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1

Dystrophin Quantification in Muscle Samples

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Transverse sections of tissue samples were sectioned (8 μm thick) and co-stained with rabbit-anti-dystrophin (Abcam) and rat anti-laminin (Sigma) as previously described30 (link). Dystrophin was quantified relative to laminin co-stain using ImagePro software (MediaCybernetics) and normalised to C57CL/10. Briefly, 4 images of dystrophin and the corresponding laminin fields were taken for each section. Following the Arechavala-Gomeza approach54 (link), 10 regions of interest were randomly placed on the laminin image which was overlaid on the corresponding dystrophin image to attain the minimum and maximum fluorescence intensity (Image-Pro, Media Cybernetics, Inc.). Data was normalised relative to C57BL/10. The percentage recovery score was calculated using the following equation: (dystrophin recovery of treated mdx mice-dystrophin recovery of untreated mdx mice)/(dystrophin recovery of C57BL/10 mice-dystrophin recovery of untreated mdx mice); as described on the TREAT-NMD website (http://www.treat-nmd.eu/downloads/file/sops/dmd/MDX/DMD_M.1.1_001.pdf).
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2

Quantitative Analysis of MBP and Cell Markers

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Quantitative image analysis was performed using ImageJ (NIH) and Image-Pro (Media Cybernetics). To quantify MBP expression, the pixel intensity of immunofluorescence was measured. All slides were immunostained with MBP antibodies, and all digital images were acquired using the same exposure parameters. To quantify PDGFR+, NeuN+, APC+, O4+, or GFAP + cells within the slices, 5–10 digital photographs were taken using the same exposure parameters from each section. The cell counter of Image-Pro software (Media Cybernetics) was used to count cells, and mean numbers were used for analysis.
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3

Quantifying Macrophage Proliferation in Atherosclerosis

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Aortic roots were frozen in OCT media (Tissue-Tek, Miles Inc.) and serial 10μm sections were cut as previously described[20 (link)]. Accumulation of lipids in lesions was visualized by staining with oil red O. Macrophages were detected using rabbit anti-mouse macrophage antisera (Accurate Chemicals)[22 (link)]. Percentage of macrophage and lipid (oil-red-o+) area in aortic root plaques was calculated using computer-assisted image analysis (Image-Pro, Media Cybernetics). Macrophage proliferation in atherosclerotic lesions was identified by immunostaining consecutive aortic root sections with antibodies against macrophages or proliferating cell nuclear antigen (PCNA, Abcam ab2426)[23 (link)]. Proliferating macrophages were identified as regions staining positive for both macrophage and PCNA and were quantified using computer-assisted image analysis (Image-Pro, Media Cybernetics). The ratio of proliferating macrophages to total macrophages at the aortic root was calculated by dividing macrophage positive areas by macrophage and PCNA positive areas.
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4

Quantifying Pancreatic Islet Morphometry

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Paraffin sections (4-µm thickness) were stained with hematoxylin and eosin (HE) for histological examination. For the immunohistochemical detection of insulin, paraffin sections were incubated with the rabbit anti-rat insulin antibody (cat#4590, Cell Signaling Technology, USA) at 1:100 dilution, followed by incubation with the HRP-conjugated anti-rabbit secondary antibody (cat#PV-9000, ZSGB-BIO, China) and development with the HRP-AEC kit (GENMED Scientifics, USA). Sections were then counterstained with hematoxylin and examined under the light microscope (Leica DM2000, Germany). For measurement of the islet area, islets in HE sections were identified and the islet area was measured using Image-Pro software (Media Cybernetics, USA). The average islet area from each rat was determined from 4-5 sections spaced >200 μm apart. The cell number per islet area in the same section was counted using Image-Pro (Media Cybernetics, USA) and the average cell number per islet from each rat was determined in the same manner as that of the islet area.
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5

Optic Nerve Axon Quantification

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Axon counts for individual optic nerves were obtained as described previously (Buckingham et al., 2008 (link); Crish et al., 2010 (link); Inman et al., 2006 (link); Joos et al., 2010 (link); Sappington et al., 2010 (link)). Briefly, a single, plastic cross-section was imaged in its entirety for each nerve by creating a montage of 20–25 adjacent frames using a 100x oil-immersion objective, differential interference contrast optics (Provis AX70; Olympus, Melville, NY), a motorized stage and a digital charge-coupled device (CCD) camera. Image montages were minimally processed for contrast- and edge-enhancing using macro routines (ImagePro; Media Cybernetics, Silver Spring, MD). All axons with an identifiable myelin sheath were counted in each frame at 1,000x digital magnification using an additional macro routine. The axon density was calculated as the number of axons divided by frame area, and the axon density for each nerve was estimated as the mean of densities across frames.
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6

