Non-human primate and murine kidney samples were fixed in 3.7% formaldehyde in PBS (Fishar), dehydrated, and embedded in paraffin. 4 μm sections were cut, rehydrated, and stained using a monoclonal anti-TNK1 antibody (LSBio) at a dilution of 1:100. For detection, the Dako real detection Alkaline phosphatase Kit (Dako) was employed. Slides were visualized using a Zeiss Axio Imager A1 microscope with five randomly chosen field of views per animal and region in 200-fold magnification and intensity of expression was quantified using ZEN pro software (Zeiss). For the non-human primate samples, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was performed in order to quantify DNA strand breaks. After sectioning and rehydration, tissues were digested in proteinase K (Roche, Basel, Switzerland) for 15 min at 37°C. Subsequently, samples were stained using the in situ Cell Death Detection Kit, TMR red (Roche) according to the manufacturer’s instructions and counterstained with DAPI. After staining, positive events per field of view in 100-fold magnification were counted in five randomly selected regions per animal using the Zeiss Axio Imager A1 microscope.
Axio imager a1 microscope
Manufactured by Zeiss
Sourced in Germany, United States, France, Canada, United Kingdom
The Axio Imager A1 is a transmission light microscope designed for routine brightfield and phase contrast microscopy. It features a stable and ergonomic stand, a compact and efficient transmitted light illumination system, and a highly corrected optics system for high-quality imaging.
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Lab products found in correlation
Axiovision software, by Zeiss (17 mentions)
Axiocam hrc camera, by Zeiss (14 mentions)
Axiovision 4, by Zeiss (11 mentions)
Axiocam mrc5, by Zeiss (9 mentions)
Hoechst 33342, by Thermo Fisher Scientific (8 mentions)
Axiocam mrm camera, by Zeiss (7 mentions)
Alexa fluor 488, by Thermo Fisher Scientific (7 mentions)
Axiocam high resolution camera, by Zeiss (6 mentions)
Axiocam mrc camera, by Zeiss (5 mentions)
Envision system hrp, by Agilent Technologies (5 mentions)
Vector vip substrate, by Vector Laboratories (5 mentions)
Axiocam, by Zeiss (5 mentions)
Paraformaldehyde (pfa), by Polysciences (4 mentions)
Axiocam mrc5 camera, by Zeiss (4 mentions)
Axiocam mrc digital camera, by Zeiss (4 mentions)
Csu10, by Yokogawa (4 mentions)
Axiocam mrm, by Zeiss (4 mentions)
Axiocam mrc, by Zeiss (4 mentions)
Axiovert 200m, by Zeiss (4 mentions)
Lsm 710, by Zeiss (4 mentions)
269 protocols using axio imager a1 microscope
1
Quantification of Kidney Injury Markers
2
Epifluorescence and Bright-field Imaging Protocols
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Epifluorescence microscopy was performed with a BIOREVO BZ-9000 (Keyence) and an Axioimager A1 microscope (Carl Zeiss). Bright-field images were taken with an MZ16F fluorescence stereomicroscope (Leica), a BIOREVO BZ-9000 (Keyence) and an Axioimager A1 microscope (Carl Zeiss).
3
Confocal and Widefield Microscopy of C. elegans
4
Macrophage Immunophenotyping via Flow Cytometry
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The PMA-treated THP-1 cells or PBMCs (1 × 105) were rinsed with PBS, fixed in 4% paraformaldehyde, and spun onto glass slides using a Shandon Cytospin 4 Cytocentrifuge (Thermo Scientific, Pittsburgh, PA, USA). The macrophages were first identified using Liu staining and examined using an Axio Imager A1 Microscope (Carl Zeiss Micro Imaging Inc., Thornwood, NY, USA). The slides were stained using either PE-conjugated mouse anti-human CD14 (25–0149, eBioscience, San Diego, CA, USA) or FITC-conjugated mouse anti- human CD68 (11–0689, eBioscience), and nuclei were identified using Hoechst 33258 (Sigma, St. Louis, MO, USA). Images were obtained using an Axio Imager A1 Microscope (Carl Zeiss Micro Imaging Inc., Thornwood, NY, USA).
5
Visualizing Fungal Septation and Nuclear Localization
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To visualize septa of the indicated strains, conidia were inoculated onto sterile glass coverslips at related temperatures prior to observation. At the detection time point, media on the coverslips were removed and germlings were washed three times with PBS. Cultured cells were then fixed with 4% paraformaldehyde (Polysciences, Warrington, PA, USA) and washed three times with PBS. CFW (Sigma-Aldrich, St. Louis, MO, USA) was used to stain hyphal septa in the dark for 5 min. CFW solution was then removed and the glass coverslip was washed three times with PBS. Images were captured with a Zeiss Axio imager A1 microscope (Zeiss, Jena, Germany) and managed with Adobe Photoshop (Adobe, San Jose, CA, USA).
For visualization of the localization of GFP-PomA and RFP-H2A, a similar strategy procedure was used as described in references.
For visualization of the localization of GFP-PomA and RFP-H2A, a similar strategy procedure was used as described in references.
