Nanozoomer xr digital slide scanner

Manufactured by Hamamatsu Photonics

Sourced in Japan

The NanoZoomer-XR Digital Slide Scanner is a high-performance imaging system designed for digitizing microscope slides. It captures high-resolution images of specimens with a maximum resolution of 0.92 microns per pixel. The device features an automated slide loading mechanism and can handle a variety of slide sizes. The NanoZoomer-XR is capable of generating digital images that can be viewed and analyzed on a computer.

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Lab products found in correlation

Tcs sp5 confocal microscope, by Leica (4 mentions) Ndp view2, by Hamamatsu Photonics (3 mentions) Mz10f stereomicroscope, by Leica (2 mentions) Dfc3000g camera, by Leica (2 mentions) Bx52 epifluorescent microscope, by Olympus (2 mentions) Cast stereology software, by Olympus (2 mentions) Dp70 digital ccd camera, by Olympus (2 mentions) Ethylene diamine tetraacetic acid (edta), by Avantor (2 mentions) Ap in situ cell death detection kit, by Roche (1 mentions) Everbrite hardset mounting medium with dapi, by Biotium (1 mentions) Ventana benchmark ultra, by Roche (1 mentions) Integrator system, by Visiopharm (1 mentions) Dmls microscope, by Leica (1 mentions) Icc50 hd camera, by Leica (1 mentions) Hematoxylin, by Merck Group (1 mentions) Hartman s fixative solution, by Merck Group (1 mentions) Vectamount permanent mounting medium, by Vector Laboratories (1 mentions) Mayer s haematoxylin, by Vector Laboratories (1 mentions) Immedge hydrophobic barrier pap pen, by Vector Laboratories (1 mentions) Nanozoomer digital pathology view, by Hamamatsu Photonics (1 mentions)

Spelling variants of this product

NanoZoomer (461 citations) NanoZoomer slide scanner (136 citations) NanoZoomer-XR (98 citations) NanoZoomer digital slide scanner (74 citations) Nanozoomer scanner (61 citations) Slide scanner (39 citations) Digital slide scanner (14 citations) NanoZoomer XR scanner (10 citations) NanoZoomer XR slide scanner (8 citations) NanoZoomer-XR Digital scanner (3 citations)

25 protocols using nanozoomer xr digital slide scanner

Apoptosis Measurement in LCLs

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Apoptosis rate in LCLs was evaluated using terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) assay, designed to detect apoptotic cells during the late stages of apoptosis, as previously described^{13 (link)}. Briefly, cells were cytospinned on glass slides and then fixed in 4% PFA for 10 min at room temperature (RT) and washed three times in phosphate buffer saline (PBS) for 5 min. Staining for apoptotic cells was performed using the AP-In situ Cell Death Detection Kit (Roche Diagnostics, Penzberg, Germany) following the manufacturer’s protocol. Slides were mounted for microscopic imaging with home-made glycerol-based mounting media with anti-fading (1,4-diazabicyclo[2.2.2]octane, DABCO). Apoptotic cells were detected with NanoZoomer-XR Digital slide scanner (Hamamatsu, Japan) for counting.

Grazioli P., Parodi C., Mariani M., Bottai D., Di Fede E., Zulueta A., Avagliano L., Cereda A., Tenconi R., Wierzba J., Adami R., Iascone M., Ajmone P.F., Vaccari T., Gervasini C., Selicorni A, & Massa V. (2021). Lithium as a possible therapeutic strategy for Cornelia de Lange syndrome. Cell Death Discovery, 7, 34.

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Wholemount Imaging and Slide Scanning Protocol

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Wholemount images were taken with a MZ10 F Stereomicroscope (Leica Microsystems), using a DFC3000 G camera (Leica Microsystems). For bright field images, stained slides were scanned with Nanozoomer-XR Digital slide scanner (Hamamatsu) and images processed using Nanozoomer Digital Pathology View. Fluorescent staining was imaged with a TCS SP5 confocal microscope (Leica Microsystems) and images processed using Fiji (Schindelin et al., 2012 (link)).

Lodge E.J., Santambrogio A., Russell J.P., Xekouki P., Jacques T.S., Johnson R.L., Thavaraj S., Bornstein S.R, & Andoniadou C.L. (2019). Homeostatic and tumourigenic activity of SOX2+ pituitary stem cells is controlled by the LATS/YAP/TAZ cascade. eLife, 8, e43996.

