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Axio imager d1

Manufactured by Zeiss
Sourced in Germany, United States

The Axio Imager D1 is a microscope system designed for routine applications in biological and material science research. It features a high-performance optical system, including LED illumination and a range of objectives, to provide clear, high-quality images. The Axio Imager D1 is a versatile and reliable instrument suitable for a variety of microscopy techniques.

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30 protocols using axio imager d1

1

Mapping Glucose-sensing Neurons in Mouse Brain

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For the chromogenic in situ hybridization, brain sections containing the PVT of 14-week-old males were prepared using a mouse brain matrix with 1 mm section dividers (CellPoint Scientific, Gaithersburg, MD, USA), fixed for 28 hours in 10% formalin and embedded in paraffin. Five μm sections were cut with a microtome and single in situ hybridization (ISH) for Gck (cat. number: 400971) or double in situ hybridization for Slc17a6 (Vglut2) and Gad67 (cat. number: 319171-C1 and 400951-C1) was performed using RNAscope® probes and RNAscope® 2-plex detection kit (ACDBio, Newark, CA, USA). Sections were counterstained with Mayer’s hematoxylin and mounted using aquatex mounting medium (cat. number: 363123S, VWR, Radnor, PA, USA) and observed using an Axio Imager D1 (Zeiss, Oberkochen, Germany).
For fluorescent in situ hybridization, 14-week-old males were transcardially perfused with 4% PFA and 20 μm cryosections were prepared. Gck mRNAs were detected using RNAscope probes (Cat# 400971-C1) and RNAscope® Fluorescent Multiplex Detection Reagents following manufacturer’s instructions. Sections were mounted using DAPI-fluoromount (SouthernBiotech®, Birmingham, AL, USA) solution. Images were acquired on a ZEISS Axio Imager.M2 microscope, equipped with ApoTome.2 and a Camera Axiocam 702 mono using the AxioVision software (Zeiss, Oberkochen, Germany).
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2

Live-cell Imaging with Formaldehyde Fixation

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Live imaging was conducted using a heated on‐stage chamber, gassed with warmed, humidified air containing 5% CO2, on an inverted microscope. For imaging of fixed cells, culture plates were washed briefly with warm foetal calf serum‐free media, then fixed in 4% formaldehyde at room temperature for a minimum of 30 min prior to imaging. Images were captured using a Zeiss AxioImager D1 (inverted) fluorescence microscope equipped with an AxioCam MRm camera and a GFP filter (excitation 470/40; emission 525/50). The 10 × objective allowed the maximum number of patterns to be captured in each image, while still giving sufficient resolution for counting protrusions.
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3

Immunofluorescence Assay for Cell Viability

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Immunostaining was performed on PFA fixed cells with the indicated antibodies and the DNA-binding dye 4′,6-diamidino-2-phenylindole (DAPI) to quantify total cell number and cell viability. Detailed protocol and a list of antibodies used in this study is provided in Supplemental Experimental Procedures. Images were captured using a Zeiss Axio Imager D1 (Thornwood, NY, USA) epifluorescence microscope and analyzed using ImageJ software.
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4

Immunohistochemical Staining of Ly6G and H3cit

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Sections were allowed to come to room temperature, before rinsing in PBS with 0.1% Tween 20 (PBST). Sections were blocked for 1 hour at room temperature with 10% FBS in PBST in a humidified chamber. Sections were incubated in the same chamber overnight at 4oC with the primary antibodies described above against Ly6G and H3cit or rat anti-CD41 [MWReg30 clone (recognizes integrin α2b), Biolegend catalog number 133901] in 10% FBS in PBST. Slides were rinsed in PBST before incubating with the secondary antibody under the same conditions as used for the primary antibody [goat anti-rat Ig (IgG) (Alexa555, 1.5 μg/mL) or donkey anti-rabbit IgG (Alexa647, 1.5 μg/mL)]. After a further wash in PBST, sections were stained with DAPI and mounted as described above. Sections were visualized using AxioImager D1 (Carl Zeiss Microscopy) and images taken using Axiocam MRc Camera (Carl Zeiss Microscopy). Zen software 2.3 (version 13) was used to analyze images. For the final images used in the figures, Alexa647 was represented using green.
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5

