Axiolmager

Manufactured by Zeiss

The Axiolmager is a high-performance microscopy system from Zeiss. It is designed for advanced imaging and analysis applications in materials science, life science, and other research fields. The Axiolmager offers a range of advanced imaging capabilities, including high-resolution imaging, multi-modal imaging, and automated image acquisition and analysis.

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Lab products found in correlation

Vector novared substrate kit, by Vector Laboratories (2 mentions) Clearmount, by StatLab (2 mentions) Antigen unmasking solution, by Vector Laboratories (2 mentions) Vectastain elite abc kit, by Vector Laboratories (2 mentions) Jmp pro, by SAS Institute (2 mentions) Em ccd, by Hamamatsu Photonics (1 mentions) Imagej 1.46r, by Adobe (1 mentions) Csu10, by Yokogawa (1 mentions) Rabbit anti rfp, by Rockland Immunochemicals (1 mentions) Plan apochromat 100x, by Zeiss (1 mentions) Vectashield containing dapi, by Vector Laboratories (1 mentions) Metamorph software, by Universal Imaging (1 mentions)

8 protocols using axiolmager

Confocal Microscopy Imaging and Analysis

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Confocal images were acquired using a camera (EM-CCD; Hamamatsu Photonics) and a spinning disk confocal microscope (CSU-10; Yokogawa) mounted on a microscope (Axiolmager; Carl Zeiss) with a Plan-APOCHROMAT 100×/1.4 oil differential interference contrast objective and controlled by by iVision software (Biovision Technologies) or microManager (Edelstein et al., 2010 ). All images within each experiment were acquired using identical settings. Acquired images were processed using ImageJ 1.46r and Photoshop (CS6 Extended; Adobe). 3D reconstructions were built from confocal z-stacks, analyzed, and exported as .mov files using IMARIS 9.0.2 (Bitplane, Inc.). Figures were constructed using Illustrator (CS6 Extended; Adobe), and graphs were exported from JMP Pro (SAS). Movies were annotated using Photoshop, compressed with Handbrake and combined to run alongside other movies using Pic Stitch. Quantitative analyses of AC-invadopodia, invasive protrusion, or BM breach formation was done using either ImageJ, Imaris, or both. For time-lapse microscopy, worms were anesthetized in 0.2% tricaine and 0.02% levamosile in M9 and then transferred to 5% noble agar pads, sealed with VALAP, and imaged at 23°C. See Kelley et. al. for detailed worm staging, microscopy and data handling protocols and video tutorials.

Kelley L.C., Chi Q., Cáceres R., Hastie E., Schindler A.J., Jiang Y., Matus D.Q., Plastino J, & Sherwood D.R. (2019). Adaptive F-actin polymerization and localized ATP production drive basement membrane invasion in the absence of MMPs. Developmental cell, 48(3), 313-328.e8.

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Intersectional Genetic Labeling of Lamp5+ Lhx6+ Cells

Cited 2 times

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To label Lamp5⁺Lhx6⁺ cells in the mouse neocortex and hippocampus, we used an intersectional genetics approach. In mouse mature cortical interneurons, Id2 and Lamp5 are expressed in nearly identical populations^{35 (link)} (and both are expressed in the cortical Lamp5⁺Lhx6⁺ type), and so we used an Id2^creER driver line^{53 (link)} (Jax stock no. 016222) in combination with an Nkx2.1^Flpo driver^{54 (link)} (Jax stock no. 028577) and the Cre/Flp-dependent tdTomato reporter Ai65^{55 (link)} (Jax stock no. 021875) to obtain selective labelling of Lamp5⁺Lhx6⁺ cells. Tamoxifen (20 mg/ml in corn oil) was administered to Id2^creER Nkx2.1^FlpoAi65 animals (3 × 5 mg by oral gavage over 5 days) between postnatal days 30 and 40 to activate CreER, after which animals were either perfused with 4% PFA in PBS and their brains processed for immunohistochemistry (20-μm cryosections; tdTomato signal was enhanced using rabbit anti-RFP from Rockland Immunochemicals; 600-401-379; 1:1,000 dilution), or acute brain slices were prepared for morphological fills as described previously^{56 (link)}. Fluorescence images were acquired on a Zeiss Axio lmager.A1 and levels and contrast adjustments were performed using Photoshop (Adobe).

Krienen F.M., Goldman M., Zhang Q., del Rosario R.C., Florio M., Machold R., Saunders A., Levandowski K., Zaniewski H., Schuman B., Wu C., Lutservitz A., Mullally C.D., Reed N., Bien E., Bortolin L., Fernandez-Otero M., Lin J.D., Wysoker A., Nemesh J., Kulp D., Burns M., Tkachev V., Smith R., Walsh C.A., Dimidschstein J., Rudy B., Kean L.S., Berretta S., Fishell G., Feng G, & McCarroll S.A. (2020). Innovations present in the primate interneuron repertoire. Nature, 586(7828), 262-269.

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Tissue Imaging with Brightfield Microscopy

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For imaging, first an overview 20x image was taken, followed by each individual tissue section imaged with 10 z-stack planes, 2 µm apart at 20x. Hematoxylin & Eosin brightfield images were acquired with a Zeiss Axiolmager.Z2 VSlide Microscope using the Metasystems VSlide scanning system with Metafer 5 v3.14.179 and VSlide software. The microscope had an upright architecture, and used a widefield system; a 20x air objective with the numerical aperture (NA) 0.80 was used. The camera was a CoolCube 4 m with a Scientific CMOS (complementary metal-oxide-semiconductor) architecture and monochrome with a 3.45 ×3.45 µm pixel size. All brightfield images were taken with a Camera Gain of 1.0 and an Integration Time/Exposure time of 0.00004-0.00008 seconds.