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Immunohistochemical Analysis of Microglia and Astrocytes

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At the end of the experiments, each mouse was deeply anesthetized with urethane 10% and then transcardially perfused with saline followed by 4% paraformaldehyde (PFA) fixative, as per previously described procedures [57 (link),58 (link)]. Brain sections of 30 μm were cut in the coronal plane with a cryostat at −20 °C and processed for immunohistochemistry (IHC) analysis. The sections were placed in PBS pH 7.4 at 4 °C and stored for later use. The nonspecific binding sites in sections were blocked with bovine serum albumin and incubated overnight with an antibody against ionized calcium-binding adaptor molecule-1 (polyclonal rabbit anti-Iba1; 1:400 dilutions; Wako Chemicals USA, Richmond, VA, USA) and antibody against glial fibrillary acidic protein (polyclonal mouse anti-GFAP; 1:300 dilutions; Wako Chemicals USA, Richmond, VA, USA). Sections were incubated in rabbit or mouse polyclonal to anti-goat immunoglobulin G secondary antibody (1:300; Vector Laboratories, TPE, TWN) to visualize the staining. Sections were developed in DAB (3,3′-diaminobenzidine) solution for 5 min and washed 3 times for 10 min with Trisbuffered saline. Iba1⁺ and GFAP⁺ cell bodies were scanned with a NanoZoomer-XR digital slide scanner (Hamamatsu, Hamamatsu City, Japan) and processed by its viewing platform (NDP.view2).

Ballon Romero S.S., Lee Y.C., Fuh L.J., Chung H.Y., Hung S.Y, & Chen Y.H. (2020). Analgesic and Neuroprotective Effects of Electroacupuncture in a Dental Pulp Injury Model—A Basic Research. International Journal of Molecular Sciences, 21(7), 2628.

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Quantifying Cell Proliferation via Ki67

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For assessing cell proliferation rate, Ki67 immunoassay^{60 (link)} was used. Slides were stained with primary antibody anti-Ki-67 (1:250, #9129 (D3B5) Cell Signaling) overnight, followed by incubation with Alexa-488 anti-rabbit secondary antibody (1:1000, #6441-30 SouthernBiotech) for 2 h. Slides were mounted for microscopic imaging with EverBrite Hardset Mounting Medium with DAPI (#23004, Biotium) and positive cells were detected and acquired with NanoZoomer-XR Digital slide scanner (Hamamatsu, Japan) for counting.

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Comprehensive Kidney Allograft Tissue Analysis

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Two-micron sections of FFPE renal allograft biopsies were stained with hematoxylin and eosin, Periodic acid–Schiff–diastase, and Jones' silver stain according to standard diagnostic practice. Subsequently, IHC stainings were performed on 4 μm FFPE cut sections with an automated, validated and accredited staining system (Ventana Benchmark ULTRA; Ventana Medical Systems, Tucson, AZ) using ultraview or optiview universal DAB detection Kit. Antibodies used (CD3, CD4, CD8, CD20, CD56, CD68, PD-1, and granzyme B) and dilutions are summarized in Table S1, SDC (http://links.lww.com/TXD/A156). FoxP3/CD4 staining was performed at MGH/Harvard, (Boston, MA). All sections were scanned at 40× magnification using Nanozoomer XR digital slide scanner (Hamamatsu, Hamamatsu City, Japan). Digital image analysis was performed using Visiopharm integrator system (Version 2017.2.4.3387) with Author module (Visiopharm, Hoersholm, Denmark). For each section, manual selection of only cortical tissue was made, excluding the medulla, artifacts, and the lumen of blood vessels larger than glomeruli. Image analysis Application Protocol Packages were developed to measure the total tissue area (μm²) and the area percentage of positive staining.

van der Zwan M., Baan C.C., Colvin R.B., Smith R.N., White R.A., Ndishabandi D., Nigg A.L., van den Bosch T.P., de Graav G.N., Clahsen-van Groningen M.C, & Hesselink D.A. (2018). Immunomics of Renal Allograft Acute T Cell-Mediated Rejection Biopsies of Tacrolimus- and Belatacept-Treated Patients. Transplantation Direct, 5(1), e418.

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Histological Analysis of Tissue Samples

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After deparaffinization and rehydration, tumors, lungs, lymph nodes or skin sections were stained with hematoxylin (Sigma-Aldrich, MO, USA; cat# GHS232) and eosin (Sigma-Aldrich, MO, USA; cat# HT110232) according to manufacturer’s instructions, dehydrated and mounted with xylene. All bright field images (skin, lymph nodes and tumor sections) were acquired using a Leica DMLS microscope (Leica, DE) coupled with a Leica ICC50 HD camera (Leica, DE) and Leica Application Suite v4.2.0, or using a NanoZoomer-XR Digital slide scanner (Hamamatsu, JP) and NDP.view 2 software (version 2.7).

Di Leo L., Bodemeyer V., Bosisio F.M., Claps G., Carretta M., Rizza S., Faienza F., Frias A., Khan S., Bordi M., Pacheco M.P., Di Martino J., Bravo-Cordero J.J., Daniel C.J., Sears R.C., Donia M., Madsen D.H., Guldberg P., Filomeni G., Sauter T., Robert C., De Zio D, & Cecconi F. (2021). Loss of Ambra1 promotes melanoma growth and invasion. Nature Communications, 12, 2550.

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Prostate Tissue Microarray Digitization

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Tissue microarrays were digitized at 40x resolution (0.23 microns per pixel) at the University Hospital Zurich (NanoZoomer-XR Digital slide scanner, Hamamatsu). Tumour stage and Gleason scores were assigned according to the International Union Against Cancer (UICC) and WHO/ISUP criteria. Cancerous regions were delineated and labeled with corresponding Gleason patterns using the TMARKER⁴¹ software. In addition, TMA spots containing only benign prostate tissue were marked as “benign” by the two pathologists.

