Bright-field images of cell culture were taken with ZEISS Axio Observer inverted microscope equipped with AxioCam MR R3 camera sensor. Images were processed by manually drawing a line around the cells and then individual cell area were measured with Fiji software distribution of ImageJ v1.51n50 (link),51 (link).
Axiocam mr r3 camera
Manufactured by Zeiss
Sourced in Germany
The AxioCam MR R3 is a high-resolution digital camera designed for microscopy applications. It features a 3.3-megapixel CMOS sensor and supports a range of resolutions up to 2080 x 1542 pixels. The camera provides reliable and reproducible image capture for a variety of microscopy techniques.
Automatically generated - may contain errors
Lab products found in correlation
Zen pro software, by Zeiss (3 mentions)
Apotome microscope, by Zeiss (3 mentions)
Plan apochromat 63 1.40 oil dic m27 objective, by Zeiss (2 mentions)
Cellomics beta catenin activation kits, by Thermo Fisher Scientific (2 mentions)
Axio vert a1 inverted microscope, by Zeiss (2 mentions)
Anti mouse alexa fluor 488, by Thermo Fisher Scientific (2 mentions)
Axio observer, by Zeiss (1 mentions)
Microwell 96 well optical bottom plate, by Thermo Fisher Scientific (1 mentions)
Evos fl cell imaging system, by Thermo Fisher Scientific (1 mentions)
4 6 diamidino 2 phenylindole (dapi), by Merck Group (1 mentions)
Xylene, by Carl Roth (1 mentions)
Plan neofluar, by Zeiss (1 mentions)
Plan apochromat, by Zeiss (1 mentions)
Mayer s hemalum solution, by Merck Group (1 mentions)
Zen 3.1 blue software, by Zeiss (1 mentions)
Eosin g 0.1, by Merck Group (1 mentions)
Axiophot microscope, by Zeiss (1 mentions)
Plan apochromat 63x 1.40 oil dic m27 objective, by Zeiss (1 mentions)
Plan apochromat 40x 0.95 objective, by Zeiss (1 mentions)
Nanozoomer, by Hamamatsu Photonics (1 mentions)
11 protocols using axiocam mr r3 camera
1
Quantifying Cell Area from Microscopy
2
Quantifying Calcium Transients in 4T1-GCaMP6s Cells
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To detect and quantify calcium transients, 2 × 104 4T1-GCaMP6s cells/well were plated in Nunc MicroWell 96-well optical bottom plates and incubated at 37 °C for 24 h. 4T1-GCaMP6s cells were infected with VSV-fluc or VSV-p15 at an MOI of 1 and cultured in 10% FBS FluoroBrite DMEM (Thermo Fisher) supplemented with 2mM L-glutamine, 10mM HEPES, 100 µg/mL streptomycin, and 100 units/mL penicillin. 4T1-GCaMP6s were illuminated with a 488 nm laser and images were captured every 0.45 s for 9 min at 20x magnification and 0.8 numerical aperture on a Zeiss Axios Observer Z.1 spinning disk confocal microscope with an AxioCam MR R3 camera. During acquisition, cells were maintained in a humified chamber at 5% CO2 and 37 °C. The Cellpose cell segmentation algorithm was used to automatically segment GCaMP6s expressing cells from an average intensity projection of the first 100 frames of the timelapse video [44 (link)]. Images were recorded using Zeiss Zen Blue software. Background fluorescence signal was subtracted using the ImageJ rolling ball algorithm [45 (link)], and F/F was calculated by dividing the mean fluorescence intensity of a cell at the time of acquisition by the cell mean intensity over the course of the time series.
3
Immunostaining of Polytene Chromosomes
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Salivary glands were dissected from 3rd instar larvae, preparation and immunostaining of polytene chromosomes was performed as described elsewhere (Eggert et al. 2004 (link)). Images were taken with Zeiss Apotome Microscope equipped with Plan-Apochromat 63×/1.40 oil DIC M27 objective, filters set (63HE for red channel, 38HE for green channel and 49 for DAPI) and AxioCam MR R3 camera. Images were processed with ZenPro software (v2.3, Zeiss) and mounted in ImageJ (v1.42h). For the list of antibodies see Table S2.
