscope system (Nikon, Shinagawa, Japan). Antibodies and their working concentrations are listed in table S2.
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3

Quantifying Macrophage Accumulation in Adipose Tissue

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For tissue harvest, a 0.9% sodium chloride solution was perfused at a constant pressure via the left ventricle, and then tissues were removed immediately. Epididymal fat pads were fixed with formalin and embedded in paraffin. Tissues were sectioned serially (5 μm) and stained with hematoxylin and eosin for general morphological examination.
For immunohistochemical detection of macrophages, sections were incubated with anti-Mac3 antibody (BD Pharmingen) and stained using the avidin-biotin complex and ImmPACT DAB Peroxidase Substrate Kit (Vector Laboratories). Each section was counterstained with hematoxylin. Macrophage accumulation in fat tissue [Mac3-positive cells (in percentage)] was analyzed using the ratio of the number of Mac3-positive cells to the number of total cells (total number of nucleus) (48 (link)). For perilipin staining, sections were stained with anti-perilipin antibody (Abcam) followed by Alexa Fluor 588–conjugated anti-rabbit immunoglobulin (Ig) antibodies (Molecular Probes). Nuclei were counterstained with Hoechst 33258. The sections were mounted using ProLong Antifade Kit (Molecular Probes) and observed under a confocal microscope (Nikon A1R confocal microscope system; Nikon Instruments Inc.).
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4

Immunostaining of Retinal Pigment Epithelium

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After enucleation, eye cups and retina were carefully removed. RPE flatmounts were fixed in 2% paraformaldehyde, stained with rabbit polyclonal antibodies against mouse ZO-1 (1:100; Invitrogen, Carlsbad, CA, USA), and visualized with Invitrogen Alexa Fluor 594 (Thermo Fisher Scientific, Waltham, MA, USA). For immunofluorescence staining for Cre expression, fresh, unfixed mouse eyes were embedded in optimal cutting temperature compound (Thermo Fisher Scientific), frozen in isopentane precooled by liquid nitrogen, and then cryosectioned. Using a Nikon A1R confocal microscope system (Nikon, Tokyo, Japan), flatmounts were imaged and assessed by a blinded operator. Degeneration in RPE flatmounts was defined using an established protocol.20 (link)
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5

Subcellular Localization Analysis of Neuronal Transcription Factors

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The 2Gi2R reporter-expressing lentivirus was included during the reprogramming of fibroblasts to hiBFCNs. Cells were replated onto astrocyte-coated and Matrigel-treated coverslips. At the indicated time points, cells were fixed with 4% PFA, followed by immunostaining with antibodies against GFP, RFP, and TUJ1. Nuclei were counterstained with DAPI. For live-cell imaging, cells at the indicated time point were maintained at 37 °C with 5% CO2 under the Nikon A1R confocal microscope system. The target cells were located under a 60x objective and imaged as 0 min. Culture medium was then replaced with prewarmed medium containing 50 nM leptomycin B (LMB). Cells were subsequently imaged every 10 min for a total of 1 h, followed by fixation with 4% PFA and immunocytochemistry. Images of single confocal plane across the center of the nucleus were obtained on the NIKON A1R confocal microscope with a pinhole setting at 2.5. Because of the complexity of neuron-astrocyte co-cultures, neuronal nucleus and soma were manually defined by using the Image J program. The mean fluorescence intensity of GFP or RFP was separately measured in the cytoplasm or nucleus of hiBFCNs. The ratios of GFPnuc/RFPnuc, GFPnuc/GFPcyt and RFPnuc/RFPcyt were calculated by Microsoft Excel and analyzed by GraphPad Prism 8.
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6

Automated NET Formation Kinetics Assay

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A microplate-based NET imaging assay was established using a motorized stage support of a confocal microscope. PMNs were seeded at a concentration of 250,000 cells/well in a 96 well plate Optical Btm Pit Polymer Base black plate (Thermoscientific, Rochester, NY). PMNs were preincubated with 10 ng/ml IL-1β prior to imaging. PMNs were then stimulated with 200 μg/ml MSU crystals for 16 hours. Nikon A1R confocal microscope system with a 10X lens was used to capture transmitted light and fluorescence images. A field of interest was chosen to perform imaging and their position was defined using the NIS elements software. The chosen field was a true representation of the entire well. Images were taken every 15 min for 12 hours using automated capture component of the NIS elements software. Mean Sytox Orange intensities of the fluorescent images were quantified using the measure region of interest (ROI) feature of the Nikon A1 Elements software. The entire image which represented the field was selected as the ROI. These measurements were used to calculate changes in SYTOX orange intensities over time (ΔMean SYTOX orange intensity). Samples were always run as three biological replicates.
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7

