Nanozoomer ht

Manufactured by Hamamatsu Photonics

Sourced in Japan

The NanoZoomer HT is a high-throughput digital slide scanning system designed for digitizing glass microscope slides. It captures high-resolution images of samples and tissue sections with the ability to scan multiple slides simultaneously. The core function of the NanoZoomer HT is to provide a digitized platform for efficient slide imaging and archiving.

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Lab products found in correlation

Ndp view, by Hamamatsu Photonics (3 mentions) Anti nf 160 primary antibody, by Merck Group (3 mentions) Alexa fluor 488 secondary antibody, by Thermo Fisher Scientific (3 mentions) Alexa fluor 555 secondary antibody, by Thermo Fisher Scientific (3 mentions) Ndp view2, by Hamamatsu Photonics (2 mentions) Collagen 1, by Southern Biotech (2 mentions) Collagen 3, by Southern Biotech (2 mentions) Anti s100, by Agilent Technologies (2 mentions) Superfrost plus slide, by Thermo Fisher Scientific (2 mentions) Axio zoom v16, by Zeiss (2 mentions) Imagescope positive pixel analysis v9.1 algorithm, by Leica (1 mentions) Ndp view software, by Hamamatsu Photonics (1 mentions) Discovery xt autostainer, by Roche (1 mentions) Click it edu alexa fluor 555 imaging kit, by Thermo Fisher Scientific (1 mentions) Illustrator cs6, by Adobe (1 mentions) Uplansapo, by Olympus (1 mentions) Oct compound, by Avantor (1 mentions) Senescence detection kit, by Abcam (1 mentions) Imagescope software, by Leica (1 mentions) Goat on rodent hrp polymer, by Biocare Medical (1 mentions)

27 protocols using nanozoomer ht

Stem Tissue Development in Shade-Treated Plants

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Longitudinal and cross‐sections from the median region of the first subapical internodes of shade‐treated and control plants were prepared for microscopic study of the development of the stem tissues. The internode sections were fixed in FAA overnight and stored in 70% ethanol. Subsequent tissue dehydration, embedding in paraffin, sectioning to 10 µm, and staining with alcian blue and safranin were performed at the histopathology laboratory at Texas A&M University School of Veterinary Medicine. The slides were scanned at 20X using Nanozoomer HT digital slide scanner, and the images were viewed using NDP.view2 software (Hamamatsu Photonics).

Kebrom T.H., McKinley B.A, & Mullet J.E. (2020). Shade signals alter the expression of circadian clock genes in newly‐formed bioenergy sorghum internodes. Plant Direct, 4(6), e00235.

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Quantitative Analysis of Renal Fibrosis

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PAS stained sections of the kidneys were analyzed and scored in a blinded fashion. The extent of interstitial fibrosis and tubular atrophy were assessed as two separate parameters as % of affected cortical area. For Collagen I and III immunohistochemistry [Collagen I (Southern Biotech) Cat No. 1310-01; Collagen III (Southern Biotech) Cat No. 1330-01], sections of formalin-fixed and paraffin-embedded renal tissues were processed for indirect immunoperoxidase staining as previously described^{26 (link)}. Using a whole slide scanner (NanoZoomer HT, Hamamatsu Photonics, Hamamatsu, Japan), fully digitalized images of immunohistochemically stained slides were further processed and analyzed using the viewing software NDP.view (Hamamatsu Photonics, Hamamatsu, Japan) and ImageJ (National Institutes of Health, Bethesda, MD). The percentage of positively stained area was analysed in the kidney cortex in blinded fashion.

Kuppe C., Ibrahim M.M., Kranz J., Zhang X., Ziegler S., Perales-Patón J., Jansen J., Reimer K.C., Smith J.R., Dobie R., Wilson-Kanamari J.R., Halder M., Xu Y., Kabgani N., Kaesler N., Klaus M., Gernhold L., Puelles V.G., Huber T.B., Boor P., Menzel S., Hoogenboezem R.M., Bindels E.M., Steffens J., Floege J., Schneider R.K., Saez-Rodriguez J., Henderson N.C, & Kramann R. (2020). Decoding myofibroblast origins in human kidney fibrosis. Nature, 589(7841), 281-286.