4
Quantifying Nuclear β-Catenin Levels
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NCI-H1703, SK-LU-1, and HLCSC were first treated with glycogen synthase kinase 3 inhibitor X (GSK3i) for 24 h upon growing overnight in order to artificially activate the Wnt/β-catenin pathway before the onset of chelerythrine chloride treatment. Immunofluorescence was performed by using Cellomics® Beta-Catenin Activation Kits (Thermo Scientific, Waltham, MA, USA) in accordance with the manufacturer’s protocol or by staining with mouse anti-beta catenin 1 (cat# 610154, BD Biosciences, Franklin Lakes, NJ, USA) and counter-stained with anti-mouse-Alexa Fluor 488 (A-11001, Thermo Fisher Scientific) and DAPI (1:1000 of 2 mg/mL, Sigma-Aldrich). Five random, non-overlapping frames were captured from each well by using Axio Vert.A1 inverted microscope equipped with HXP-120V light source and Axiocam MR R3 camera (Carl Zeiss, Oberkochen, Germany) or EVOS FL cell imaging system (Thermo Fisher Scientific). Cells harboring nuclear β-catenin were manually counted by using Image’s J cell counter plugin and the positive counts were divided by the respective total number of cells in the captured frames to obtain the percentage of cells with positive nuclear β-catenin [58 (link)]. Treated samples were compared with untreated Wnt-activated negative control.
5
Quantifying Nuclear β-Catenin Translocation
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Immunofluorescence assay was performed as described previously [23 (link)]. SK-LU-1 and HLCSC were first treated with GSK3i for 24 h upon growing overnight in order to optimally increase β-catenin localization before the onset of phytochemicals treatments. Immunofluorescence was performed by using Cellomics® Beta-Catenin Activation Kits (Thermo Scientific, Waltham, MA, USA) in accordance with the manufacturer’s protocol. Five random, non-overlapping frames were captured from each well by using Axio Vert.A1 inverted microscope equipped with HXP-120V light source and Axiocam MR R3 camera (Carl Zeiss, Oberkochen, Germany). Cells harboring nuclear β-catenin were manually counted by using ImageJ’s cell counter plugin and the positive counts were divided by the respective total number of cells in the captured frames to obtain percentage of cells with positive nuclear β-catenin [32 (link)]. Treated samples were compared with untreated Wnt-activated negative control.
6
Visualizing Bacterial Infections in Bone
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Formalin-fixed paraffin embedded (FFPE) bone slices of the right pelvis of the infected mouse and of the non-infected control mouse were de-paraffinised using xylene (Carl Roth) and hydrated in a series of graded alcohols. Briefly, slides were placed 2× in xylene, 1× in xylene:ethanol (1:1), 2× in 100% ethanol, and subsequently in 95% ethanol, 70% ethanol, and 50% ethanol followed by rinsing with tap water. The slides were left in each solution for 3 min before proceeding to the fresh next solution. Subsequently, bone slices were either stained with hematoxylin and eosin (Mayer’s hemalum solution and Eosin G 0.1%, both Merck, Darmstadt, Germany) to reveal the tissue structure, or Gram staining was performed according to the manufacture’s protocol (Carl Roth, Karlsruhe, Germany) to visualise bacteria.
Bright field images were acquired using an Axio Observer.Z1 (Carl Zeiss, Jena, Germany) equipped with an AxioCam MR R3 camera (Carl Zeiss) and a Plan Apochromat 40×/0.95 objective or a Plan-Neofluar 63×/1.3 oil immersion objective. The whole slices were scanned in tile-scan mode and stitched using the Zen 3.1 blue software (Carl Zeiss).
Bright field images were acquired using an Axio Observer.Z1 (Carl Zeiss, Jena, Germany) equipped with an AxioCam MR R3 camera (Carl Zeiss) and a Plan Apochromat 40×/0.95 objective or a Plan-Neofluar 63×/1.3 oil immersion objective. The whole slices were scanned in tile-scan mode and stitched using the Zen 3.1 blue software (Carl Zeiss).
