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Nanozoomer 2.0 rs slide scanner

Manufactured by Hamamatsu Photonics
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Sourced in Japan

The NanoZoomer 2.0-RS is a high-performance digital slide scanner developed by Hamamatsu Photonics. It is designed for scanning and digitizing biological and pathological tissue samples mounted on glass microscope slides. The NanoZoomer 2.0-RS captures high-resolution images at up to 40x magnification, enabling detailed examination and analysis of the sample.

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Lab products found in correlation

Histostain sp kit, by Thermo Fisher Scientific (1 mentions) Dab peroxidase kit, by Vector Laboratories (1 mentions) Hematoxylin h, by Vector Laboratories (1 mentions) Vectastain elite abc hrp kit, by Vector Laboratories (1 mentions) Cleaved caspase 3, by Cell Signaling Technology (1 mentions) Dm6000b microscope, by Leica (1 mentions) Mouse anti muc5ac, by Thermo Fisher Scientific (1 mentions) Goat anti amylase, by Santa Cruz Biotechnology (1 mentions) Vectastain elite abc kit, by Vector Laboratories (1 mentions) Mouse anti ki67, by BD (1 mentions) Cryotome, by Leica (1 mentions) Dab substrate kit, by Abcam (1 mentions) Rabbit polyclonal antibody against col 2, by Abcam (1 mentions) Alexa fluor 488, by Thermo Fisher Scientific (1 mentions) Rat anti mouse f4 80 monoclonal antibody, by Bio-Rad (1 mentions) Oct compound, by Sakura Finetek (1 mentions) Bz x800, by Keyence (1 mentions) Ndp view2, by Hamamatsu Photonics (1 mentions) Histochoice clearing agent, by Merck Group (1 mentions) Nbp2 50 037, by Novus Biologicals (1 mentions)

Close spelling variants of this product

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18 protocols using nanozoomer 2.0 rs slide scanner

1

Quantifying Pathological Lesions in Histology

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Pathology images were captured at 10x magnification on a Hamamatsu NanoZoomer 2.0RS slide scanner. The resulting image files were converted to JPEG format (lossless compression) with NDPItools (https://www.imnc.in2p3.fr/pagesperso/deroulers/software/ndpitools/) for further analysis. Background over-staining was subsequently removed in in FIJI (FIJI Is Just ImageJ) using the Subtract Background plugin (settings: rolling ball radius of 50 pixels, light background, separate colors). Following that, deconvolution was performed in using the Color Deconvolution plugin FIJI (using custom trained vectors for H-DAB staining) (Schindelin et al., 2012 (link)). Anaconda/Python scripts calling the numpy, scipy, skimage, pandas, seaborn and matplotlib libraries were used for further analysis. A sliding window of 10001 and 1001 pixels (necrotic lesions and NNGI granulomas respectively) was used to calculate running averages for DAB stain intensity projected on the major axis (normalized to 1.0) of a rectangular region traversing each granuloma, lesion or appropriate control region. The same size rectangular region was used for each necrotic lesion and granuloma, respectively.
Chinta K.C., Rahman M.A., Saini V., Glasgow J.N., Reddy V.P., Lever J.M., Nhamoyebonde S., Leslie A., Wells R.M., Traylor A., Madansein R., Siegal G.P., Antony V.B., Deshane J., Wells G., Nargan K., George J.F., Ramdial P.K., Agarwal A, & Steyn A.J. (2018). Microanatomic Distribution of Myeloid Heme Oxygenase-1 Protects against Free Radical-Mediated Immunopathology in Human Tuberculosis. Cell Reports, 25(7), 1938-1952.e5.
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2

