Images were analyzed using Nikon NIS-elements Advanced Research Imaging Software, version 4.30.01. Cell borders were traced guided by the Pan-Cadherin signal and saved as Regions-of-Interest (ROIs). Software-generated measurements of ROI size, equivalent to cell size, and of mean 640 nm signal intensity for each ROI, representing the Mitotracker signal, were exported for analysis.
Nis elements advanced research imaging software
Manufactured by Nikon
Sourced in United States
NIS-Elements Advanced Research is an imaging software designed for microscopy applications. It provides a comprehensive platform for acquiring, processing, and analyzing digital images from various types of microscopes. The software offers a wide range of tools and features to support advanced research and image analysis tasks.
Automatically generated - may contain errors
Lab products found in correlation
Eclipse 80i microscope, by Nikon (2 mentions)
F 3008, by Merck Group (1 mentions)
T4026, by Merck Group (1 mentions)
4 6 diamidino 2 phenylindole (dapi), by Merck Group (1 mentions)
Bond rx, by Leica (1 mentions)
Vectastain elite abc kit, by Vector Laboratories (1 mentions)
Image pro plus ams software, by Media Cybernetics (1 mentions)
90i microscope, by Nikon (1 mentions)
Hoechst 33342, by Thermo Fisher Scientific (1 mentions)
Bovine serum albumin pbs, by Merck Group (1 mentions)
Alexa fluor 594 conjugated secondary antibody, by Thermo Fisher Scientific (1 mentions)
Bovine calf serum (bcs), by Cytiva (1 mentions)
Polyclonal rabbit anti gfap antibody, by Agilent Technologies (1 mentions)
Alexa fluor 488 conjugated goat anti rabbit igg, by Thermo Fisher Scientific (1 mentions)
Ti e inverted microscope, by Nikon (1 mentions)
Ds ri2 camera, by Nikon (1 mentions)
Cytoseal xyl, by Thermo Fisher Scientific (1 mentions)
Originpro 8, by OriginLab (1 mentions)
D7008, by Merck Group (1 mentions)
A1r scanning confocal microscope, by Nikon (1 mentions)
11 protocols using nis elements advanced research imaging software
1
Quantification of Cellular Mitochondrial Density
2
Visualizing Microtubules and DNA in DU 145 Cells
3
Quantifying Lung Inflammation via CD45
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Histologic analysis of inflammatory cell infiltrate was performed on lung tissue collected 24 h after infection (n = 6–7 per group). Lungs were inflated with melted 2% agarose solution and removed into 4% paraformaldehyde (PFA). The lung was immersion fixed in 4% PFA for 24 h at room temperature prior to dehydrating in 70% ethyl alcohol (EtOH). Dehydrated tissue was then embedded in paraffin and sectioned at 4 µm. Mounted sections were deparaffinized for immunohistochemistry with CD45 staining, a pan-leukocyte marker which stains all leukocytes brown under bright field microscopy. The Biocare Medical Decloaker was used to acquire the heat-induced epitope prior to slide staining with Leica’s Bond Rx instrument. Slides were then treated with primary CD45 antibodies (1:50 solution, BD Biosciences, Franklin Lakes, NJ, USA) and developed with Vectastain Elite ABC kit (Vector laboratories, Newark, CA, USA). Random imaging of ten high-powered fields (HPF) at 20x magnification was performed for each sample. The number of CD45-positive cells per HPF was quantified by a blinded researcher using an automated counting algorithm on NIS Elements—Advanced Research imaging software (Nikon Instruments, Melville, NY, USA). The 10 fields per sample were then averaged and compared between treatment groups.
4
Quantitative Luxol Fast Blue Analysis
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All the slides were imaged at 10× and 20× objectives on a Nikon 90i microscope (Nikon Instruments Europe BV, Amsterdam, The Netherlands) equipped with a Nikon DS-Ri2 CMOS 16Mp color camera and the Nikon NIS-Elements Advanced Research imaging software.
For Luxol fast blue assessment, images were captured utilizing the same exposure and illumination settings of the microscope and software.
For Luxol fast blue stained sections, the area of the blue signal and its intensity were assessed using the integrated optical density measuring tool in the Image ProPlus AMS software (Media Cybernetics, Bethesda, MD, United States).
For this purpose, the regions of interest of the blue color dye were automatically selected in each image utilizing a single predefined RGB profile of the color.