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Standardized Breast Tumor Immune Profiling

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All assessments were conducted by experienced breast pathologists (YR and RS) and a trained pathology research scientist (PG). One of the pathologists (RS) is the founding member of a five-step standardized scoring system developed by the International Immuno-oncology Biomarker Working Group (21 (link)), along with modifications specific to the post neoadjuvant residual disease setting (22 (link)). First, we assessed RCB scores on surgical specimens of non-pCR patients using the Web-based MD Anderson RCB calculator (23 (link)). All available hematoxylin and eosin (H&E) tissue–stained sections were digitized using Hamamatsu (Nanozoomer HT) scanner, and images were used to assess the degree of lymphocytic infiltration associated with tumor stroma as per the above-mentioned internationally recognized guidelines (21 (link)) and as in previous studies of residual disease (9, 17 (link)). In brief, stromal TIL scores were defined as the percentage of the tumor–stroma area that was occupied by mononuclear inflammatory cells. TILs in tumor areas with crush artifacts and necrosis were excluded. The percentage of stromal TILs was considered a continuous parameter indicating how much of the demarcated stromal area exhibits dense mononuclear infiltrates. The mean values of the histopathologic evaluation by RS and YR were used for the analyses presented.

Gazinska P., Milton C., Iacovacci J., Ward J., Buus R., Alaguthurai T., Graham R., Akarca A., Lips E., Naidoo K., Wesseling J., Marafioti T., Cheang M., Gillett C., Wu Y., Khan A., Melcher A., Salgado R., Dowsett M., Tutt A., Roxanis I., Haider S, & Irshad S. (2022). Dynamic Changes in the NK-, Neutrophil-, and B-cell Immunophenotypes Relevant in High Metastatic Risk Post Neoadjuvant Chemotherapy–Resistant Early Breast Cancers. Clinical Cancer Research, 28(20), 4494-4508.

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Kidney Injury Biomarker Quantification

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Immunohistochemical staining of NGAL, KIM-1, and Neutrophil Elastase on formalin-fixed paraffin-embedded human kidney tissue was performed as described (Supplemental Digital Content 1, http://links.lww.com/CCX/A103). To quantify NGAL and KIM-1 immunostaining, the sections were first scanned using a Nanozoomer HT (Hamamatsu Photonics, Hamamatsu, Japan). Morphometric analysis was performed using the Aperio Imagescope positive pixel analysis v9.1 algorithm (Aperio Technologies, Vista, CA) as described previously (23 (link)). Neutrophil infiltration was quantified by counting the number of neutrophils (neutrophil Elastase positive) present in all glomeruli of the kidney sections.

Jou-Valencia D., Koeze J., Popa E.R., Aslan A., Zwiers P.J., Molema G., Zijlstra J.G., van Meurs M, & Moser J. (2019). Heterogenous Renal Injury Biomarker Production Reveals Human Sepsis-Associated Acute Kidney Injury Subtypes. Critical Care Explorations, 1(10), e0047.

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Immunohistochemical Analysis of Regenerated Tissue

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Example 22

Longitudinal sections of the delivery system and regenerated tissue were cut at 10 mm on a cryostat. Slides were stained for S100 with 1:500 rabbit anti-S100 (Dako; GA504) primary antibody followed by goat anti-rabbit Alexa Fluor 555 secondary antibody (ThermoFisher; A-21428), and stained for neurofilament with monoclonal anti-NF-160 primary antibody (Sigma N-5264) followed by goat anti-mouse Alexa Fluor 488 secondary antibody (ThermoFisher; A-11029) using standard immunohistochemistry techniques. Sections were imaged at 20× using the Nanozoomer HT (Hamamatsu, Bridgewater, N.J.) with appropriate optical filters.

US10682309B2. Hydrogel microparticle scaffold with gradients of degradability and methods thereof (2020-06-16). None [US], None [US]. Inventors: Donald L. Elbert [US], Jacob Roam [US].

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Quantifying Kidney Fibrosis and Inflammation

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The sections were scanned using a NanoZoomer HT (Hamamatsu Photonics K.K., Shizuoka Pref., Japan). The extent of cortico-interstitial α-SMA, fibronectin, type I and III collagens, and CD3 expression was measured as numbers of positive pixels, and the numbers of podoplanin-positive vessel-like structures were counted in 30 cortical areas using Aperio ImageScope software (version 9.1.772.1570, Aperio Technologies Inc, Vista, CA, USA) at 200x magnification. For CD31 staining, 10 cortical areas at 400x magnification were selected, and the percentage of CD31 positive area was measured using ImageJ 1.46r (Rasband, W.S., U.S. National Institutes of Health).