Volumetric and Histological Brain Analysis

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Animals in both groups were euthanized and intracardially perfused when behavioral testing completed. Brains including cerebellum were removed, weighed, and fixed for coronal sectioning and cresyl violet staining. Criteria for brain abnormality was chosen based on the brain weight after extraction33 (link), and no animal was excluded from analysis for abnormal brain weight. The stained sections were imaged using a Nanozoomer 2.0RS slide scanner (Hamamatsu, Japan) for histological analysis and presentation. From the coronal sections, measurements included cortical and dorsal hippocampal (dHPC) volumetrics, neuronal density, and cortical thickness in both hemispheres. Furthermore, in order to enhance the accuracy of the histology, six animals from B6 group and one animal from the BTBR group were excluded from histological assessments and also from all other corresponding volumetric analyses because of damages to one or both hemispheres, and technical issues such as missing and/or damaged sections.
Faraji J., Karimi M., Lawrence C., Mohajerani M.H, & Metz G.A. (2018). Non-diagnostic symptoms in a mouse model of autism in relation to neuroanatomy: the BTBR strain reinvestigated. Translational Psychiatry, 8, 234.
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3

Myelin Assessment of Mouse Brains

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Two mice were sacrificed (one at 12 weeks of TX and one at 12 weeks with no TX), and perfused intracardially with 4% paraformaldehyde in phosphate buffer saline. The extracted brains were then post-fixed overnight at 4°C in the same fixative, cryoprotected for several hours at 4°C in phosphate buffer saline containing 30% sucrose, and frozen in melting isopentane. The brains were then sliced in 20 μm thick sections with a Microm cryostat for myelin assessment with PLP/GFP (proteolipid protein/green fluorescent protein). Microscopic scans of whole sections (pixel size 0.25 μm2) were acquired with a Nanozoomer 2.0-RSslide scanner (Hamamatsu Photonics, Hamamatsu Japan). Co-localization of brain regions with MR images was performed using anatomical landmarks from similar slices.
Petiet A., Aigrot M.S, & Stankoff B. (2016). Gray and White Matter Demyelination and Remyelination Detected with Multimodal Quantitative MRI Analysis at 11.7T in a Chronic Mouse Model of Multiple Sclerosis. Frontiers in Neuroscience, 10, 491.
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4

Immunohistochemical Staining of Teratomas and Arteries

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Teratomas and human arteries were fixed in 4% paraformaldehyde (PFA) and embedded in paraffin. Sections were cut and mounted on positively charged slides. Sections were deparaffinized with xylene and rehydrated in a graded ethanol series. Endogenous peroxidase was quenched by placing the slides in 3% hydrogen peroxide in methanol for 10 min. Heat-induced epitope retrieval was performed by boiling the slides for 6 min in citrate buffer solution (pH 6.0) (Invitrogen). Slides were washed with phosphate-buffered saline and then stained with the monoclonal antibody MAB2909, which recognizes alkaline phosphatase (R&D Systems), using the Histostain-SP Kit (Invitrogen) according to the manufacturer’s instructions. In brief, after exposure to serum blocking solution, the sections were incubated successively with primary antibody, biotinylated secondary antibody, and streptavidin–horseradish peroxidase (HRP) conjugate. Visualization was performed with 3,3′-diaminobenzidine (Molecular Probes), which generates a brown-colored oxidation product upon reaction with the HRP-labeled streptavidin. Nuclei were stained with hematoxylin. For images, slides were scanned by NanoZoomer 2.0-RS slide scanner (Hamamatsu Photonics).
Jin H., Hilaire C.S., Huang Y., Yang D., Dmitrieva N.I., Negro A., Schwartzbeck R., Liu Y., Yu Z., Walts A., Davaine J.M., Lee D.Y., Donahue D., Hsu K.S., Chen J., Cheng T., Gahl W., Chen G, & Boehm M. (2016). Increased activity of TNAP compensates for reduced adenosine production and promotes ectopic calcification in the genetic disease ACDC. Science signaling, 9(458), ra121.
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5

