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Nis element ar 3

Manufactured by Nikon
Sourced in Japan

NIS-Element AR 3.0 is a comprehensive imaging software platform for Nikon microscopes. It provides advanced image acquisition, analysis, and processing capabilities to support a wide range of microscopy applications.

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7 protocols using nis element ar 3

1

Image Processing Techniques for Microscopy

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All Western blot and Northern blot images were processed with Adobe Photoshop CS4 for all linear adjustments and cropping. All images captured on Nikon Eclipse Ti microscope were analyzed and processed with Nikon NIS ELEMENT AR 3.1 software. Image cropping was done using Adobe Photoshop CS4.
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2

Keratinocyte Migration Dynamics Analysis

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Single-cell migration was evaluated to determine the migration rate of keratinocytes under subconfluent conditions. As described in the previous section, time-lapse images were captured from five randomly selected positions per well. Cell migration was analysed using NIS Element AR 3.1 software (Nikon, Minato City, Tokyo, Japan). At least 150 cells from each condition were chosen randomly and tracked every 20 min for 1 h (36 h after seeding). The migration rate of the cells was evaluated every 20 min using Equation (3).
Migration rate=(x2x1)2+(y2y1)2t2t1
where (x1, y1) and (x2, y2) indicate the centre of the cell evaluated by the software at time t1 and t2, respectively. The overall migration rate for a cell was evaluated by averaging migration rate for three 20 min segments.
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3

Lysosomal Ca2+ Dynamics Monitoring

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The cells in each group were washed three times with PBS, and the intracellular lysosome was extracted by lysosome extraction kit (Sigma-Aldrich, St. Louis, MO, USA). Then, 3 µmol/L Fluo-3AM solution was immediately added, and incubated in a incubator at 37°C for 30 min. After aspirating the working fluid, lysosome was rinsed with PBS for three times, and PBS was added to balance for 10 min, and finally for observation. By using Ca2+ analyzer, the image and time was obtained with real-time monitoring via NIS-Element AR3.0 (Nikon) software system, with a period of 6 min. Lysosomal Ca2+ intensity was expressed as R340/380 (Wavelengths at 340 and 380 nm, respectively). Each experiment was detected at least 10 cells, baseline was also detected (baseline fluctuates within a relatively small range), with each experiment repeating at least three times.
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4

Intracellular Calcium Dynamics Measurement

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HPAEC grown to confluence on 25mm glass coverslips (Fisher Scientific) were loaded with 2µM Fura-2 AM (Invitrogen), a cell permeable fluorescent probe used for measuring change in cytosolic Ca2+, for 30 minutes. After dye loading, the cells were washed twice with Ca2+ free HBSS buffer, and the coverslips were mounted on an inverted microscope (Eclipse TE2000-E, Nikon). Calcium release from the intracellular stores was determined by perfusing Ca2+ free imaging buffer and stimulating cells with thrombin (2.5U). Store-operated Ca2+ entry was measured, following addition of 1.26 mM Ca2+. Images were captured at 510nm using a digital CCD camera (CoolSNAP HQ2, Photometrics) and an imaging software (NIS-Element AR 3.0, Nikon) after alternating excitations at 340 and 380nm. Fura-2 ratio (F-ratio 340/380) was calculated and analyzed later offline with NIS-Element AR 3.0 Software (13 (link)).
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5

Fura-2 Ca2+ Imaging for Intracellular Stores and SOCE

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HPAEC grown to confluence on 25 mm glass coverslips (Fisher Scientific) were loaded with 2 µM Fura-2 AM (Invitrogen), a cell permeable fluorescent probe used for measuring change in cytosolic Ca2+, for 30 minutes. After dye loading, the cells were washed twice with Ca2+ free HBSS buffer, and the coverslips were mounted on an inverted microscope (Eclipse TE2000-E, Nikon). Calcium release from the intracellular stores was determined by perfusing Ca2+ free imaging buffer and stimulating cells with thrombin (2.5U). Store-operated Ca2+ entry was measured, following addition of 1.26 mM Ca2+. Images were captured at 510 nm using a digital CCD camera (CoolSNAP HQ2, Photometrics) and an imaging software (NIS-Element AR 3.0, Nikon) after alternating excitations at 340 and 380 nm. Fura-2 ratio (F-ratio 340/380) was calculated and analyzed later offline with NIS-Element AR 3.0 Software.
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6

Microscopic Analysis of Oocyte Chromosomes

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Stained oocytes or chromosome spreads were examined with a Nikon A1R microscope using a 100× oil-immersion objective. Optical sections were captured at 2-μm intervals. Images were analysed with NIS-Element AR3.0 software (Nikon). To clearly highlight the location of CENP-F and chromosomes in Supplementary Fig. 1a, the corresponding channels were inverted to black and white by ImageJ software. For live cell imaging, oocytes were cultured in CZB medium under a humidified atmosphere of 5% CO2 at 37 °C in the incubator chamber; images were acquired with a Zeiss LSM780 microscope equipped with a ×40 objective. Zeiss Blue software (version 2.3) was used to analyse the data.
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7

Lignin Quantification via Safranin O Staining

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Safranin O staining and analyses were performed as previously described [31 (link)]. Images from 3 independent biological replicates for each genotype and tissue were acquired. A Nikon A1R confocal equipped with a 60×/1.4 aperture oil immersion objective (Plan APO VC) and the NIS Element AR3.0 software was used (Nikon, Tokyo, Japan). Acquisition parameters were the following: track 1 (ex: 488 nm, BP: 525/50), track 2 (ex: 561 nm, BP: 595/50). Images were treated using FIJI v2.0 [56 (link)] and analyzed with the associated macro developed for this method as previously described [31 (link)]. Lignin appears in colors ranging from purple (low amounts) to red (high amounts).
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