6
Microscopic Observation of Protein Co-localization
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For microscopic observations, conidia were inoculated onto pre-cleaned glass coverslips overlaid with liquid media. To observe co-localization of GFP-AkrA and mRFP-PHOSBP, strain ZYA13 (S1 Table ) was cultured at 37°C for 10 h in non-inducing medium (non-inducing conditions for the alcA(p) driving expression of AkrA) and shifted for 6 h to the inducing medium (in which the alcA promoter was induced) before microscopic observation [34 (link)]. Differential interference contrast (DIC) and fluorescence images of the cells were captured with a Zeiss Axio imager A1 microscope (Zeiss, Jena, Germany) equipped with a Sensicam QE cooled digital camera system (Cooke Corporation, Germany). The images were processed with MetaMorph/MetaFluor software (Universal Imaging, West Chester, PA) and assembled in Adobe Photoshop (Adobe, San Jose, CA).
7
Histological Evaluation of HCC Tumor Necrosis and Immune Infiltration
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Tumor specimens were diagnosed as HCC based on the established classification of neoplastic liver lesions. After standard processing and embedding in paraffin, 4 μm sections were prepared, deparaffinized, stained with hematoxylin-eosin (H&E), studied with a Zeiss Axio Imager A1 microscope (Carl Zeiss, Oberkochen, Germany) by a pathologist blinded to the treatment arm. Morphometric study of areas of necrosis was compared to the size of the tumor sections by counting view fields at medium objective magnification. IHC staining with mouse anti-rat CD3 (BD Biosciences, San Jose, CA, USA) was performed on 5 µM paraffin sections of posttreatment tumor tissues obtained after tumor reached over 2 cm. Images of at least 7 randomly selected fields (unit area of each field, 0.34 mm2) were captured by observers blinded to sample identity. Identical exposure times and image settings were used within each experiment. Images were analyzed with ImageJ software (http://rsb.info.nih.gov/ij , Bethesda, MD, USA).
8
MPIO Labeling Visualization Protocol
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To visualize MPIO labeling, labeled cells were affixed to a glass slide with a ThermoFisher Cytospin 4 cytocentrifuge and fixed with a Methanol/Acetic acid solution. Slides were then stained with a Perl’s Prussian Blue (PPB) solution and counterstained with Nuclear Fast Red. Slides were dehydrated with increasing concentrations of ethanol, cleared with xylene, and coverslipped with a xylene-based mounting medium. These PPB-stained slides were examined to assess the localization of MPIO within the cell to determine the labeling efficiency using a Zeiss AXIO Imager A1 Microscope (Zeiss Canada, Toronto, ON, Canada). Iron oxide particles appear dark blue, and cells appear light pink in color.
9
Fungi Morphology and Spectroscopic Analysis
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Morphology graph of the fungi was collected with Zeiss Axio Imager A1 microscope (Zeiss, Jena, Germany). IR spectra were obtained from a Nexus 670 spectrometer with scanning range of 4000–400 cm-1 (Nexus, Nicolet, USA). The NMR spectra were recorded on a Bruker AV-400 spectrometer (400MHz for 1H and 13C; Bruker, Faellanden, Switzerland) in DMSO-d6. HPLC was carried out on Agilent LC 1100 with an VWD detector (Agilent Technologies, Santa Clara, CA, USA). Semi-preparation HPLC was performed on Agilent 1200 with an VWD detector (Agilent Technologies, Santa Clara, CA, USA). LC-MS was conducted on an Agilent 6460 HPLC, coupled to negative electrospray ionization (ESI) tandem mass spectrometry (MS/MS) method. Mass spectra in the negative ion mode was operated under the following conditions: fragmenter voltage of 5 eV, voltage of 3500 V, nebulizer pressure of 45 psi, capillary temperature of 300°C, m/z range from 50 to 1000.
10
Chromosome Aberration Assay Protocol
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Lymphocytes for the chromosome aberration test were obtained by culturing aliquots of heparinised whole blood with the Gibco® PB-MaxTM karyotyping medium (Catalogue No. 12557-021, ThermoFisher Scientific, Life Technologies Corporation, Grand Island, NY, USA) at 37 °C for 48 h. In the last three hours, the cultures were added colchicine (Sigma-Aldrich Co., St. Louis, MO, USA) in the final concentration of 2.5 μg/mL according to the standard procedure described elsewhere (12 ).
Slides were analysed under a Zeiss Axio Imager A1 microscope (Carl Zeiss, Jena, Germany) with the ISIS imaging software package (MetaSystems Hard & Software GmbH, Altlussheim, Germany). At least 200 metaphase spreads were analysed at 10–100× magnification for chromosome aberrations (chromosome and chromatid breaks, dicentric and ring chromosomes, acentric fragments, stable aberrations, and radial figures) (13 ).
Slides were analysed under a Zeiss Axio Imager A1 microscope (Carl Zeiss, Jena, Germany) with the ISIS imaging software package (MetaSystems Hard & Software GmbH, Altlussheim, Germany). At least 200 metaphase spreads were analysed at 10–100× magnification for chromosome aberrations (chromosome and chromatid breaks, dicentric and ring chromosomes, acentric fragments, stable aberrations, and radial figures) (13 ).
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