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Nis elements imaging software 3

Manufactured by Nikon
Sourced in Netherlands

NIS-Elements Imaging Software 3.00 is a comprehensive imaging software package designed for microscopy applications. It serves as a platform for acquiring, processing, analyzing, and managing digital images captured through Nikon microscopes. The software provides a suite of tools for tasks such as image acquisition, 3D reconstruction, and advanced image analysis.

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8 protocols using nis elements imaging software 3

1

Quantifying Cellular Markers in Hippocampus and Hypothalamus

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BrdU, IdU, c-Fos, and GFAP-ir nuclei and cells that came into focus were manually counted from Bregma −2.16 to −4.20 mm at hippocampal and hypothalamic levels (Paxinos & Watson, 2007) using a standard optical microscope with a 40× objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) coupled to the NIS-Elements Imaging Software 3.00 (Nikon, Tokyo, Japan).
Focusing on the hippocampus, BrdU-ir nuclei were counted in the SGZ of the DG, while IdU-ir nuclei and c-Fos and GFAP-ir cells were counted in the whole hippocampus (DG, CA3, and CA1 areas). Focusing on the hypothalamus, counting was performed in the paraventricular (PVH), ventromedial (VMH), and arcuate (ARC) nuclei and median eminence.
Immunostained cells located in the uppermost side that came into focus while moving down through the thickness of the section were counted. Overall, quantification was expressed as the average number of cells per area (mm2) in each experimental group.
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2

Quantifying Hippocampal Neurogenesis in Rats

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5-bromo-2′-deoxyuridine and IdU-immunoreactive (+) cell nuclei that came into focus were manually counted using a standard optical microscope with the 40 × objective (Nikon Instruments Europe B.V., Amstelveen, Netherlands) coupled to the NIS-Elements Imaging Software 3.00 (Nikon). Brain structure analyzed consisted of approximately 8 coronal sections (from −2.16 to −4.20 mm Bregma levels), which resulted in one of every eight equidistant sections (one representative section for each 240 μm) according to the rostro-caudal extent. Estimations of the number of positive cells in the hippocampal neurogenic niche SGZ in both hemispheres were calculated per sections (30 μm deep), according to a rat brain atlas and cytoarchitectonic criteria (Paxinos and Watson, 2007 ). Quantification was expressed as the average number of positive cells per section for each experimental group.
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3

Immunoreactivity Assessment in Submandibular Gland

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All sections were reviewed by researchers blinded to the clinical information (E.F.E. and J.S.). Sections with positive immunoreactivity were visualized using a standard optical microscope (Nikon Instruments Europe B.V., Amstelveen, the Netherlands), coupled to the NIS-Elements Imaging Software 3.00 (Nikon). We screened 4–6 serial sections per subject with the anti-nitro-α/β-synuclein antibody and the anti-IYD polyclonal antibody. The degree of immunoreactive inclusions within different regions of the submandibulary gland was assessed in contiguous tissue sections according to a five-point rating scale: not detectable (0), mild (1), moderate (2), frequent (3), and very frequent (4). These regions encompassed acini, ducts, and interlobular connective tissue (that contain blood vessels and autonomic nerves supplying the gland). The presence of immunoreactive inclusions was also assessed in other intraglandular cells such as adipocytes, endothelial, and mononuclear blood cells [24 (link)].
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4

Quantifying Cell Density in Mouse Brain

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The average density of positive cells per animal was quantified. Thus, the estimation of the number of cells per section (30 μm deep) in both hemispheres was calculated. Each structure analyzed consisted of ~6 coronal sections, which resulted in one of every five equidistant sections (one representative section for each 180 μm) according to the rostro-caudal extent. To outline the area of study, the region of interest was drawn in each structure, the identification of which was performed at Bregma −1.58 to −2.46 mm in hippocampal and hypothalamic levels and at Bregma 1.42 to −0.10 mm in striatal levels according to a mouse brain atlas and cytoarchitectonic criteria [58 ]. Thus, the BrdU-immunoreactive (+) nuclei and IdU-immunoreactive (+) nuclei that came into focus were manually counted in the hypothalamus and the subventricular zone (SVZ) of the lateral ventricles. Regarding the hypothalamus, counting was performed in the ventromedial (VMH) and arcuate (ARC) nuclei of the hypothalamus and median eminence. Quantification was performed using a standard optical microscope with 40× objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) coupled to NIS-Elements Imaging Software 3.00 (Nikon). The data were expressed as the number of positive cells per section.
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5