Arvaniti E., Fricker K.S., Moret M., Rupp N., Hermanns T., Fankhauser C., Wey N., Wild P.J., Rüschoff J.H, & Claassen M. (2018). Automated Gleason grading of prostate cancer tissue microarrays via deep learning. Scientific Reports, 8, 12054.

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Azoxymethane and Dextran Sulfate-Induced Colorectal Cancer in Mice

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8–12-week-old male C57BL/6 mice (Lab), LabR and WildR mice received a single intraperitoneal injection of azoxymethane (AOM; 10 mg/kg of body weight) on day 0. This treatment was followed by three 7-day cycles of 2–2.5% dextran sodium sulfate (DSS) in drinking water (day 5–12; day 26–33; day 48–55). Mice were monitored for weight loss and euthanized on day 85 to assess colorectal tumor burden. Images of dissected colorectal tissue were analyzed using ImageJ software (NIH, MD), in a blinded manner with regards to the groups the samples were assigned to. For histological analysis, colorectal tissue was fixed in 10% buffered formalin for over night followed by 70% ethanol. Paraffin blocks were made and serial step sections were processed. Every 10_th slide was stained with hematoxylin and eosin (HE) and Movat. All slides were digitally scanned on a Nanozoomer-XR digital slide scanner (Hamamatsu Photonics K. K., Japan) for semi-quantitative analysis of invasiveness and inflammation. Invasiveness was scored based on tumor location as follows: tumors located within lamina propria (score of 1), muscularis mucosae (score of 2), submucosa (score of 3), muscular propria (score of 4), subserosa or serosa (score of 5). Inflammation was scored based on inflammatory cell infiltration; 1=mild, 2=moderate, 3=severe.

Rosshart S.P., Vassallo B.G., Angeletti D., Hutchinson D.S., Morgan A.P., Takeda K., Hickman H.D., McCulloch J.A., Badger J.H., Ajami N.J., Trinchieri G., de Villena F.P., Yewdell J.W, & Rehermann B. (2017). Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell, 171(5), 1015-1028.e13.

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Retinal Morphology Analysis in Ocular Models

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Oriented ocular globes were fixed for at least 24 h in Hartman’s fixative solution (Sigma-Aldrich, St. Louis, MI, USA) and embedded in paraffin. Five-µm sagittal sections containing optic nerve (ON) were performed and stained with hematoxylin and eosin (HE). HE sections from 3 consecutive slides were examined by light microscopy at a magnification of 20× and color images were obtained using a NanoZoomer-XR Digital slide scanner (Hamamatsu Photonics, Hamamatsu city, Japan). Images were analyzed using NDP View software. The outer nuclear layer (ONL thickness) in the LID model or the total retinal thickness (from the internal limiting membrane to the retinal pigment epithelium) and the outer retinal thickness (from the outer plexiform layer to the retinal pigment epithelium) in the MNU rat model were measured every 500 µm from the ON to the inferior and the superior ciliary processes. Thickness profiles along the retina were generated by averaging, for each distance, the values obtained for all eyes, as previously described [30 (link)] and values are expressed as mean ± sem. The photoreceptor ratio was calculated as the percentage of outer retinal thickness/total retinal thickness, as previously described [40 (link)].

Bigot K., Gondouin P., Bénard R., Montagne P., Youale J., Piazza M., Picard E., Bordet T, & Behar-Cohen F. (2020). Transferrin Non-Viral Gene Therapy for Treatment of Retinal Degeneration. Pharmaceutics, 12(9), 836.

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Quantifying Brain Plaque-Associated Microglia

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The human biopsy brain tissue sections were imaged with Hamamatsu NanoZoomer-XR Digital slide scanner with 20x (NA 0.75) objective (Hamamatsu Photonics K.K.). Due to the small size of the biopsy specimen, all plaques with microglia within or around the plaque in the grey matter area of the specimen were included in the analysis. Size of the β-amyloid plaques was obtained by manually outlining the plaques in NDP.view2 software (Hamamatsu Photonics K.K.). Plaque-associated microglia were manually counted, and the number of microglia within the plaque area and around the plaque area were recorded separately. Only microglia with clearly visible soma were included in the count. Counting and analysis was performed by an investigator blinded to sample identity.

Natunen T., Martiskainen H., Marttinen M., Gabbouj S., Koivisto H., Kemppainen S., Kaipainen S., Takalo M., Svobodová H., Leppänen L., Kemiläinen B., Ryhänen S., Kuulasmaa T., Rahunen E., Juutinen S., Mäkinen P., Miettinen P., Rauramaa T., Pihlajamäki J., Haapasalo A., Leinonen V., Tanila H, & Hiltunen M. (2020). Diabetic phenotype in mouse and humans reduces the number of microglia around β-amyloid plaques. Molecular Neurodegeneration, 15, 66.

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