Sounart H., Voronin D., Masarapu Y., Chung M., Saarenpää S., Ghedin E, & Giacomello S. (2023). Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale. Nature Communications, 14, 6500.

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Brightfield Imaging of H&E Stained Samples

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Hematoxylin & Eosin brightfield images were acquired with a Zeiss Axiolmager.Z2 VSlide Microscope using the Metasystems VSlide scanning system with Metafer 5 v3.14.179 and VSlide software. The microscope has an upright architecture, uses a widefield system, and a 20X air objective with a numerical aperture (NA) of 0.80 was used. The camera was a CoolCube 4 m with a Scientific CMOS (complementary metal–oxide–semiconductor) architecture and monochrome with a 3.45 × 3.45 µm pixel size. All brightfield images were taken with a Camera Gain of 1.0 and an Integration Time/Exposure time of 0.00011 s.

Sounart H., Lázár E., Masarapu Y., Wu J., Várkonyi T., Glasz T., Kiss A., Borgström E., Hill A., Rezene S., Gupta S., Jurek A., Niesnerová A., Druid H., Bergmann O, & Giacomello S. (2023). Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections. Genome Biology, 24, 237.

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Immunohistochemical Staining Protocol

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For immunohistochemical staining, the procedures followed the instructions of the Vectastain Elite ABC Kit (PK-6101) and Vector NovaRED Substrate Kit (SK-4800). Briefly, 5 μm paraffin sections were deparaffinized and hydrated through xylenes and graded alcohol series, followed by antigen retrieval through boiling in antigen unmasking solution (Vector Labs). Slides were blocked in blocking serum (1.5% normal serum), and incubated with primary antibodies diluted in blocking serum overnight at 4°C. Biotinylated secondary anti-rabbit antibody from Vectastain Elite ABC Kit was diluted 1:200 in blocking serum. The signal was enhanced using the Vectastain Elite ABC system and visualized with the NovaRed Substrate Kit. The slides were counterstained with Harris Modified Hematoxylin (1:10 diluted in H₂O) and mounted with Clearmount (American MasterTech). Primary antibodies and dilutions used are listed in the key resources table. H&E staining was performed using standard protocols as previously described. Histology slides were visualized using a Zeiss Axiolmager.

Liu Y., Wang J., Horton C., Yu C., Knudsen B., Stefanson J., Hu K., Stefanson O., Green J., Guo C., Xie Q, & Wang Z.A. (2022). Stromal AR inhibits prostate tumor progression by restraining secretory luminal epithelial cells. Cell reports, 39(8), 110848.

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Fixation and Immunostaining of Yeast Cells

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Cells samples were fixed overnight in 1 ml KPF (0.1 M KH₂PO₄ pH6.4, 3.7% formaldehyde), then washed and digested for 1 h in SBC buffer (1.2 M sorbitol, 0.1 M KH₂PO₄, pH 5.9, 0.7% citric acid) containing 20 μl Glusulase (Perkin Elmer, NEE154001EA) and 5 μl 10 mg/ml lyticase. Digested cells were placed on poly-l-lysine coated glass slides, immune-stained with rat monoclonal anti-tubulin YOL1/34 (Serotec) and mounted in Vectashield containing DAPI (Vector Laboratories) for visualization of mitotic spindles and the nuclei, respectively. For in vivo imaging of Ddc2-Citrine tagged cells and cells containing N-terminal half-Venus-Pds1 and Esp1-Venus-C-terminal half, cells were washed once with PBS and resuspended in 5 μl of Vectashield before imaging. Images were captured with Plan Apochromat 100X objective of the Zeiss Axiolmager motorized microscope equipped with EXFO 120 W metal halide illuminator and a Photometrics CoolSNAP HQ2 high sensitivity monochrome camera. The microscope is driven by the Metamorph software (Universal imaging Corporation).

Yam C.Q., Chia D.B., Shi I., Lim H.H, & Surana U. (2020). Dun1, a Chk2-related kinase, is the central regulator of securin-separase dynamics during DNA damage signaling. Nucleic Acids Research, 48(11), 6092-6107.

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Multimodal Imaging of Cellular Processes

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Fixed samples were imaged on an Andor Dragonfly inverted confocal spinning disc microscope operated using Fusion and Imaris software. Images were acquired using 60x, 1.4 NA Plan Apo objective. Fixed samples were imaged on Upright Zeiss Axiolmager widefield microscope operated using Zeiss ZEN blue 3 software. Images were acquired using 40x, 0.95 NA Plan Apo objective or 63x, 1.40 NA Plan Apo objective.
Time-lapse imaging after calyculinA treatment and for PUMA-induced apoptotic extrusion was performed on Nikon Ti-E deconvolution microscope operated using NIS elements software was used. Images were acquired using 20X, 0.75 NA Plan Apo objective. Time-lapse imaging for laser-induced apoptotic extrusion was performed on Zeiss LSM 710 Meta confocal microscope equipped with Mai Tai multi-photon laser operated using Zen Black software. Images were acquired using 43X, 1.3 NA Plan Apo objective.
Subcellular distribution of E-cadherin and Desmoglein 2 was visualised on Leica SP8 STED 3X FLIM super resolution microscope operated using Leica LASX software. Images were acquired using HC Plan Apochromat 93×1.30 glycerol objective.

Nanavati B.N., Noordstra I., Verma S., Duszyc K., Green K.J, & Yap A.S. (2023). Desmosome-anchored intermediate filaments facilitate tension-sensitive RhoA signaling for epithelial homeostasis. bioRxiv.

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Immunohistochemical Staining Protocol

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