Neutrophil Extracellular Trap Formation

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As previously detailed [21 , 26 ], 2 × 106 human neutrophils in assay medium were incubated for 4 hrs at 37 °C with or without 100 nM PMA and 100 μg/ml MSU crystals in 35 mm glass bottom dishes (MatTek, Ashland, MA) pre-coated for 1 hr with 1% human serum albumin (Sigma Aldrich, St Louis, MO, USA). 2.5 μM Sytox Orange (Invitrogen, Grand Island, NY, USA) was added prior to fluorescence imaging (exc/em: 547/570 nm). Images were collected using a Nikon A1R confocal microscope system equipped with a Nikon Eclipse Ti-E inverted microscope, built in Perfect Focus, high-speed motorization and NIS Elements software (Nikon Instruments, Melville NY). Live cell imaging was carried out using a Tokai Hit INY-G2A-TIZ incubator (Tokai Hit CO, Ltd, Shizuoka-kenwith Japan) for temperature, humidity and CO2 control. The Coherent Sapphire 561nm 20mW laser was used to excite Sytox Orange using a CFI Plan APO VC 60X Oil NA 1.4 WD 0.13 mm objective. Optical sections of neutrophils were analyzed, Z-stacks spanning 1 μm were acquired and 3-D image reconstructions were processed using the Nikon NIS Element Version 4 software. Final image preparation was carried out using Adobe Photoshop.
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8

Visualizing mTmG Expression in Myogenic Cells

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Rosa26mTmG/+;Myf6-Cre+ mice were anesthetized with isoflurane and trans-cardially perfused with 1% PFA. Their tissues were harvested and fixed with 4% PFA overnight. The tissues were then washed with PBS, equilibrated in 30% sucrose overnight, embedded in optimal cutting temperature (OCT) medium, sectioned into 20 μm slices using cryotome (Leica), and mounted on slides with mounting medium (Vector Laboratories). Fluorescent signals were then visualized using a Nikon A1R confocal microscope system.
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9

Live Imaging of CD8 T Cell Interactions

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Confocal fluorescent microscopy was carried out on scanning laser Nikon A1R + confocal microscope system equipped with Nikon TiE inverted microscope, Nikon A1plus camera, and four lasers with excitation lines at 405, 488, 561, and 640 nm. The system was fitted with heated stage, objective heater, and a motorized stage with autofocus. The ibidi chamber with preformed bilayers was placed on stage preheated at 37 °C. The cell samples were injected into the entry ports of the slide containing bilayer with displayed ligands. The stage positions were chosen during first two minutes after the sample loading. The selected stage positions were imaged every 2 min for 30 min using 60X/1.4NA objective of the microscope preheated at 37 °C. Bright-field, reflected light, and two fluorescent channels (Alexa Fluor 488 for anti-CD3 imaging and Cy5 for ICAM-1 imaging) of the confocal microscope were utilized to acquire images of interface formed by CD8 T cells interacting with the bilayer surface. The acquisition of the images was performed with Nikon NiS-Elements AR software (v. 4.50.00). MetaMorph (v7.7.2.0) and Nikon NiS-Elements AR (v. 4.50.00) software were employed for analysis and quantification of the images.
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10

Confocal Microscopy Imaging Protocol

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Fluorescence images were captured on a Nikon A1R confocal microscope system (UGA College of Veterinary Medicine Cytometry Core Facility) using a 100X 1.45NA (Nikon) objective, equipped with an S-P 50 mW multiline Ar laser for imaging GFP and Alexa 488, a Coherent Sapphire 561nm 20 mW laser for imaging dsRed, and a Coherent Cube 640nm 40mW laser for imaging Alexa 647. Images were captured using NIS Elements software and processed with the Fiji (ImageJ v. 1.48) software package (Schindelin et al., 2012 (link); Schneider et al., 2012 (link)).
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