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63 protocols using image pro premier 9

1

Quantitative Histological Analysis of Mucosal Immune Markers

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Digitally fixed images of mucosal tunica were analyzed at 200× and 1000× magnification using an optical microscope (Olympus, Hamburg, Germany) equipped with an image analyzer (Image Pro Premier 9.1, MediaCybernetics, Rockville, MD, USA). The immunohistochemical data for TLR4, NF-kB p65, NF-kB p50, COX2, iNOS, TNF-α, IL-1β, Cas-3 and Cas-8 were qualitatively evaluated by a blinder examiner and were expressed as negative (−), very weak (−/+), weak (+), moderate (++) and strong (+++) positivity. Additionally, a blinder examiner evaluated immunostaining also quantitatively, as Integrated Optical Density (IOD) using an image analyzer (Image Pro Premier 9.1, MediaCybernetics, Rockville, MD, USA) [47 (link),48 (link)]. The data were pooled to represent a mean value and a statistical analysis was applied to compare the results obtained from the different experimental groups. The analysis was performed on five sections for each sample spacing 70 μm and evaluating six random fields with the same area (52 × 103 μm2) per section.
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2

Quantifying Hepatocyte Lipid Droplets and Fibrosis

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The lipid droplets in hepatocytes were assessed on hematoxylin–eosin-stained sections by measuring the diameter (μm) of randomly chosen 100 lipid droplets/groups at a final magnification of 400×. The morphometric analyses were performed by two different observers blinded to the experimental group, using a computer image analysis software (Image Pro Premier 9.1, Media Cybernetics, Rockville, MD, USA).
NAFLD is characterized by liver histopathological features including steatosis, hepatocyte ballooning, inflammation, and fibrosis, as previously described [9 (link),26 (link)]. Perivascular hepatic fibrosis evaluation was assessed using Masson trichrome staining and liver fibrosis (blue: collagen fibers; red: hepatocyte cytoplasm). The percentage of perivascular hepatic fibrosis was calculated using a computerized image analyzer (Image Pro Premier 9.1, MediaCybernetics Inc., Rockville, MD, USA) evaluating 20 randomly chosen liver fields per experimental animal [9 (link),26 (link)].
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3

Quantitative Histological Analysis of Aortic Remodeling

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Transverse sections (5 µm) of paraffin-embedded proximal ascending aorta were used for histological stains with Masson’s Trichrome (HT15, Sigma-Aldrich) for collagen, hematoxylin and eosin (H&E) for nuclei, and Verhoeff Van Gieson (VVG; 87017, Thermo Fisher) for elastin. Brightfield photomicrographs were randomly captured by a researcher (XYK) blinded to the treatment groups using the Olympus BX51 microscope and Image-Pro Premier 9.2 (Media Cybernetics).
Total fibrosis was measured by ImageJ (v1.52a, NIH) with Colour Deconvolution-Masson’s Trichrome expressed as a percentage of collagen stained area over total tissue area. Media thickness was measured as the intima-media distance using the incremental distance tool at a calibrated step of 10 μm on Image-Pro Premier 9.2 (Media Cybernetics) and reported as an average of 62–142 measurements per section.
Adventitial area and SMC nuclei were quantified in H&E stained sections as described67 (link). Adventitial area was expressed as a percentage of total tissue area. SMC nuclei were expressed as nuclei counts over media area. Elastin area fraction was expressed as the elastin area over total tissue area. Elastin breaks were counted and expressed normalized to the media area.
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4

Soft Agar Colony Formation Assay

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Agar (0.35%, 1 mL) in culture media was added to the bottom layer of each well in a 12‐well plate. For the top layer in each well, 1 × 103 cells were resuspended in 1 mL of a mixture comprising 0.2% agar and RRMI 1640 media. The cells were incubated at 37°C with 5% CO2 for 2 weeks, after which the colonies were stained with crystal violet, photographed by inverted phase‐contrast microscopy (Leica, Wetzlar, Germany) and counted using ImagePro premier 9 (Image‐Pro Premier 9.0, Media Cybernetics, MD, USA).
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5

Liver Histomorphometry via Paraffin Sections

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Liver paraffin-embedded sections were deparaffinized, rehydrated, and then stained with haematoxylin-eosin, following standard protocols. In detail, haematoxylin-eosin staining was used to evaluate liver morphology and also to measure the hepatocyte nuclear area [13 (link), 40 (link)]. The hepatocyte nuclear area was calculated using a computerized image analyzer (Image Pro Premier 9.1, Media Cybernetics Inc., Rockville, USA) evaluating 20 randomly chosen liver fields per experimental animal. Two blinded investigators performed the morphometrical analysis and their evaluation was assumed to be correct if the values were not significantly different. If there was disagreement concerning the interpretation, the case was reconsidered to reach a unanimous agreement.
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6

