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27 protocols using axiocam microscope

1

Histochemical Staining Protocols for Plant Tissues

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For DAB (diaminobenzidine tetrahydrochloride; Applichem Lifescience) and NBT (nitroblue tetrazolium chloride; Molekula/VWR Chemicals) staining in maize (B83 inbred line), the root segments were embedded in 6% agarose with 0.5% gelatine and 100-μm-thick sections were cut with a vibratome. Sections were immediately transferred for 1 h to NBT staining solution (0.1% NBT in 10 mM potassium phosphate buffer, pH 7.8) according to the methods of Kawai-Yamada et al. (2004) (link) or for 2-3 h to DAB staining solution [1 mg/ml DAB, Tween 20 (0.05% v/v) and 10 mM Na2HPO4, pH>6.8] according to the methods of Daudi and O'Brien (2012) . Upon signal development, sections were mounted with distilled water and immediately imaged with an AxioCam microscope (Zeiss).
For DCFH-DA (dichloro-dihydro-fluorescein diacetate; Sigma-Aldrich) staining in Arabidopsis, 5 dag seedlings were stained for 15 min in DCFH staining solution (50 μM DCFH-DA in 50 mM phosphate buffer) in darkness according to the methods of Shin et al. (2005) (link). Seedlings were washed briefly in phosphate buffer alone before imaging by confocal microscopy using an LSM5 microscope (Axiovert, Zeiss).
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2

Immunophenotyping of Cardiac Tissue

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Serial 8 µm frozen sections from LV tissue were fixed in 1% paraformaldehyde for 10 min at room temperature and post-fixed in Ethanol/Acetic acid (2:1) for 5 min at 20 °C. Sections were blocked with PBS BSA 1% for 1 h before immunolabeling with primary antibodies against: α-SMA (Abcam), and Ki67 (anti-Ki67; ThermoFischer Scientific). A fluorescent secondary antibody tagged alexa-red-555 was used against the primary antibody. Stained sections were scanned using an epifluorescence Zeiss Axiocam microscope equipped with a digital camera. The α-SMA + and Ki67 + mean fluorescence was calculated with NIH ImageJ software (NIH) in each section, comparing it with the size of the whole area.
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3

Spheroid Culture on Extracellular Matrices

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Spheroids were generated by plating 1×104 KPC cells in ultra-low attachment spheroid microplates (Corning). The next day, spheroids were transferred to 24-well plates containing synthetic ECM or fibroblast-derived ECM using a P1000 pipette at one spheroid per well. Synthetic ECM was generated by gelating different concentrations of high-concentration rat tail collagen I (Corning) and growth-factor reduced Matrigel (Corning) at a final concentration of 20% in a 37°C incubator for 1h. Spheroids were cultured on top of fibroblast-derived or synthetic ECM in DMEM with 10% FBS and were imaged 2–3h after transfer on ECM (d0) and the three following days with a Zeiss AxioCam microscope. Spheroid area, including outgrowing cells, was quantified manually in Fiji (v2.0).
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4

Quantifying Colonic Mucus Cells

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Colon tissue was fixed in 10% phosphate-buffered formalin and 5 uM sections of tissue were stained with Alcian Blue staining by UCD VMTH Histopathology laboratory. Pictures were taken on Axiocam Microscope (Zeiss) with 2.2μm*2.2μm pixel distance dimensions. Quantification of mature Alcian blue-positive cells were calculated based on comet like features of the cells with dense blue staining on the apical side of colonic crypt within the frame. Each measurement was conducted based on 5 pictures per mouse on at 40x magnification.
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5

Microscopic Analysis of Blood Smears

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Air-dried thin-smear blood films were fixed and stained according to manufacturers instructions and imaged on a Zeiss AxioCam microscope equipped with a 100X oil-immersion objective. Raw images were analysed using ImageJ34 (link).
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6

