Nanozoomer xr scanner

Manufactured by Hamamatsu Photonics

Sourced in Japan

The NanoZoomer XR scanner is a high-resolution digital slide scanner designed for wide-field imaging of tissue samples. It captures high-quality digital images of microscope slides at up to 40x optical magnification. The NanoZoomer XR scanner is capable of capturing images with a maximum resolution of 0.23 microns per pixel.

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Lab products found in correlation

Ventana benchmark autostainer, by Roche (1 mentions) Image pro plus 7, by Media Cybernetics (1 mentions) Bloxall, by Vector Laboratories (1 mentions) Ep3095, by Merck Group (1 mentions) Ventana benchmark xt, by Roche (1 mentions) Ultraview universal dab detection kit, by Roche (1 mentions) Rm2125rt, by Leica (1 mentions) Dia 310, by Dianova (1 mentions) Tissue studio, by Definiens (1 mentions)

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NanoZoomer (461 citations) NanoZoomer-XR (98 citations) Nanozoomer scanner (61 citations) NanoZoomer-XR Digital slide scanner (25 citations) NanoZoomer XR slide scanner (8 citations) NanoZoomer-XR Digital slide scanner C12000 (6 citations) NanoZoomer-XR Digital scanner (3 citations) NanoZoomer-XR whole-slide scanner (2 citations) NanoZoomer-XR Scanner C12000 (2 citations) NanoZoomer-XR digital whole slide scanner (2 citations)

10 protocols using nanozoomer xr scanner

Quantifying Tumor-Infiltrating Lymphocytes in Adenocarcinoma

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Sections were scanned at 40× magnification using a NanoZoomer XR scanner (Hamamatsu, Japan). The image format was NanoZoomer Digital Pathology Image (*.ndpi) with a resolution of 226 nm/pixel (112,389 dots per inch, i.e., 4.4 × 4.4 pixels/μm corresponding to a final magnification of ×1.558). The quantification of TILs was performed by digital image analysis using Visiopharm Integrator System software (VIS; Visiopharm A/S, Hoersholm, Denmark) (Figure 1). Regions of interest were manually delineated by the observer in the software as an invasive area outlined as the outermost front of the adenocarcinoma, including the deepest invasive front of the tumor, areas with tumor budding and/or irregular tumor islands. TILs were quantified as immune densities (cells/mm²) within both cancer epithelium (intratumoral) and tumor-associated stroma (peritumoral) as previously described [18] (link). In brief, we used an app-based image analysis algorithm developed specifically for counting of CD3+ and CD8+ lymphocytes. Artifacts, including tissue folds and clefts, mucin, fatty tissue, and necrosis, were automatically excluded to avoid contributions from regions of no interest.Figure 1

Photomicrographs of CD3 and CD8 immunohistochemistry. The panels on the top show high cell densities, and the panels on the bottom show low densities.

Figure 1

Eriksen A.C., Sørensen F.B., Lindebjerg J., Hager H., dePont Christensen R., Kjær-Frifeldt S, & Hansen T.F. (2018). The Prognostic Value of Tumor-Infiltrating lymphocytes in Stage II Colon Cancer. A Nationwide Population-Based Study. Translational Oncology, 11(4), 979-987.

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Automated Quantification of Tumor-Infiltrating T Cells

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In center 1, slides were digitized on the NanoZoomer HT scanner (Hamamatsu Photonics, Japan) with the ×20 magnification and 0.45 µm/pixel resolution. A customized IS module integrated into Developer XD digital pathology software (Definiens, Munich, Germany) was used to quantify CD3+ and CD8+ T cells in the CT and IM, divided in tiles (720 µm per side). In center 2, the NanoZoomer XR scanner (Hamamatsu Photonics) was used, with the identical setting. An upgraded version of the IS module (Immunoscore Analyzer, HalioDx) was used to quantify CD3+ and CD8+ cells. In both centers, the mean and distribution of the intensity of stained cells were used as internal quality controls of each immunostaining. Automatic tissue detection (tumor, healthy non-epithelial tissue and epithelium) and IM defined as a region of 720 µm width; 360 µm on each side of the border between malignant cells and peritumoral stroma were generated automatically. If required, automated detection of the CT region was manually corrected and validated by a pathologist.