Quantification of IBA-1+ Microglia in Brain Regions

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Representative counting frames were obtained using a standard optical microscope equipped with the 40 × objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) and coupled to the NIS-Elements Imaging Software 3.00 (Nikon). The brain regions of interest for this study were the following: PrL, Str, BLA, and the hippocampal areas CA1 and CA3 and the dentate gyrus. A minimum of eight coronal sections per brain region were analyzed, which resulted in one of every six equidistant sections (one representative section for each 180 µm) according to the rostro-caudal extent. Estimations of the number of IBA-1-immunoreactive ( +) cells per area (mm2) in both hemispheres were manually counted according to stereological methods and calculated based on the following formula (Rivera et al., 2018 (link)): Na=ΣQ-/Σastr, where ΣQ − is the total number of positive ( +) cells counted per animal, and astr is the area (mm2) of the structure analyzed. Cell number quantification was expressed as the average number of IBA-1 + cells per area (mm2) for each experimental group. For densitometric analysis, quantification of IBA1 immunoreactivity is determined using ImageJ software (NIH, USA) and expressed as arbitrary units of average intensity of the image field that corresponds to representative areas of the brain regions.
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6

Quantifying Microglia Density in Brain Regions

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Representative counting frames were obtained using a standard optical microscope equipped with the 40x objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) and coupled to the NIS-Elements Imaging Software 3.00 (Nikon). The brain regions of interest for this study were: PrL, Str, BLA, and the hippocampal areas CA1 and CA3, and the dentate gyrus. A minimum of 8 coronal sections per brain region was analyzed, which resulted in one of every six equidistant sections (one representative section for each 180 µm) according to the rostro-caudal extent. Estimations of the number of IBA-1immunoreactive (+) cells per area (mm 2 ) in both hemispheres were manually counted according to stereological methods and calculated based on the following formula (Rivera et al., 2018) (link):
where ΣQ-is the total number of positive (+) cells counted per animal, and a str is the area (mm 2 ) of the structure analyzed. Cell number quanti cation was expressed as the average number of IBA-1+ cells per area (mm 2 ) for each experimental group. For densitometric analysis, quanti cation of IBA1 immunoreactivity is determined using ImageJ software (NIH, USA) and expressed as arbitrary units of average intensity of the image eld that corresponds to representative areas of the brain regions.
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7

Quantifying Hippocampal Immune Cells

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The average density of immunoreactive cells per animal was manually quantified using stereological methods. Estimations of the number of cells per sections (30 µm deep) and area (mm 2 ) in both hemispheres were calculated according to the following formula: Na = Σ(Q-)/ Σ(astr), where ΣQ-is the total number of positive (+) cells counted per animal, and astr is the area of the structure analyzed. Each structure analyzed consisted of approximately 8 coronal sections (from -2.16 to -4.20 mm Bregma levels), which resulted in one of every eight equidistant sections (one representative section for each 240 µm) according to the rostrocaudal extent. IBA-1+, iNOS+, GFAP+, CX3CR1+, CCR2+, CCR4+ and CXCR4+ cell counts were performed in the dentate gyrus (DG) and CA3 and CA1 hippocampal areas.
Representative counting frames were evaluated using a standard optical microscope with the 40x objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) coupled to the NIS-Elements Imaging Software 3.00 (Nikon). Quantification was expressed as the average number of positive cells per area (mm 2 ) for each experimental group.
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8

Quantitative Analysis of Immunomarkers

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Positive (+) immunoreactive and immunofluorescent nuclei and cells that came into focus were manually counted. Representative counting frames from sections with immunoreactivity were evaluated using a standard optical microscope with the 40× objective (Nikon Instruments Europe B.V., Amstelveen, The Netherlands) coupled to the NIS-Elements Imaging Software 3.00 (Nikon). For immunofluorescent cell counting, the sections were visualized with a confocal laser (spectral) scanning microscope (Leica TCS NT; Leica Microsystems) equipped with a 561 nm DPM laser (argon 30%) and a 40× objective (HCX PL APO CS 40.0x1.25 OIL UV). The emission filter settings were 500-550 nm for PMT2 (green) and 610-700 nm for PMT3 (red). Depending on the level of zoom used in each image, the XY voxel size was from 100 to 77 nm, approximately. Settings of light and brightness/contrast were adjusted by using the Leica LAS AF Lite imaging software.
Phospho-H3+ and BrdU+ nucleus counts were performed in the subventricular zone (SVZ) of the lateral ventricles, while GFAP, Iba-1, iNOS, FosB, cleaved caspase-3 and PPARα+ cell counts were carried out in the whole striatum. Overall, quantification was expressed as the average number of cells per area (mm 2 ) for each experimental group.
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