Immunohistochemistry and H&E Staining Protocol

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Samples for immunohistochemical analysis and hematoxylin and eosin (H&E)
staining were fixed in a solution of 1% paraformaldehyde and Gurr®.
After overnight fixation at room temperature, they were stored in 70%
ethanol. When required, they were processed using a Shandon Citadel 2000 tissue
processor (Thermo Scientific) and embedded in paraffin wax in a Shandon
HistoCentre 3 embedding center (Thermo Scientific). Sections
(5 µM) were cut using a Shandon Finesse 325 microtome (Thermo
Scientific). The DakoCytomation EnVision® Dual Link System-HRP (DAB+)
kit (Dako Ltd, High Wycombe, UK) was used to carry out immunohistochemical
analysis of 5-µM sections according to manufacturer’s instructions.
Sections were stained using antibodies against β-Gal (Promega z3781) or
HO-1 (AbCam, ab13243) at a dilution of 1:100, and counterstained with
hematoxylin.
For H&E staining, 5-µM liver sections were deparaffinized in xylene,
rehydrated in decreasing alcohol concentrations, stained with H&E,
dehydrated in increasing alcohol concentrations, and mounted using DPX mounting
media (Sigma), all according to standard procedures. The sections were
photographed under bright field conditions on a Zeiss Axiocam microscope; the
resulting images were processed with AxioVision software (Zeiss).
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7

Quantifying Worm Fluorescence Intensity

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After RNAi treatment, one-day-old adult worms were selected and images were taken using a 20X objective with the Zeiss AxioCam microscope. Fluorescence intensity was quantified using the Axio Cam software (AxioVs40 V4.8.2.0). The Student’s t-test was performed to determine statistical significance.
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8

Visualizing Macropinosomes in 2D and 3D Cultures

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Macropinosome visualization experiments were performed14 (link) for 2D culture and with some modifications for the 3D culture conditions. Briefly, cells were collected in 15 ml tubes in GSC medium. Macropinosomes were marked using a high-molecular TMR–dextran (Life Technologies) at a final concentration of 1 mg ml−1 for 1 h at 37 °C with or without EIPA/MCP pretreatment for 1 h at 0.5 µg ml−1 or 0.5%, respectively. At the end of the incubation period, cells were rinsed three times in cold PBS and immediately fixed in 2% cold formaldehyde. Cells were DAPI-treated for 10–15 min to stain nuclei and GSCs were coverslips mounted onto slides using Fluorsave (Calbiochem). Images were captured using an LSM800 Airyscan confocal microscope with 1.4 NA 63× oil-immersion lens using minimum pinhole (30 µm), or with Zeiss AxioCam microscope with 60×, 40×, and 20× objectives, leading to the calibration of 0.33 µm/pixel and 0.67 µm/pixel. Data were analyzed using the “Analyze Particles” feature in ImageJ (National Institutes of Health).
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9

Imaging Gas Vesicle-Expressing Cells

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For TEM imaging, cells expressing GVs were diluted to OD600 ~1 in 10 mM HEPES (pH 7.5) or culture media. Then, 3 µl of the sample was applied to a freshly glow-discharged (Pelco EasiGlow, 15 mA, 1 minute) formvar/carbon-coated, 200 mesh copper grid (Ted Pella) for 1 minute before being reduced to a thin film by blotting. Grids with cells were washed three times in 10 mM HEPES (pH 7.5), blotted, air-dried and imaged without stain. Image acquisition was performed using a Tecnai T12 (FEI, now Thermo Fisher Scientific) electron microscope operated at 120 kV, equipped with a Gatan Ultrascan 2,000 × 2,000 CCD camera.
For PCM imaging, cells expressing GVs were scraped off from plates and re-suspended in PBS at an OD600 of 1–2, or liquid cultures were used directly. Suspensions were transferred to glass slides, and PCM images were acquired using a Zeiss Axiocam microscope with a ×40 Ph2 objective.
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10

NP-Ptx Cellular Uptake Visualization

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SKOV3 and COV318 cells were plated at a density of 3 × 104 cells in Lab-Tek® II Chamber Slide™ (Nunc, NY, USA) and cultured for 24 h. Cells were then exposed to 1 mg/ml of NP-Ptx or NP-Ptx-b labeled with DiO in a CO2 incubator at 37°C for different time points. After 10 washes in PBS, cells were fixed with 3% PFA at room temperature for 20 min and rinsed 3x5 min in PBS before being incubated with 1% (v/v) rhodamine-phalloïdin in PBS for 20 min at room temperature. Cells were then rinsed with PBS and a slide was mounted with Vectashield® and observed with an Axiocam microscope (Zeiss, Oberkochen, Germany).
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