Marliot F., Chen X., Kirilovsky A., Sbarrato T., El Sissy C., Batista L., Van den Eynde M., Haicheur-Adjouri N., Anitei M.G., Musina A.M., Scripcariu V., Lagorce-Pagès C., Hermitte F., Galon J., Fieschi J, & Pagès F. (2020). Analytical validation of the Immunoscore and its associated prognostic value in patients with colon cancer. Journal for Immunotherapy of Cancer, 8(1), e000272.

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Immunoprofiling of Liver Tumor Biopsy

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IHC of FFPE slices were obtained from liver tumor biopsy taken at pre-vaccination and at every 12-week intervals. First hematoxylin and eosin staining was applied to assess the proportion of tumor area in the whole tissue and the percentage of tumor cells in the tumor area. Then Immunoscore CR TL assay was done that consists of immunostaining on two consecutive slides for quantification of positive CD3⁺ and CD8⁺ cells in the core tumor (CT) and invasive margin (IM). All immunostainings were performed on the automated system Ventana BenchMark autostainer (Roche Diagnostics). Image acquisition was done on the Hamamatsu, NanoZoomer XR scanner.
IHC and gene expression measurements were performed by HalioDx SA.

Hubbard J.M., Tőke E.R., Moretto R., Graham R.P., Youssoufian H., Lőrincz O., Molnár L., Csiszovszki Z., Mitchell J.L., Wessling J., Tóth J, & Cremolini C. (2022). Safety and Activity of PolyPEPI1018 Combined with Maintenance Therapy in Metastatic Colorectal Cancer: an Open-Label, Multicenter, Phase Ib Study. Clinical Cancer Research, 28(13), 2818-2829.

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Quantifying Leydig and Sertoli Cells

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The testes were fixed in Bouin’s solution for 24 h and then dehydrated and embedded as previously described [31 (link)]. CYP11A1 was used as an LC marker [31 (link)]. Because HSD11B1 only exists in immature LCs, not in progenitor LCs [25 (link)], this marker was also used for LC maturity. SOX9 was used as a Sertoli cell marker [32 (link)]. Immunohistochemical staining was carried out as previously described [31 (link)]. In brief, the slide was blocked, the antigen was unmasked, and CYP11A1, HSD11B1, or SOX9 antibodies were incubated, and then a secondary antibody was combined. Staining was shown, and Mayer hematoxylin was used as a counterstain. Non-immune rabbit IgG was used as the negative. The slide was scanned as a digital file with a Nano Zoomer XR scanner (Hamamatsu, Japan). Image-Pro Plus 7.0 software (Media Cybernetics, Silver Spring, MD, USA) was used for the analysis of CYP11A1⁺, HSD11B1⁺ LCs, and SOX9⁺ Sertoli cells, which were stereologically enumerated as previously described [33 (link)].

Li H., Su M., Lin H., Li J., Wang S., Ye L., Li X, & Ge R. (2023). Patulin Stimulates Progenitor Leydig Cell Proliferation but Delays Its Differentiation in Male Rats during Prepuberty. Toxins, 15(9), 581.

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Quantifying Placental S100P and HLA-G Levels

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Serial sections of human placental tissue were stained for S100P and human leukocyte antigen-G (HLA-G) as previously described [8 (link),9 (link)]. Briefly, sample tissue sections were deparaffinised, and heat-induced antigen-retrieval was carried out for 10 min using citrate buffer (pH 6.0) by heating with a microwave at 800 Watts. Blocking was achieved after incubating sections with BLOXALL (Vector Laboratories, Peterborough, UK) for 10 min and then with 2.5% (w/v) goat serum for 30 min. Staining was carried out using monoclonal anti-S100P or anti-HLA-G antibodies (Abcam, Cambridge, UK) incubated at 4 °C overnight (Supplementary Table S1). Following washing in PBS, the appropriate conjugated second antibody (Supplementary Table S1) was used. Images were acquired using NDP software and the staining was analysed using a Nano Zoomer XR scanner (Hamamatsu, Shizuoka, Japan). Analysis for the presence of S100P and HLA-G at the plasma membrane was carried out using ImageJ plot profile function (https://imagej.nih.gov/ij/docs/examples/calibration/ (accessed on 20 June 2019)). Matched images after staining for S100P and HLA-G were taken, and the same region of interest (ROI) was drawn across each cell with the membrane being placed at the midpoint of the region. Signal density was measured across a grey scale to reflect concentration of the epitopes.

