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Imagej

Manufactured by Universal Imaging
Sourced in United States

ImageJ is a free, open-source image processing software. It is designed to analyze and manipulate digital images. ImageJ provides a wide range of tools and features for image processing, measurement, and analysis.

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5 protocols using imagej

1

Quantitative Image Analysis of Cells

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Analysis of cells and clusters during time-lapse experiments was performed using ImageJ (public domain) and a custom MATLAB script (MathWorks; Natick, MA). Analysis of vessel characteristics was performed using ImageJ (public domain) and MetaMorph (Universal Imaging, Downingtown, PA). Analysis of stress fibers was performed using ImageJ (public domain) and a custom MATLAB script developed in the laboratory (MathWorks; Natick, MA) (60 (link)). Analysis of GFP-ECFCs in vivo was performed using Imaris (Bitplane, Belfast, UK) and ImageJ (public domain). All graphs were made using GraphPad Prism 6 (GraphPad Software Inc.).
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2

Quantifying Basilar Artery Vasospasm in SAH

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This protocol was conducted in a as previously described in Dr. Huang et al. (2017) [24 (link)]. Three cross sections from the middle-third BA in each animal were analyzed by a trained research staff blinded to the experimental groups. The thickness of BA was defined as the largest vertical distance between the inner surface of endothelium and the outer surface of adventitia. The arterial cross-sectional area was calculated using computer-based morphometric analysis (Image J; Universal Imaging Corp., USA). The average area of BA cross sections from each rat was calculated to obtain mean values for the degree of vasospasm at 48 h after SAH.
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3

Mammary Gland Whole Mount Analysis

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Mammary gland whole mount analysis was carried out as described by Kleinberg et al. [23] (link). All chemicals came from Merck (Darmstadt, Germany), unless otherwise stated. After harvesting, tissues were fixed in ice-cold 4% paraformaldehyde for 2 h. Mammary glands were stored in 70% ethanol until further analysis. In short, following 3 washes with aceton for 30 min, mammary glands were rehydrated in 100% and 95% ethanol (30 min each). The glands were stained for 1 h with filtered hematoxylin, followed by thorough rinsing with tap water. Background staining was minimized by incubation (3×35 min) in a solution of 150 ml 100% ethanol, 150 ml aqua dest. and 7.5 ml HCl 1N (Sigma-Aldrich Chemie GmbH, Munich, Germany). Subsequently tissues were dehydrated in 70%, 95% and 100% ethanol (2×30 min for each step), followed by an incubation in Xylol (Roth, Karlsruhe, Germany) overnight. For long term storage mammary gland whole mounts were placed in methylsalicylate. Digital images of squash preparations were taken by a transmitted-light microscope stand mounted with a NIKON D200 camera (Nikon GmbH, Düsseldorf, Germany) at a distance of 60 cm all in one day. Picture analysis was performed using MetaVue software (MetaVue, Universal Imaging Corp., Downingtown, PA, USA) and ImageJ [34] (link). Pixel size was 11.125 µmx11.125 µm and pixel area was 123.766 µm2.
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4

Basilar Artery Vasospasm Analysis

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Three cross-sections from the middle-third BA from each animal were analyzed by a trained member of research staff who was blinded to the experimental groups. The BA thickness was defined as the largest vertical distance between the inner surface of the endothelium and the outer surface of the adventitia. The arterial cross-sectional area was calculated using a computer-based morphometric analysis (ImageJ; Universal Imaging Corp., Hialeah, FL, USA). The average area of the BA cross-section from each rat was calculated to obtain the mean values for the degree of vasospasm at 48 h after SAH.
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5

Raichu FRET Probes for GTPases

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We used pRaichu-Rac1 and pRaichu-Rab5 as FRET probes for Rab5 and Rac1 GTPases, respectively. Raichu-Rac1 consists of YFP, CRIB of PAK1, Rac1, CFP (amino acids 1–237), and the CAAX box of Ki-Ras (Itoh et al., 2002 (link)). Raichu-Rab5 consists of Venus, the amino-terminal Rab5-binding domain of EEA1 (amino acid residues 36–218), SECFP, and Rab5a (Kitano et al., 2008 ). FRET analysis for Rac1 and Rab5 was conducted as described previously (Aoki and Matsuda, 2009 (link)). Briefly, control and DRG2-depleted MCF7 cells were transfected with pRaichu-Rac1 or pRaichu-Rab5. Images were captured using the ratiometric FRET module in the FluoView program of the LSM FV1000 confocal microscope (Olympus, Tokyo, Japan). CFP and YFP images were processed by ImageJ and MetaMorph software (Universal Imaging, West Chester, PA). After background subtraction, FRET ratio images were generated using MetaMorph software and visualized in intensity-modulated display mode. In this display mode, eight colors from red to blue are used to represent the FRET ratio (YFP/CFP), with the intensity of each color indicating the mean intensity of YFP and CFP.
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