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14 protocols using metamorph imaging system

1

Calcium Imaging and cGMP Sensing

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cGMP and Calcium imaging was performed as described elsewhere [15 (link), 40 (link)]. Briefly, a single adult animal that expressed genetically encoded cGMP indicator cGi-500 [25 (link)] or that express calcium indicator GCaMP3 [48 (link)] and tagRFP in AFD was placed on a 10% agar pad on a cover slip with 0.1 μm polystyrene beads (Polysciences, Warrington, PA, USA) and covered by another cover slip for immobilization [49 (link)]. The immobilized animals were placed on a Peltier-based temperature controller (Tokai Hit, Fujinomiya, Japan) on a stage of BX61WI microscope (Olympus, Tokyo, Japan). The cyan and yellow, or red and green fluorescence was separated by the Dual-View optics system (Teledyne photometrics, AZ, USA), and the images were captured by an EM-CCD camera C9100-13 ImageEM (Hamamatsu Photonics, Hamamatsu, Japan) at 1 Hz frame rate. Excitation pulses were generated by SPECTRA light engine (Lumencor, Beaverton, OR, USA). The fluorescence intensities were measured by the MetaMorph imaging system (Molecular Devices). Change of fluorescence ratio R (CFP/YFP for cGMP imaging with cGi-500 and GFP/RFP for Ca2+ imaging with GCaMP3 and tagRFP), (R–R0) / R0, was plotted, where R0 is average of R from t = 1 to t = 31.
Expression of PDE-5::GFP was observed with LSM880 confocal microscope (Zeiss, Oberkochen, Germany).
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2

Multimodal Imaging of Tumor Hypoxia and Extracellular Matrix

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Tumor sections were imaged using a fluorescence microscope (BD CARV II Confocal Imager; BD Biosciences), a Quentem 512sc Photometrics camera (Photometrics), and a MIV2000 motorized x-y stage (MetaMorph Imaging System; Molecular Devices), at the following excitation/emission (Ex/Em) wavelengths: HA, DiI, and CD31: 562 nm/624 nm; Hypoxyprobe-1, ColI, and α-SMA: 490 nm/520 nm.
Captured Hypoxyprobe-1 and ColI images were then analyzed with Image-Pro Analyzer 7.0 software (Media Cybernetics). For α-SMA quantification, bright field slides were scanned using the Aperio AT2 scanner (Leica Biosystems), and images were analyzed with HALO image analysis software (Indica Lab). Necrotic regions were excluded from analysis. The percent fluorescent positive area was calculated as the fluorescent signal area divided by the entire tumor area (% positive area = positive signal area/total area). HA levels were quantified using the Spectrum Positive Pixel Count V9 Aperio scoring algorithm (Leica Biosystems).
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3

Quantitative Microscopic Analysis of Neural Markers

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Light photomicrographic images were acquired using a Nikon Optiphot microscope (Nikon Inc., Tokyo, Japan) fitted with a Nikon digital camera (DXM1200), using the Nikon ACT-1 image capture software (ver. 2.2). NeuN- and GFAP-positive cells in the M1, M2 and hippocampus were measured using the MetaMorph Imaging System (Molecular Device, Sunnyvale, CA, USA). The images were imported into Adobe Photoshop (ver. 7.0, Adobe Systems Inc., San Jose, CA, USA) and were adjusted for brightness and contrast to optimize the clarity.
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4

Flagellar Tip Imaging and Intensity Analysis

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Bright-field and fluorescence images were acquired at a 400× magnification using a Nikon Eclipse E600W compound microscope equipped with a CoolSNAP-ES CCD camera (Photometrics, Tucson, AZ) and MetaMorph imaging system (Molecular Devices, Sunnyvale, CA). The MetaMorph program was also used for pseudocolor with a standard rainbow color palette. ImageJ 1.50i was used to subtract background, and the line tool was used to draw across the brightest region near the flagellar tip to obtain plot profiles. The peak value from each profile was used to calculate intensity ratios. Thin-section EM of axonemes was performed as previously described (Kamiya, 1988 (link)).
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5