Lancaster T., Tabrizi M.E., Repici M., Gupta J, & Gross S.R. (2023). An Extracellular/Membrane-Bound S100P Pool Regulates Motility and Invasion of Human Extravillous Trophoblast Lines and Primary Cells. Biomolecules, 13(8), 1231.

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Tumor Histopathology and Vascular Characterization

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Guided by T₂-weighted anatomical images, tumors were
carefully excised and orientated for subsequent histopathological processing.
Formalin-fixed and paraffin embedded tumors were cut in 3μm sections and
were stained with hematoxylin and eosin (H&E) and for the murine vascular
endothelial marker endomucin (rabbit EP3095, Millipore, Watford, UK).
Whole-Slide images were digitized using a Hamamatsu NanoZoomer XR scanner (20x
magnification, 0.46μm resolution, Hamamatsu, Japan).

Zormpas-Petridis K., Jerome N.P., Blackledge M.D., Carceller F., Poon E., Clarke M., McErlean C.M., Barone G., Koers A., Vaidya S.J., Marshall L.V., Pearson A.D., Moreno L., Anderson J., Sebire N., McHugh K., Koh D.M., Yuan Y., Chesler L., Robinson S.P, & Jamin Y. (2019). MRI Imaging of the Hemodynamic Vasculature of Neuroblastoma Predicts Response to Anti-angiogenic Treatment. Cancer research, 79(11), 2978-2991.

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Prognostic Factors for Seminoma Relapse

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Detailed information about the study cohort and methods, including prognostic factors for relapse after orchiectomy for stage I seminoma, has been published previously. [10, 11] In brief, all patients with CSI TGCC diagnosed in Denmark between 1 January 2013 and 31 December 2018 were identified in the prospective Danish Testicular Cancer (DaTeCa) database. [12] By individual-level data linkage to the Danish National Pathology Registry, [13] using the civil registration number, [14] the histologic slides from the orchiectomy specimens were collected and converted into digital images (using a Hamamatsu NanoZoomer XR scanner, Hamamatsu Photonics, Hamamatsu city, Japan). Information on clinical and follow-up data, vital status, emigration, and time of death was obtained by medical record review and by linkage to the Danish Civil Registration System. [14] Exclusion criteria were prior TGCC, synchronous TGCC, registration in the Register of Human Tissue Utilisation, [13] orchiectomy abroad, loss to follow-up within 30 days of orchiectomy and not CSI-NS disease.
This study is reported in accordance with STROBE and TRIPOD (Supplementary).
The study protocol was approved by the Regional Ethics Committee, the Danish Patient Safety Authority and the Data Protection Agency.

Wagner T., Toft B.G., Lauritsen J., Bandak M., Christensen I.J., Engvad B., Kreiberg M., Agerbæk M., Dysager L., Carus A., Rosenvilde J.J., Berney D, & Daugaard G. (2024). Prognostic factors for relapse in patients with clinical stage I testicular non-seminoma: A nationwide, population-based cohort study. European journal of cancer (Oxford, England : 1990), 202.

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Tumor-Infiltrating Lymphocyte Quantification

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One to three core needle biopsies of the tumor were collected before the first treatment and at resection. The biopsies were embedded in paraffin, sectioned and stained with hematoxylin and eosin for quality assessment and evaluation of necrosis by a pathologist (Veracyte, France). Sectioned tissue biopsies were stained by IHC for CD3, CD4 and CD8. Staining was performed on slides using the Roche Ventana Benchmark XT autostainer. After antigen retrieval, staining was performed on consecutive slides using CD8 antibodies (clone C8/144B, Veracyte), CD3 antibodies (clone MRQ39, Veracyte), and CD4 antibodies (clone SP35, Roche) and detected with secondary antibody using the Ultraview Universal DAB detection kit. Image acquisition was performed using the Hamamatsu Nanozoomer XR scanner. The Veracyte Digital Pathology Platform was used for quantification of CD3, CD8 and CD4 density in the whole tumor area.