Immunohistochemical Analysis of Lung Tissue

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Hematoxylin and eosin (H&E) staining and immunohistochemistry were performed on paraffin-embedded lungs using standard protocols. Immunohistochemistry was performed using antibodies directed against Ki67 (1:100, BD Biosciences,) and Cleaved caspase 3 (1:400, Cell Signaling Technologies). Briefly, paraffin sections were re-hydrated, unmasked in 10mM Sodium Citrate buffer with 0.05% Tween 20 in a pressure cooker for 10 minutes, the peroxidase was quenched for 15 minutes in 3% H2O2, sections were blocked for 30 minutes in TBS with 0.025% Triton X-100 supplemented with 10% serum and 1% BSA, and incubated overnight at 4°C with primary antibody. On the next day, the sections were incubated for 30 minutes with biotinylated antibody compatible with the primary antibody used (1:1000, Vector Laboratories) and were subsequently incubated with VECTASTAIN Elite ABC HRP Kit (Vector Laboratories), according to manufacturer’s instructions. The sections were washed with TBS in between steps. Staining was performed using the DAB peroxidase kit (Vector Laboratories) and hematoxylin (H-3401, Vector Laboratories) for counter-staining. A Leica DM6000B microscope (Leica Microsystems) or NanoZoomer 2.0-RS slide scanner (Hamamatsu) was used for imaging.
Bieging-Rolett K.T., Kaiser A., Morgens D.W., Boutelle A.M., Seoane J.A., Van Nostrand E.L., Zhu C., Houlihan S.L., Mello S.S., Yee B.A., McClendon J., Pierce S.E., Winters I.P., Wang M., Connolly A.J., Lowe S.W., Curtis C., Yeo G.W., Winslow M.M., Bassik M.C, & Attardi L.D. (2020). Zmat3 is a key splicing regulator in the p53 tumor suppression program. Molecular cell, 80(3), 452-469.e9.
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6

In Situ Hybridization Visualization of Trophoblast Genes

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In situ hybridization was performed on primary cell cultures seeded on chamber slides at 90% confluency (106 cells/well) (Thermo Fisher Scientific, UK). Cells were fixed in 4% PFA for 30 min, washed twice with PBSX1, dehydrated in increasing concentrations of ethanol and stored in 100% ethanol at −20 °C. In situ hybridization was performed using the RNAScope 2.5 RED chromogenic assay kit following the manufacturer’s instructions (Bio-Techne, UK). Briefly, slides were allowed to equilibrate to room temperature and rehydrated in PBSX1. RNAscope® Hydrogen Peroxide was applied to the slides for 10 min at RT, followed by RNAscope® Protease Plus in RT for 10 min. Slides were then incubated with the target or control probes at 40 °C for 2 h (negative control probe (310043), positive control probe (313911), Tpbpa-probe (405511), Prl8a8-probe (528641), Gjb3-probe (508841), and Hand1-probe (429651) in a HybEZ oven for 2 h at 40 °C. Next, slides were washed twice with wash buffer and were subjected to six rounds of amplification and the probe signal was developed via a reaction with fast red. Slides were then counterstained with Haematoxylin and mounted in EcoMount. Slides were scanned on a NanoZoomer 2.0-RS slide scanner (Hamamatsu, Hamamatsu City, JP) at ×40 magnification.
Napso T., Zhao X., Lligoña M.I., Sandovici I., Kay R.G., George A.L., Gribble F.M., Reimann F., Meek C.L., Hamilton R.S, & Sferruzzi-Perri A.N. (2021). Placental secretome characterization identifies candidates for pregnancy complications. Communications Biology, 4, 701.
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7

Digitally Capturing Microscopic Samples

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Digital images were captured using the NanoZoomer 2.0- RS slide scanner (Hamamatsu, Japan) under 40x magnification.
Craciun L., de Wind R., Demetter P., Lucidi V., Bohlok A., Michiels S., Bouazza F., Vouche M., Tancredi I., Verset G., Garaud S., Naveaux C., Galdon M.G., Gallo K.W., Hendlisz A., Derijckere I.D., Flamen P., Larsimont D, & Donckier V. (2020). Retrospective analysis of the immunogenic effects of intra-arterial locoregional therapies in hepatocellular carcinoma: a rationale for combining selective internal radiation therapy (SIRT) and immunotherapy. BMC Cancer, 20, 135.
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8

