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42 protocols using dp25 camera

1

Histological Analysis of Harvested Kidneys

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Harvested kidneys were fixed in 4% paraformaldehyde (Wako Pure Chemical Industries, Osaka, Japan), and then embedded in paraffin. Paraffin-embedded kidney sections (4 μm thick; cut with a microtome; TU-213, Yamato, Saitama, Japan) were used for histological analysis. The sections were dewaxed in xylene and stained with periodic acid-Schiff, Masson trichrome, and Oil-Red. Glomerular size, evaluated by the Bowman’s capsule area, and lipid droplets in the renal tubules, calculated as the relative area of droplets to the tubular area, were quantified in the periodic acid-Schiff-stained sections. Interstitial fibrosis was evaluated in the Masson trichrome-stained sections. Accumulations of neutral lipids were observed in glomeruli and renal tubules in Oil-Red-stained sections. Olympus BX51N microscope and Olympus DP25 camera (Olympus, Tokyo, Japan) were used for acquiring images. ImageJ software 1.53c (National Institute of Health, Bethesda, MD, USA) was used for the quantification.
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2

Histological Analysis of Thrombectomy Clots

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The clots retrieved by thrombectomy were fixated in 10% formalin. The formalin-fixed species were then embedded in paraffin, cut at 4μm thickness, and stained with hematoxylin and eosin. These stained sections were examined and photographed using an Olympus microscope and Olympus DP25 camera (Olympus Corporation. Tokyo, Japan). Qualitative histologic analysis was done by two experienced pathologists, who independently evaluated and described the histoarchitecture of the clot. Quantitative thrombus composition analysis was also performed to determine the percentage of fibrin, red blood cells (RBC) and white blood cells (WBC) in each thrombus. Hematoxylin and eosin stained slides were scanned in via Aperio digital scanner (Leica Biosystems. Buffalo Grove, IL). Automated histologic quantification was performed on the digitized images using Orbit Image Analysis Software (www.orbit.bio) per a standard operating procedure.13 (link)
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3

Quantifying Immune Cell Subsets in Skin Biopsies

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Biopsy samples for histopathology and immunohistochemistry were immediately placed in formalin and processed by routine histologic methods and assessed by a board certified pathologist. Immunohistochemistry was performed on formalin fixed, paraffin embedded specimens following antigen retrieval with Diva or Borg decloaking solution (Biocare Medical). Adjacent 10 μm sections were stained for CD3+ (rabbit anti-human CD3, DAKO, USA; biotinylated goat anti-rabbit IgG, Vector Labs, USA; streptavidin, Biogenix; DAB, DAKO, USA), or FoxP3+ (rat anti-FoxP3, Ebioscience, USA; rat-on-mouse HRP probe/polymer, Biocare, USA; AEC, Biocare, USA). CD3+ and FoxP3+ cells in the dermis and epidermis were quantified from images captured at 400x magnification using a DP25 camera and BX53 microscope (Olympus, USA).
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4

Tissue Histological Analysis for Extravasation

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Tissues were fixed in Excel fixative (American Master Tech Scientific, Lodi, CA, USA) and processed with paraffin-embedding procedures. Sections (5 μm in thickness) were cut and stained with hematoxylin and eosin, and the stained sections were observed under a light microscope (Olympus BX41, Center Valley, PA, USA) to assess extravasation of blood cells. Images were captured with an Olympus DP25 camera.
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5

Murine Organ Harvesting and Analysis

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Murine organs (lungs, spleens) were harvested from surviving mice at the conclusion of each experiment, or from mice at predetermined time points throughout the experiments. The right lung was prepared for bacterial titer; the left lung was processed for histology. Organs for titer were homogenized in sterile PBS via a Bullet Blender (Next Advance, Averill Park, NY, USA) for 5 min. A 200-μl aliquot was removed from the 1-ml homogenate, serially diluted and plated on LB agar. Organs for histology were washed in PBS, fixed in 10% neutral buffered formalin, dehydrated in ethanol and embedded in paraffin; 5-μm sections were stained with Hematoxylin and Eosin. Images were obtained using an Olympus DP25 camera and BX40 light microscope.
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6

