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24 protocols using ndp viewer

1

Quantifying Placental Vascular Remodeling

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Tissue volumes were determined from serial sections using the Cavalieri method48 . In brief, cross-sectional areas on serial sections were determined and volumes calculated using the spacing between sections. Arterial remodelling was assessed in the central 2/4 of the decidua basalis on sagittal sections to avoid inclusion of veins that have been shown to be more peripherally located39 (link). Three to five implantation sites (corresponding to one uterine horn chosen at random) were analysed per litter. For each implantation site, the five largest vessels were measured in triplicate (three sections 49 μm apart from each other). For all stereological measurements, uterine arteries were tied before dissection to minimize bleeding. Size of lumens and vessels was determined by measuring cross-sectional areas with NDP viewer (Hamamatsu) as this was found to yield more reproducible results than measuring diameters. Differences in size and relative thickness of vessels were confirmed by smooth muscle actin staining. For determination of trophoblast invasion, H&E and cytokeratin stainings were used and analysed as described before8 (link) using the most distal section from the fetus that contained fetal red blood cells as a marker for the base of the ectoplacental cone and the most distal section positive for cytokeratin staining as its apex.
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2

Mouse Ear Lymphatic Vessel Analysis

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Ears from 8- to 10-week-old mice were collected and fixed in 4% paraformaldehyde overnight at 4°C. For each ear, the dorsal skin was separated from the rest of the tissue (central cartilage and the adhering ventral skin). Whole dorsal ear skins were fixed in methanol for 1 hour at –20°C and then blocked with 3% milk and 0.2% Triton X-100 for 1 hour at room temperature. They were then incubated with a polyclonal goat anti-LYVE1 antibody (1:200; AF2125, R&D Systems) and rat anti-CD31 antibody (1:150, DIA-310, Dianova) overnight at room temperature. After washing in PBS, an Alexa Fluor 488–coupled rabbit anti-goat antibody (1:200; A21222, Invitrogen) was added for 2 hours at room temperature. After washes with PBS, Alexa Fluor 546–coupled goat anti rat antibody (1:200; A11081, Invitrogen) was incubated at room temperature for 2 hours. Slides were then washed with PBS and mounted using Dako fluorescent mounting medium (Dako). Slides were scanned using a Nanozoomer 2.0 scanner (Hamamatsu) and visualized using NDPviewer (Hamamatsu). The lymphatic vessel frequency, density, and thickness were quantified using ImageJ software.
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3

Quantifying Glomerular Injury and Podocyte Density

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Podocyte density was calculated in each glomerulus as p57 + cell number/glomerular area. Glomerular planar area and glomerular diameter were calculated using a virtual slide system (NDP viewer, Hamamatsu Photonics). We measured all the glomeruli encountered in each section (on average, 93.1 glomeruli/animal). CD44-positive glomeruli were quantified by the incidence of glomeruli having CD44 + cells. Similar to p57, we analyzed CD44 + glomeruli among all the glomeruli encountered in each section (on average, 97.7 glomeruli/animal). To express the degree of glomerular injury in each animal, glomerular scoring was performed. Glomerular lesions were divided into four grades using PAM-stained slides depending on the glomerular area involved by crescent; S0 (no change), S1 (< 50%), S2 (> 50%), S3 (global sclerosis). All the glomeruli in the single section in each animal were individually scored, and the average value in each animal was calculated. On average, over 90 glomeruli per section were examined. Fibrinoid exudate was estimated by MT staining showing red-colored amorphous deposition in the tuft or urinary space. The incidence of fibrin-positive glomeruli per section was calculated.
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4

Immunohistochemical Analysis of Neurological Markers

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The tissue microarrays (TMAs) were constructed as previously described and immunohistochemistry (IHC) was performed as our previous study [19 (link)]. Anti-human rabbit monoclonal antibodies for monoamine oxidase A (MAO-A) (1:200; #ab126751, Abcam, Cambridge, UK), anti-human mouse monoclonal antibodies for beta-tubulin III (1:100; #4466S, CST, Massachusetts, USA), anti-human rabbit monoclonal antibodies for tyrosine hydroxylase (TH) (1:300; #58844S, CST, Massachusetts, USA), anti-human mouse monoclonal antibodies for vesicular acetylcholine transporter (VACHT) (1:100; #MA5-27,662, ThermoFisher, Waltham, USA) and anti-human rabbit monoclonal antibodies for CD56 (1:200; #99746S, CST, Massachusetts, USA) were used as primary antibodies to detect the expression of MAO-A, TH, VACHT and CD56, respectively. Automated digital pathological slice scanner, KF-PRO-120 (KONFOONG biotech international CO.LTD., Ningbo, China) and NanoZoomer S360 (Hamamatsu Photonics CO.LTD., Beijing, China), were used to scan images of IHC slides, and slides were photographed by Digital slices view software K-Viewer (KONFOONG biotech international CO.LTD., Ningbo, China) and NDP-viewer (Hamamatsu Photonics CO.LTD., Beijing, China).
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5