7
Immunostaining of Polytene Chromosomes
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Immunostaining of polytene chromosomes was done essentially as described previously (67 (link), 71 (link)). The antibodies used in the protocol are listed in table S1. Preparations were analyzed using a Zeiss Axiophot microscope (Plan Apochromat 40×/0.95 objective) equipped with a KAPPA DX20C CCD camera and with a Zeiss Apotome Microscope [Plan Apochromat 63×/1.40 oil DIC M27 objective; filter set: 63HE for red channel, 38HE for green channel, and 49 for 4′,6-diamidino-2-phenylindole (DAPI)] equipped with AxioCam MR R3 camera. For comparisons of targeting between different genotypes, the protocol was run in parallel, and nuclei with clear cytology were chosen on the basis of DAPI staining and photographed. At least 20 nuclei per slide were used in these comparisons and at least five slides per genotype. Images were processed with ZenPro software (v2.3, Zeiss).
8
Immunolabeling Barley Root Cell Walls
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Fresh root tips (5 mm) were collected from barley seedlings (5 dpg) and fixed in TEM fixative in PBS (0.25% glutaraldehyde, 4% paraformaldehyde, 4% sucrose) overnight with at least 1 h of vacuum infiltration. The fixed root tips were rinsed in PBS twice for 8 h. Root tips were then embedded in 4% agarose gel to the desired angle and orientation, and the agarose gels were shaped to cuboid. The following dehydration and LR White Resin embedding steps were carried out according to Burton et al. (2011 (link)). Longitudinal sections at 1‐μm intervals were sectioned using a Leica Microtome EM UC6 with either a glass or a diamond knife. The sections were mounted onto glass slides and dried on a hot plate at 60°C for at least 1 h. The antibodies specific to (1,3;1,4)‐β‐glucan, callose, AGP, mannan, arabinoxylan and pectin were used for immunolabelling. The immunolabelling was performed as described by Burton et al. (2011 (link)). Images were taken and processed by an Axio Imager M2 microscope using an AxioCam MR R3 camera and Zeiss zen imaging software.
9
Immunostaining of Polytene Chromosomes
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Immunostaining of polytene chromosomes was done essentially as described previously (Johansson et al. 2012; (link)Lundberg et al. 2013a ). The antibodies used in the protocol are listed in Supplementary Table S1. Preparations were analysed using a Zeiss Axiophot microscope (Plan Apochromat 40x/0.95 objective) equipped with a KAPPA DX20C CCD camera and with Zeiss Apotome Microscope (Plan Apochromat 63x/1.40 oil DIC M27 objective, filters set: 63HE for red channel, 38HE for green channel and 49 for DAPI) equipped with AxioCam MR R3 camera. For comparisons of targeting between different genotypes, the protocol was run in parallel and nuclei with clear cytology were chosen on the basis of DAPI staining and photographed. At least 20 nuclei per slide were used in these comparisons and at least five slides per genotype. Images were processed with ZenPro software (v2.3, Zeiss).
10
Quantifying Lung Tissue Fibrosis
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Mouse lung tissue was fixed in formalin and embedded in paraffin. Tissue blocks were sectioned (4−6 μm) and mounted on glass slides for haematoxylin and eosin (H&E; Surgipath and Sigma) and PicroSirius Red staining (VWR and Raymond Lab) or Goldner trichrome, for general morphological analysis and collagen deposition, respectively (Thoua et al., 2012 (link)). Sections were imaged using the NanoZoomer (Hamamatsu), and analysed using 10X magnification in the NDP View software, or imaged using a Zeiss Axio Observer apotome microscope and Axio Cam MR R3 camera and viewed in ZEN Blue microscopy software. The modified Ashcroft score was used to quantify the extent of fibrosis, as described previously (Hubner et al., 2008 (link)). Multiple fields were scored following a raster-like pattern until the entire section was covered. The sum of the grades was divided by the number of fields to obtain a fibrotic index. In every field, the predominant degree of fibrosis was recorded as that occupying more than half of the field area while areas dominated by bronchial or tracheal tissue were omitted.
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