Gastrocnemius Muscle Fiber Analysis

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Serial paraffin gastrocnemius sections were stained with hematoxylin-eosin and the sections were then observed with a light microscopy at final magnification of 400× (Olympus, Hamburg, Germany). Feret’s diameter of 50 myotubes for each animal gastrocnemius was determined using an image analyzer (Image Pro Premier 9.1, Media Cybernetics, Rockville, MD, USA). Two blinded investigators performed the morphometrical analysis and their evaluation was assumed to be correct if the values were not significantly different. If there was disagreement concerning the interpretation, the case was reconsidered to reach a unanimous agreement.
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7

Quantifying Reactive Oxygen Species in Heart

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Reactive oxygen species were analyzed using fluorescent probe dihydrorhodamine 123 (Invitrogen; Thermo Fisher Scientific, IL, United States) applied to frozen heart sections. The sections were mounted and observed with fluorescent microscopy (i50 Eclipse, Nikon, Hamburg, Germany) at a final magnification of 400×. Twenty random fields from a total of five non-consecutive sections per animal were analyzed, and the fluorescence staining was calculated using an image analyzer (Image Pro Premier 9.1, Media Cybernetics, Rockville, MD, United States) and expressed as arbitrary units (AU). Two blinded investigators performed the analysis, and their evaluations were assumed correct if the values were not significantly different. If there was disagreement concerning the interpretation, the case was reconsidered in order to reach a unanimous agreement.
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8

Liver Fibrosis Assessment by Sirius Red and Immunofluorescence

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Liver fibrosis was assessed by Sirius red staining to quantify collagen deposition in liver sections [14 (link)]. Following Sirius red staining, slides were scanned by a digital scanner (SCN400; Leica Microsystems, Buffalo Grove, IL) and quantified by the Image-Pro Premier 9.1 (Media Cybernetics, Inc., Rockville, MD). In addition, immunofluorescence staining was performed for Col1a1 co-stained with CK-19 and desmin in frozen liver sections (8 μm). Immunofluorescent staining was visualized using Leica TCS SP5 X system (Leica Microsystems Inc.) and Olympus F300 from Texas A&M Integrated Microscopy Imaging Laboratory. We also measured the expression of Col1a1, Fn1 and TGF-β1 in isolated cholangiocytes and total liver samples by qPCR.
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9

Histomorphometric Analysis of Skeletal Muscle

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Gastrocnemius samples were fixed in 4% buffered paraformaldehyde for 24 h, dehydrated in progressive ethanol solutions, xylene and embedded in paraffin wax, following the standard procedures. Subsequently, 7 mm-thick paraffin sections were cut with a microtome and so the serial paraffin sections were dewaxed in xylene, rehydrated through decreasing scale of ethanol and stained with haematoxylin-eosin, following standard protocol. Then the sections were observed with an optical light microscope (Olympus, Deutschland, Germany) at the final magnification of 200×. Digital images of gastrocnemius were captured and the Feret’s diameter (expressed in µm) of 50 myotubes for each animal muscle was determined using an image analyser (Image Pro Premier 9.1, Media Cybernetics, Rockville, MD, USA) by two observers blinded to the treatment, whose evaluation was assumed to be correct if the values were not significantly different. In case of dispute concerning interpretation, the case was reconsidered to reach an agreement [73 (link),74 (link)].
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10

Quantification of Kv7 Protein Expression

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Coronary artery segments of 1 to 2 mm from domestic or Ossabaw pigs were formalin-fixed, paraffin embedded, and cross-sectioned. The sections were deparaffinized with xylene, hydrated, and subjected to the standard acidic antigen retrieval procedure. The primary goat Kv7.4 antibody (dilution factor: 1:100, Santa Cruz Biotechnology, Dallas, TX) or rabbit Kv7.5 antibody (dilution factor: 1:50, Alomone Labs, Jerusalem, Israel) were added to the prepared sections. After overnight incubation at 4°C with the corresponding primary antibody, the sections were then incubated with the secondary biotin-conjugated antibody (dilution factor 1:1,000, The Jackson Laboratory, Sacramento, CA). After the secondary antibody was removed by multiple washes, the sections were treated with horseradish peroxidase-conjugated to streptavidin. The color was developed using diaminobenzidine and appeared brown. The color density of staining was analyzed using the DAB analysis module of Image-Pro Premier 9.1 (Media Cybernetics Inc., Warrendale, PA). The ratio of the background-corrected intensities of media/intimal layer and the adventitia layer staining was calculated to quantify the relative expression levels of Kv7 proteins. No staining was observed in “no primary antibody” controls (S1 Fig).
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