Western Blotting of Hep-2 Cell Lysates

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Western blotting was performed as previous reported [36 (link), 37 (link)]. Briefly, Hep-2 cells were grown in the mid-log phase, washed with phosphate buffered saline and lysed for 30 min on ice. The lysis buffer with pH 6.8 contained 10% glycerol, 5% 2-mercaptoethanol, 2% sodium dodecyl sulfate (SDS), 62.5 mmol/L Tris-HCl. The SDS–PAGE analysis was performed and membranes were incubated overnight at 4°C with antibodies directed against the indicated proteins. The antibodies were obtained from the following companies: anti-TrkB, anti-β-actin, anti-p-Akt, anti-cyclin D1, anti-p-s-Src and anti-c-Src were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA); anti-RUNX3 and anti-Keap1 were purchased from Cell Signaling Technology (Danvers, MA, USA); anti-E-cadherin, anti-N-cadherin, anti-vimentin, anti-Twist-1 and anti-Twist-2 were purchased from BD Biosciences (San Jose, CA, USA). Membranes were washed, incubated with the appropriate secondary antibodies and exposed with the ECL chemiluminescent substrate kit (Pierce, Rockford, IL, USA). Images were analyzed with ImagePro (Media Cybernetics, Bethesda, MD, USA) and densitometry data were analyzed by using either conventional Student’s t-test. Results are reported as mean ± SD. A P-value <0.05 was considered significant and all were two-tailed.
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7

Aortic Plaque Quantification by Oil-red-O

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Fixed aortas were rinsed in absolute propylene glycol and stained with Oil-red-O (01516, Sigma Aldrich). After washing in 85% propylene glycol solution and distilled water, the aortas were opened longitudinally to the iliac bifurcation and a coverslip was placed to flatten down the aorta with endothelial surface facing upwards. Images were acquired using Olympus SZX7 fitted with a 1x lens and image processing was performed using Image-Pro (Media Cybernetics). The plaque area was quantified as a percentage of the area of both the total aorta and the aortic arch.
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8

BMDM Inflammasome Activation Assay

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BMDM were stimulated as described above, supernatants were collected, and proteins were precipitated by methanol-chloroform extraction. Cell pellets were suspended in lysis buffer. Immunoblot analysis was performed using following primary antibodies: anti-mouse IL-1β (AF-401-NA; R&D System, MN USA), rabbit polyclonal anti-Caspase-1 (Santa Cruz Biotechnology), anti-β-actin (C4; Santa Cruz Biotechnology). For ASC oligomerization assay in lysates, cells suspension was washed with PBS and incubated with 2 mM disuccinimidyl suberate (DSS, No-Weigh™ Format, Pierce Protein Biology) for 30 minutes in room temperature. After washing with ice cold PBS, precipitates were suspended in lysis buffer. Immunoblot analysis was performed using rabbit anti-mouse ASC (N15; Santa Cruz Biotechnology). The supernatants were also used for anti-mouse ASC immunoblot and anti-phosphotyrosine (4G10; EMD Millipore, MA USA) immunoblot analysis. For immunoprecipitation, anti-phosphotyrosine agarose beads (PY20; EMD Millipore) were added into the supernatants and incubated for overnight, washed with lysis buffer for 3 times, and used for immunoblot with HRP conjugated rabbit anti-mouse ASC (LifeSpan Biosciences, Inc., WA USA). Image densitometry was performed using Image-Pro (MEDIA Cybernetics, INC., MD USA).
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9

Thermal Imaging of Bee Nest Temperatures

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The experimental nests (e.g. Fig 1) were filmed through 200 h of observation time from a distance of 1.5 m with a high-definition (HD) camera (Panasonic HVX 200) and in parallel, with an infrared (IR) camera (Flir A320; resolution: 640 x 560 pixel; 9 Hz). The color-coded (rainbow-900 palette) IR images were transferred from the IMG-format (providing adjustable temperature scales when operated by Flir-Researcher 2.9) into the fixed-scale BMP-format, which was further analysed by the Image-Pro software (MediaCybernetics 7.0). In total, > 30 000 frames were selected for the final evaluation representing 120 min recording time. Selected images from both HD and IR films were processed by the ThermaCAM Reporter 9.1 Professional (Flir) and Image-Pro and superposed by triangulation to the view of the IR camera. This allowed the identification of the temperature values of bee bodies and of the cavities between.
Data loggers (HOBO U12) were mounted one meter in front and behind the nest and registered ambient humidity, irradiation and ambient temperature (Tamb), which latter was also used to calibrate the IR camera.
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10

Quantifying Cell Viability in Tissue Constructs

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Cell viability was quantified on 20 digital photomicrographs (TIFF, 10 × ) of the construct surface, 250 μm apart, that were generated with a spectral confocal laser scanning microscope digital imaging system (Leica TCS SP2; Leica Microsystems, Buffalo Grove, IL). Constructs were rinsed with phosphate-buffered saline and incubated at room temperature in darkness with assay reagents (Invitrogen LIVE/DEAD® Viability/Cytotoxicity kit; Thermo Fisher Scientific) for 30 min.30 The numbers of live (green) and dead (red) cells in each section were quantified (Image-Pro; Media Cybernetics, Bethesda, MD) to calculate live cell percentage (live cells/total cells × 100) for each construct.
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