Finally, all resulting behavioral and imaging data were plotted in Microsoft Excel as average ±standard error of the means (SEM), and statistical differences were sought utilizing a student’s t test. A value of P <0.05 was considered to be statistically significant.
For Luxol fast blue assessment, images were captured utilizing the same exposure and illumination settings of the microscope and software.
For Luxol fast blue stained sections, the area of the blue signal and its intensity were assessed using the integrated optical density measuring tool in the Image ProPlus AMS software (Media Cybernetics, Bethesda, MD, United States).
For this purpose, the regions of interest of the blue color dye were automatically selected in each image utilizing a single predefined RGB profile of the color.
Finally, all resulting behavioral and imaging data were plotted in Microsoft Excel as average ±standard error of the means (SEM), and statistical differences were sought utilizing a student’s t test. A value of P <0.05 was considered to be statistically significant.
5
Quantifying DNA Damage in HeLa Cells
6
Astrocyte Immunofluorescence Quantification
7
Acidic Toluidine Blue Staining of Mouse Tissue
8
Quantifying Membrane Peptide Internalization
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The experiments were performed using a confocal laser scanning microscope (Nikon Ti-E, Tokyo, Japan), equipped with LU4 Four-Laser Module with AOTF, a Plan Fluor 40x DIC M N2 objective and a DS-F1camera. An Alexa Fluor 488 tracer was excited using a line of 457–514 nm argon ion laser, TAMRA-TAT peptide with a diode laser emitting at 561 nm, and Dy647P1-peptides with a 642 nm diode laser. To observe the accumulation and internalization of peptides and the efflux of fluorescent tracers, the freshly prepared GUVs were transferred to a solution of glucose containing 2 µM fluorescently labeled peptide, to provide a homogeneous distribution of peptides to membranes. For each type of experiment, at least 10–15 GUVs with a diameter of 30–40 μm from two independent experiments were analyzed. Successive images were collected using the Nis-Elements Advanced Research imaging software (Nikon) and then quantification of fluorescence was performed using Fiji ImageJ [14 (link)]. The resulting data were then analyzed with Origin Pro 8.5 (OriginLab Corporation, Northampton, MA, USA).
9
Quantifying Intracellular ROS in Microglia
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The cell permeable uorescent dye dihydroethidium (DHE; Millipore, D7008) was used to detect intracellular ROS 68 . After 24h treatment of microglia with LPS/IFNγ ± ClGBI, DHE (5 µM) was added and incubated for 30 min at 37˚C and 5% CO 2 . Cells were then washed and mounted on microscope slides.
Images were obtained with a Nikon Eclipse Ti epi uorescence microscope (Nikon, Tokyo, Japan) using a 10X objective, and processed with NIS-Elements Advanced Research Imaging software (version 4.30.02, Nikon). In a separate set of experiments, cells were washed with PBS and MHB medium was added for direct quanti cation. Determination of nal point DhE uorescence was performed using a microplate reader at 610 nm when excited at 535 nm. Data is expressed in relative uorescence units (RFU; mean ± SEM of at least three independent experiments performed by triplicate).
Images were obtained with a Nikon Eclipse Ti epi uorescence microscope (Nikon, Tokyo, Japan) using a 10X objective, and processed with NIS-Elements Advanced Research Imaging software (version 4.30.02, Nikon). In a separate set of experiments, cells were washed with PBS and MHB medium was added for direct quanti cation. Determination of nal point DhE uorescence was performed using a microplate reader at 610 nm when excited at 535 nm. Data is expressed in relative uorescence units (RFU; mean ± SEM of at least three independent experiments performed by triplicate).
10
Quantitative Analysis of BBB Permeability
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Evaluation of BBB permeability was performed as detailed [72 (link)]. Briefly, animals were placed under anesthesia and transcardially perfused with a 10mg/ml solution of FITC-Dextran (10kDA) (Sigma-Aldrich). Immediately after the perfusion was completed, the brains were removed, fixed and cryoprotected. The brains were segmented using a brain matrix and then embedded in OCT for cryosectioning. The segments containing the injection site were sectioned at 50 microns and visualized by a Nikon A1R scanning confocal microscope. Image analysis were performed using the Nikon NIS Elements Advanced Research imaging software. The detection of the fluorescence tracer in the CNS parenchyma was performed by using particle analysis and binary image conversion to exclude the vasculature. Pixel intensity in the parenchymal areas of the injection site were then measured as a function area. Thus, the results are presented as mm2 of tracer positive areas.
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