Immunofluorescence Staining of LKB1 Protein

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Cells seeded on 12 mm coverslips were fixed in PBS 4% paraformaldehyde (Santa Cruz Biotechnology, USA). Coverslips were then blocked and permeabilized with PBS containing 0.1% BSA, 10% goat serum and 0·2% Triton X-100 for 30 min at RT. After blocking, the coverslips were washed in PBS and incubated overnight in a humid chamber with the primary antibody (FLAG 1:100) in PBS. Coverslips were washed in PBS and incubated during 1 h at RT in blocking solution with DAPI but no Triton X-100 with secondary antibody (dilution 1:200, Cy3 conjugated anti-mouse or FITC-conjugated anti-rabbit, Jackson ImmunoResearch laboratories, USA). Coverslips were mounted in Dako fluorescence mounting medium (Dako, Denmark). Five Images from each experimental condition were taken using an Axioimager D1 (Zeiss). Blind quantification of LKB1 positive nuclear cells versus total number of stained cells was performed manually by an immunohistochemistry technician.
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6

Cell Morphology and Identification

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Cell morphology was examined using an Axio Imager D1 light microscope (Zeiss, Oberkochen, Germany) equipped with a phase-contrast unit. Electron micrographs were obtained by using a JEOL model JEM-100C transmission electron microscope and negative staining with 2% (w/v) sodium phosphotungstate. Gram reaction was determined using the Gram-staining kit (Deltalab, Barcelona, Spain).
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7

Quantifying Cell Viability in Collagen Gels

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Cell viability in cell-seeded dense collagen gels was assessed using a Live/Dead® assay (Thermofisher, Waltham, MA, USA) on day 24 post-culture. After rinsing twice with PBS, samples were stained with a 2 µM calcein-AM and 4 µM ethidium homodimer-1 solution and incubated at 37 °C for 30 min. Then, the gels were rinsed three times with PBS to stop the reaction before imaging. Live cells were viewed by green fluorescence and dead cells by red fluorescence using a fluorescent microscope (Axio Imager D.1, Zeiss, Jena, Germany) or a Leica SP5 upright confocal microscope (Leica DMI6000 Upright TCS SP5) under 10× and 20× magnification, respectively. Three image fields were taken for each scaffold and processed with Image J (version 1.53f51).
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8

Histological Analysis of Liver Morphology

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The liver samples were fixed in 4% paraformaldehyde and embedded in paraffin. Serial slices (3–4 μ m thickness) of the liver of the control and experimental rats were mounted on poly-L-lysine coated glass slides and routinely stained with hematoxylin and eosin (H&E Staining Kit (HE; ab245880; Abcam, Cambridge, MA, USA). All histochemical reactions were carried out according to the manufacturer’s protocols. Next, the slides underwent general histological examination to investigate potential acute or chronic changes within the liver. The samples were independently examined by experienced histologists and pathomorphologists in blinded manner to avoid potential bias. Images from slides stained with HE were acquired with the usage of the microscope Axio Imager D1 (Carl Zeiss) and the AxioCam MRc5 camera with the 2572×1928 pixels resolution for HE under objective 40×.
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9

Histological Analysis of mdx Mouse Muscle

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Serial sections (5 μm) were cut transversely through the right TA muscle of mdx mice from GLY and ALA groups using a refrigerated (−20 °C) cryostat (CTI Cryostat; IEC, Needham Heights, MA). Sections were stained with hematoxylin and eosin (H&E) for visualization of general muscle architecture26 (link). Muscle collagen content was assessed from Van Gieson-stained cross-sections as described previously26 (link). Digital images of stained sections were captured using an upright microscope with camera (Axio Imager D1, Carl Zeiss, Wrek Göttingen, Germany), controlled by AxioVision AC software (AxioVision AC Rel. 4.8.2, Carl Zeiss Imaging Solutions, Wrek, Wrek Göttingen, Germany). Images were quantified using AxioVision 4.8.2 software as described previously.
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10

Quantification of Pathogen-Induced Innate Immune Response

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Twenty-five microliters of overnight PA14 cultures was spread onto NGM agar plates56 (link) and incubated at 24 h at 37 °C, followed by 24 h at 25 °C. Thirty to 35 young adult worms containing the irg-1::gfp transgene (strain AU133) were picked onto the PA14-seeded plates and incubated at 25 °C. For visualization of irg-1::gfp activation, worms were exposed to PA14 for 12 h, immobilized in 10 mM levamisole in water, mounted on a 2% agarose pad on a glass slide, and imaged at 20x on a Zeiss Axio Imager D1 epifluorescence microscope with an AxioCam MRm. GFP fluorescence intensity was quantified using ImageJ/Fiji51 (link). Using the polygon tool, an ROI is drawn around the worm body for each image and the sum gray value (integrated density) was measured and plotted.
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