Immunohistochemical Analysis of AXL and MITF

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For immunocytochemistry, five days after seeding, cells were scraped in cold PBS, formalin-fixed, paraffin-embedded, and processed as below. For immunohistochemistry, 4 μM sections of formalin-fixed, paraffin-embedded specimens were heated at 60°C, deparaffinized in xylene, and hydrated in a series of ethanol dilutions. Epitope retrieval was by microwaving (5 min at 850w, 15 min at 150w) in 10 mM Tris-EDTA buffer pH 9.0. Slides were blocked 10 minutes in 3% BSA in TBST (Tris pH 7.6, 0.05% Tween-20). Primary antibodies were as follows: MITF, 1:100 in 3% BSA in TBST, clone D5 (Dako M3621); AXL, 1:100 in 3% BSA in TBST, clone C89E7 (CST 8661). Slides underwent 10 min peroxidase block in 3% H2O2. Secondary antibodies were: goat anti-mouse IgG-HRP (BioRad 170-6516, 1:200 in 3% BSA in TBST; Dako EnVision anti-rabbit (K4003, ready-to-use). Slides were developed with DAB+ (Dako K3468) for 10 min and counterstained 1 min with hematoxylin (Vector H-3401) prior to dehydration and mounting. Slides were imaged on an Olympus BX51 microscope with Olympus DP25 camera using Olympus WHN10X-H/22 oculars, Olympus UPlan FL N -20×/0.50 and -40×/0.50 objectives, an Olympus DP25 camera, and images acquired using Olympus DP2-TWAIN software and Adobe Photoshop 7.0. Slides were scored for intensity and distribution of AXL and MITF by a dermatopathologist blinded to clinical outcome.
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7

Anchorage-independent Cell Growth Assay

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48 hours after infection, 3000 cells/well were added to 6-well plates in growth medium with 0.35% noble agar (BD Difco) on top of a solidified layer of 0.5% noble agar prepared in growth medium. Cells were fed with fresh growth medium twice a week for 8 weeks, after which colonies were stained with 0.005% crystal violet and analyzed under Olympus CKX41 microscope using Olympus DP25 camera and DP2-BSW application software. For each condition, five fields per well were analyzed. From each field, three images (each focused on a different layer) were taken. Only the colonies that were in the focus and bigger than 30 μm in diameter were counted. Total colony numbers were calculated from 15 images for each well. For each condition, average colony number per well, which was calculated from three independent experiments, was plotted. Colony diameter was calculated using all of the counted colonies for each condition. Colony number per well and diameter values represent the mean±S.D. of three independent experiments. Two-tailed Student’s t-test was used to calculate statistical significance.
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8

Histological Analysis of Fish Intestinal Tissues

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After excision of the pyloric ceca (PC), proximal intestine (PI), and distal intestine (DI) parts, sectional samples from six fish per treatment were carefully rinsed with autoclaved seawater to remove residual faeces and immediately fixed in 10% neutral buffered formalin. Samples were routinely processed for histology, sectioned at 3–5 μm thickness. A total of two slides were made from each block. One slide of each treatment was stained with Mayer’s haematoxylin and eosin (HE) or alcian blue/periodic acid-Schiff stain (AB/PAS, pH = 2.5), respectively. After dehydration, slides were cleared in xylene and cover slipped with NeoMount. HE stained slides were used to assess possible degenerative changes and/or inflammation. Slides were examined under the Olympus BX51 light microscope coupled with Olympus DP25 camera. For more details, see the Additional file 1: Supplementary methods.
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9

Mitochondrial ROS Quantification

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Approximately 30,000 cells/well were plated on a four-well glass chamber slide (Millipore). Cells were washed in PBS 24 hours later and treated with vehicle, cetuximab (100nM) and/or honokiol (20uM). Again, 24 hours later cells were washed with PBS again. Cells were treated with 3uM MitoSox in HBSS for 30 minutes. Cells were washed in PBS and then fixed at room temperature with 4% methanol-free formaldehyde for 15 minutes. Cell were washed with PBS and treated with DAPI (Molecular Probes) for 5 minutes. Slides were mounted with Prolong gold mounting solution (Life Technologies). An Olympus BX41 microscope and Olympus DP25 camera was used for fluorescent microscopy and photography. Quantified average cell fluorescence of ~20 cells per treatment arm using ImageJ analysis.
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10

Assessing Placental Vascular Leak in ZIKV Infection

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To examine vascular leak across the placenta during ZIKV infection, Evans Blue dye was administered intravenously to pregnant AIR mice at embryonic day 17–18 as previously described25 (link). Following injection, whole fetuses were dissected and fixed with 10% neutral buffered formalin. Whole pups were imaged with an Olympus SZX16 dissection scope coupled to an Olympus DP25 camera. Following whole pup imaging, samples were cut in half sagittally and sectioned for IHC and confocal microscopy as described above.
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