Quantifying Aortic Remodeling Markers

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To quantitate aortic remodeling, IMT was measured using hematoxylin and eosin staining; elastin breaks were counted via Elastin Verhoeff's–Van Gieson staining; and collagen deposition was evaluated with Masson's trichrome staining. Hematoxylin and eosin, Elastin Verhoeff's–Van Gieson, and Masson trichrome staining were performed using MasterTech stain kits (StatLab, McKinney, TX). Staining of aortic walls was performed as described in previous studies.18 In brief, aortic paraffin sections (5 μm in thickness) were used for immunostaining with antiproliferating cellular nuclear antigen, tissue necrosis factor‐alpha (TNF‐α), intercellular adhesion molecule 1 (ICAM1), vascular cell adhesion molecule 1 (VCAM1), and collagen type I antibodies. Details of primary antibodies used are listed in Table 1. The ratios of target immunohistochemical staining positive area to the total tissue or cell area were determined via a computer‐imaging program according to the instruction provided by manufacture (MetaMorph Imaging System; Molecular Devices, San Jose, CA).
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6

Imaging Expression and Calcium Dynamics

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Expression of OLA-1::GFP and ZYG-8::GFP in head region were observed with BX53 upright microscope (Olympus, Tokyo, Japan). OLA-1::GFP expression in the whole body was observed with LSM880 confocal microscope (Zeiss).
Calcium imaging was performed as described elsewhere [37 (link),41 (link)]. Briefly, a single adult animal that expressed genetically encoded calcium indicator GCaMP3 [59 (link)] and/or XCaMP-R [60 (link)] was placed on a 10% agar pad on a cover slip with 0.1 μm polystyrene beads (Polysciences, Warrington, PA, USA) and covered by another cover slip for immobilization [92 (link)]. The immobilized animals were placed on a Peltier-based temperature controller (Tokai Hit, Fujinomiya, Japan) on a stage of BX61WI microscope (Olympus, Tokyo, Japan). The red and green fluorescence was separated by the Dual-View optics system (Molecular Devices, Sunnyvale, CA, USA), and the images were captured by an EM-CCD camera C9100-13 ImageEM (Hamamatsu Photonics, Japan) at 1 frame per second. Excitation pulses were generated by SPECTRA light engine (Lumencor, Beaverton, OR, USA). The fluorescence intensities were measured by the MetaMorph imaging system (Molecular Devices).
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7

Retinal Imaging with Confocal Microscopy

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Digital images of flat-mounted retinas were captured using an Olympus FluoView 1000 Laser Scanning confocal microscope. For imaging retinal sections, a Nikon TE2000 fluorescence microscope equipped with Photometrics CoolSNAP HQ2 camera was used. A minimum of three random fields was captured for each retina. Colocalization of green (for GFP+ cells) and red (stained vascular endothelium or other retinal cells) fluorescence was examined and area of fluorescence calculated using MetaMorph imaging system (Molecular Devices, Downingtown, PA).
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8

Live-Cell Confocal Imaging of Cell Motility

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Digital images of cell motility were obtained by using an Olympus live-cell confocal microscope system IX81 with a disk scan unit (DSU) (Olympus America Inc., Melville, NY). The two-color fluorescent images were taken alternatively by switching the excitation light paths. Fluorescent images were collected at 1–2 min intervals. MetaMorph® Imaging System (Molecular Devices Corporation, Sunnyvale, CA) was used to capture and store the images in a computer. Olympus filters for GFP (U-MGFPHQ) and RFP (DSU-MRFPHQ) were used.
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9

Bright-field and Fluorescent Microscopy

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Bright-field and fluorescent images were captured with a Nikon Eclipse E600W compound microscope at 400× magnification using a CoolSNAP-ES charge-coupled device camera (Photometrics, Tucson, AZ) and a MetaMorph imaging system (Molecular Devices, Sunnyvale, CA).
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10

Cardiac Cluster Calcium Transient and Contraction Analysis

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For calcium transient analysis, cardiac clusters were dissociated into single cells and
stained with Fluo-4, AM (Thermo Fisher Scientific) for 15 min at 37°C. Using C-Pace EP
(IonOptix, MA, USA), cells were paced at either 0.25 or 0.5 Hz and calcium transients were
recorded using MetaMorph Imaging System (Molecular Devices, CA, USA). Calcium transients
were analysed using pCLAMP 10 (Molecular Devices). For contraction analysis, cardiac
clusters were paced at 0.25 Hz using C-Pace EP (IonOptix) and video recordings were
acquired using CKX41 Inverted Microscope (Olympus). The acquired videos were first
analysed using Musclemotion20 (link)
and the raw data generated was then re-analysed using pCLAMP 10 (Molecular Devices).
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