Poosti F., Bansal R., Yazdani S., Prakash J., Beljaars L., van den Born J., de Borst M.H., van Goor H., Hillebrands J.L, & Poelstra K. (2016). Interferon gamma peptidomimetic targeted to interstitial myofibroblasts attenuates renal fibrosis after unilateral ureteral obstruction in mice. Oncotarget, 7(34), 54240-54252.

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Pituitary Volume and Cell Number Estimation

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Pituitary volume was estimated using the Cavallieri method (Howard and Reed, 1998 ). Briefly, the pituitary was exhaustively sectioned then sections were collected at regular, non-overlapping intervals throughout the gland from a random starting point and stained with H&E. Images of each H&E-stained section were acquired using a NanoZoomer HT (Hamamatsu) and processed using NDP.view2 software (Hamamatsu) to calculate the pituitary cross sectional area (CSA) at least 20 times per pituitary, which was then converted to volume. Samples were blinded prior to counting. Estimating total cell number: For each animal the maximal CSA was determined from the volumetric analysis above. At this level 3 independent sections were used to measure anterior pituitary CSA and count haemotoxylin-stained nuclei (using the cell detection tool in QuPath v0.3.2 [Bankhead et al., 2017 (link)], standard Hematoxylin OD settings except with threshold intensity set to 0.05), giving a mean cells/CSA measurement per individual. This number was multiplied by the AP volume to give the total cell number.

Scagliotti V., Vignola M.L., Willis T., Howard M., Marinelli E., Gaston-Massuet C., Andoniadou C, & Charalambous M. (2023). Imprinted Dlk1 dosage as a size determinant of the mammalian pituitary gland. eLife, 12, e84092.

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Quantitative Histomorphometric Analysis

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For morphometric analyses, stained sections were scanned using a whole‐slide scanner (NanoZoomer HT; Hamamatsu Photonics), and imaging software (NDP.view and ImageJ; National Institutes of Health) was used as follows: For each slide, 8–16 images in ×40 magnification were obtained and the percentage of positively stained area of each slide was quantified. All analyses and quantifications were performed in a blinded manner.

Buhl E.M., Djudjaj S., Klinkhammer B.M., Ermert K., Puelles V.G., Lindenmeyer M.T., Cohen C.D., He C., Borkham‐Kamphorst E., Weiskirchen R., Denecke B., Trairatphisan P., Saez‐Rodriguez J., Huber T.B., Olson L.E., Floege J, & Boor P. (2020). Dysregulated mesenchymal PDGFR‐β drives kidney fibrosis. EMBO Molecular Medicine, 12(3), e11021.

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Immunohistochemical Analysis of Regenerated Tissue

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Example 22

US10137082B2. Hydrogel microparticle scaffold with gradients of degradability and methods thereof (2018-11-27). None [US], None [US]. Inventors: Donald L. Elbert [US], Jacob Roam [US].

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Digitizing Medical Microscopy Education

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WSIs were acquired by using Hamamatsu NanoZoomer HT with a ×40 objective. Eighty-five of a total of 122 iconographic documents analyzed in the practical sessions were WSI. Activity regarding the digital microscopy usage, during four semesters of implementation (2015–2016), was measured by selecting the number of “clicks” performed by students as the simplest and easiest metric to interpret the overall usage. In this context, a “click” is any action taken when using the WSI viewer: moving around, changing magnification, selecting an area, etc.
The study obtained written approval of the Joint Institutional Bioethics Committee for Health of the Faculty of Medicine of the Eduardo Mondlane University and Maputo Central Hospital (CIBS FM and HCM) (meeting minute 12/2017, protocol number CIBS FM and HCM/87/2017).

David L., Martins I., Ismail M.R., Fernandes F., Sidat M., Seixas M., Fonseca E, & Carrilho C. (2018). Interactive Digital Microscopy at the Center for a Cross-Continent Undergraduate Pathology Course in Mozambique. Journal of Pathology Informatics, 9, 42.

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