Histological Analysis of Tissue Response

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All stained slides were scanned with the NanoZoomer 2.0-RS slide scanner (Hamamatsu, Sendai City, Japan). Stained sections were independently scored by three blinded individuals to assess tissue response. Fibrous capsule thickness and inflammatory cells were evaluated semi-quantitatively using NanoZoomer Digital Pathology software. Data are presented as mean ± standard deviation. Statistical significance was analyzed using one-way analysis of variance (ANOVA) with Tukey’s post-hoc analysis. A value of p < 0.05 was considered statistically significant.
Fu Y., Both S.K., Plass J.R., Dijkstra P.J., Zoetebier B, & Karperien M. (2022). Injectable Cell-Laden Polysaccharide Hydrogels: In Vivo Evaluation of Cartilage Regeneration. Polymers, 14(20), 4292.
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9

Quantifying Lung Tissue Collagen

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Lung tissues were fixed with 10% formalin before paraffin embedding. Tissue sections of 4 µm were stained with Masson’s trichrome by the Histology Platform at the Université de Sherbrooke. TKS5 (NBP1-90454) immunohistochemical staining was detected using diaminobenzidine and counter-stained with Harris hematoxylin. Microscope slides were scanned at 20× and 40× magnifications with the Hamamatsu NanoZoomer 2.0 RS slide scanner (Hamamatsu Photonics, Bridgewater, NJ, USA). Collagen quantification was performed as described by Chen et al. [54 ]. The percentage of collagen-positive areas was measured for each patient specimen on two separate samples (~0.5 cm3) and on two non-serial sections.
Lebel M., Cliche D.O., Charbonneau M., Adam D., Brochiero E., Dubois C.M, & Cantin A.M. (2022). Invadosome Formation by Lung Fibroblasts in Idiopathic Pulmonary Fibrosis. International Journal of Molecular Sciences, 24(1), 499.
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10

Comprehensive Tissue Analysis Protocol for Pancreatic Lesions

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Tissue specimen processing, sectioning, and H&E staining were performed using standard protocols. Immunohistochemistry was performed using the VectaStain Elite ABC kit (Vector Laboratories) according to the manufacturer's protocol. The antibodies used were mouse anti-MUC5AC (1:500; ThermoFisher), mouse anti-Ki67 (1:100; BD Pharmingen), rat anti-Ck19 (1:750; University of Iowa), and goat anti-amylase (1:100; Santa Cruz Biotechnology). The sections were counterstained with hematoxylin or Alcian blue/nuclear fast red using the NovaUltra Alcian blue stain kit (IHC World) according to the manufacturer's instructions. For Ck19 and amylase staining, the sections were stained using anti-goat Alexa 488 (1:200; Invitrogen) and anti-rat Alexa 594 (1:200; Invitrogen) and counterstained with DAPI. Pictures were taken using a Leica microscope and/or with a NanoZoomer 2.0-RS slide scanner (Hamamatsu). Analysis of the PanIN and mucinous cystic lesion areas and Ki67 staining was performed using ImageJ. To simulate the size criterion used to diagnose IPMNs in humans, we also used a size criterion (diameter ≥280) to call cystic lesions/IPMNs. This size was based on the ability to distinguish large cystic lesions from PanIN lesions. Further classification of these lesions was performed based on their lining using H&E and Muc5ac staining.
Mello S.S., Sinow C., Raj N., Mazur P.K., Bieging-Rolett K., Broz D.K., Imam J.F., Vogel H., Wood L.D., Sage J., Hirose T., Nakagawa S., Rinn J, & Attardi L.D. (2017). Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes & Development, 31(11), 1095-1108.
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