Quantitative Amyloid Deposition in 5XFAD Mice

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Quantitative analysis of fibrillar amyloid deposition was performed on 8-10 month old 5XFAD/apoEm/m, 5XFAD/apoEm/4 and 5XFAD/apoE4/4 mice as previously described [18 (link)]. Briefly, three sections per mouse (Bregma, -1.4 mm caudal to Bregma, -2.0 mm caudal to Bregma) were stained with X-34 and then scanned using a Nanozoomer slide scanner (Hamamatsu Photonics). Images were exported with NDP viewer (Hamamatsu Photonics), converted to grayscale, thresholded to highlight positive staining of plaques or CAA, and analyzed using ImageJ (National Institutes of Health). The average area covered by X-34 from the 3 sections/mouse was used to represent each mouse. The quantification was performed by an investigator who was blinded for the genotype of the animals.
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6

Quantitative Analysis of Uterine Vascular Remodeling

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Tissue volumes were quantified from serial sections using the Cavalieri method (40 (link)). Briefly, MLAp cross-sectional areas were calculated on serial sections and volumes were calculated by accounting for the spacing between the sections as previously described (41 (link)). Arterial remodeling was evaluated in the central decidua basalis on sagittal sections and veins localized at the periphery were excluded. Three to five implantation sites from randomly chosen uterine horn were analyzed per litter. In every implantation site, three to five largest vessels were measured in triplicate (three sections with distance of 49 μm apart). Lumen area and vessel-to-lumen ratios were quantitated by using outlines tools from NDP viewer (Hamamatsu) and Aperio ePathology (Leica Biosystems) softwares. SMA IHC staining was used for further qualitative assessment of arterial remodeling (41 (link)).
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7

Histological Assessment of Murine Colonic Tissues

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Murine colonic tissues were fixed with 4% paraformaldehyde in 0.1 M phosphate-buffered saline for 3 h at RT, embedded in paraffin, microtome-sectioned (3 μm thick), mounted on glass slides and stained with hemalun, phloxin, and saffron (HPS). Images were acquired with a slide scanner (Hamamatsu Nanozoomer 2.0HT, Massy, France) and viewer software (NDPViewer). Colonic tissue integrity was monitored by scoring the mucosal architecture, cellular infiltration, and muscle thickening, as 0, 1, 2, 3 (from best to less preserved). Multiplication of the score by 1, 2, 3, or 4 was applied if the observed damage covered 25%, 50%, 75%, or 100%, respectively, of the analyzed tissue fragment.
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8

Immunohistochemical Analysis of RCC and Colon Cancer

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Human tissue samples were obtained from excised RCC, normal renal tissue, colon cancer and normal colon tissues of patients at Hokkaido University Hospital. Frozen sections of excised tissues were prepared as previously described.(14 (link),26 (link)) Human sections were double-stained with anti-human CD31/Alexa Fluor 594 rat anti-mouse IgG and anti-SBSN/Alexa Fluor 488 goat anti-rabbit IgG. All samples were counterstained with DAPI (Roche Diagnostics, Mannheim, Germany) and examined using an Olympus FluoView FV10i confocal microscope (Olympus, Tokyo, Japan).
For AKT staining, formalin-fixed paraffin-embedded specimens from two cases of colon cancer were prepared. Immunohistochemical analysis was performed using serial sections that were stained with anti-SBSN (1:250 dilution), AKT (1:100 dilution) and CD31 (Leica Microsystem, UK; 1:500 dilution), followed by antibody detection using a peroxidase-conjugated streptavidin-diaminobenzidine (DAB) readout system (DAKO), and counterstaining with DAPI. Images were randomly captured using a nanozoomer slide scanner and NDPViewer (Hamamatsu, Japan).
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9

Quantifying Retinal Vascular Network

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Vessels were stained with 0.01 mg/ml IB4-FITC (Life Technologies, I21411). IB4-labeled retinas were imaged with a Nanozoomer slide scanner (Hamamatsu). Branch point numbers were quantified with Biologic CMM Analyser Software developed by N. Elie51 (link), and the retinal area was calculated with NDP-Viewer (Hamamatsu). Vascular density and vascular progression analysis were quantified with ImageJ. To measure retinal vascular density, we quantified the surface area of IB4 staining and of the total retina to obtain a ratio of coverage. To determine vascular progression, we measured the radius of the retina (D) and the distance from the optic nerve to the developing vascular front (d) and calculated the ratio d/D. At least 12 ratio (d/D) measurements were completed for each retina.
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10

Quantitative Analysis of Brain Immunostaining

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Immunostained brain sections were scanned using a Nanozoomer slide scanner (Hamamatsu Photonics). Quantitative analysis of immunopositive staining was performed as previously described [33 (link)]. Briefly, images of immunostained sections were exported with NDP viewer (Hamamatsu Photonics), converted to 8-bit grayscale using ACDSee Pro 2 software (ACD Systems) and threshold was set to highlight positive staining and analyzed using ImageJ (National Institutes of Health). 3 sections per mouse (Bregma, −1.4 mm caudal to Bregma, −2.0 mm caudal to Bregma) were quantified (the cortex immediately dorsal to the hippocampus) and the average was used to represent each mouse.
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