Nielsen M., Monberg T., Sundvold V., Albieri B., Hovgaard D., Petersen M.M., Krarup-Hansen A., Met Ö., Camilio K., Clancy T., Stratford R., Sveinbjornsson B., Rekdal Ø., Junker N, & Svane I.M. (2023). LTX-315 and adoptive cell therapy using tumor-infiltrating lymphocytes generate tumor specific T cells in patients with metastatic soft tissue sarcoma. Oncoimmunology, 13(1), 2290900.

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Quantitative Histological Analysis of Tumor Samples

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The other tumour half was fixed in formalin and embedded in paraffin. Serial formalin‐fixed paraffin‐embedded (FFPE) tissue sections (5 μm) were cut using a microtome (RM2125RT, Leica, Milton Keynes, UK). Tinctorial haematoxylin and eosin (H&E) staining was performed for the assessment of nuclear density, morphology and necrosis. HA was detected by an affinity histochemistry assay using a biotinylated, recombinant HA‐binding protein (modified TSG‐6 probe HTI‐601, Halozyme Therapeutics) [21 (link)]. Collagen I & III were detected by picrosirius red staining (PRC/R/109, Pioneer Research Chemicals, Colchester, UK). Blood vessels were detected by CD31 immunohistochemistry using a rat anti‐mouse CD31 primary antibody (DIA‐310, Dianova, Hamburg, Germany) and Rat Histofine MAX PO (414311F, Nichirei Bioscience, Tokyo, Japan).
Whole‐slide images were digitised using a Nanozoomer XR scanner (Hamamatsu, Welwyn Garden City, UK). Nuclear density, HA (%) and blood vessel density were quantified at 40× magnification from H&E, HTI‐601 and CD31 staining, respectively, using definiens tissue studio® (Definiens, Carlsbad, CA, USA). The extent (%), fractal dimension and entropy associated with collagen I & III were quantified at 20× magnification from picrosirius red staining as previously described [18 (link)].

Reeves E.L., Li J., Zormpas‐Petridis K., Boult J.K., Sullivan J., Cummings C., Blouw B., Kang D., Sinkus R., Bamber J.C., Jamin Y, & Robinson S.P. (2023). Investigating the contribution of hyaluronan to the breast tumour microenvironment using multiparametric MRI and MR elastography. Molecular Oncology, 17(6), 1076-1092.

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Quantitative Brain Tissue Analysis

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Immunofluorescence brain sections were imaged using a Nikon Eclipse fluorescence microscope (20 × lens 0.75NA; 10 × lens 0.45NA; 4 × lens 0.20NA; 2 × lens 0.10NA). The 2 × lens was used to image four consecutive NeuN positive-coronal sections (30 µm thickness) for each replicate to study lateral ventricle size. FIJI software was used to calculate the area of the lateral ventricle.^{20 (link)} Brain sections stained with Haematoxylin/Eosin or Haematoxylin/DAB were imaged using a Nanozoomer-XR scanner (Hamamatsu). The thickness of the corpus callosum was measured in 15 consecutive Haematoxylin/Eosin-coronal sections (30 µm thickness) for each replicate using the NanoZoomer Digital Pathology software's ruler function. The thickness of the corpus callosum in each section was normalized to the thickness of the entire section. Haematoxylin/DAB sections (for ATG9A) were analysed using QuPath Quantitative Pathology & Bioimage Analysis software.^{21 (link)} The Haematoxylin and DAB signals were separated using the QuPath colour transforms function, and ATG9A-DAB positive cells are shown in Fig. 4 after manually drawing a region of interest around the cortex, the brainstem or the hippocampus. Image analysis of brain regions was conducted by an operator blinded to the genotype of each animal.

Scarrott J.M., Alves-Cruzeiro J., Marchi P.M., Webster C.P., Yang Z.L., Karyka E., Marroccella R., Coldicott I., Thomas H, & Azzouz M. (2023). Ap4b1-knockout mouse model of hereditary spastic paraplegia type 47 displays motor dysfunction, aberrant brain morphology and ATG9A mislocalization. Brain Communications, 5(1), fcac335.

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