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Nanozoomer digital pathology slide scanner

Manufactured by Hamamatsu Photonics
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Sourced in Jersey, United States

The NanoZoomer Digital Pathology slide scanner is a high-resolution imaging system designed for digitizing microscope slides. It captures detailed images of tissue samples with a maximum resolution of 0.46 micrometers per pixel. The device is capable of scanning up to 210 slides in a single batch.

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Lab products found in correlation

Zen 2009, by Zeiss (4 mentions) Lsm meta confocal microscope, by Zeiss (4 mentions) Skor2, by Novus Biologicals (2 mentions) Neuronal nuclei (neun), by Merck Group (2 mentions) Calbindin, by Swant (2 mentions) Vectashield dapi, by Vector Laboratories (2 mentions) Silanized slides, by Agilent Technologies (1 mentions) Formaldehyde neutral buffer solution, by Merck Group (1 mentions) S1700, by Agilent Technologies (1 mentions) Peroxidase blocking solution, by Agilent Technologies (1 mentions) Hrp conjugated goat anti rabbit igg antibody, by Nichirei Biosciences (1 mentions) Anti hsv 1 antibody, by Agilent Technologies (1 mentions) Dab peroxidase substrate kit, by Vector Laboratories (1 mentions) Blocking one, by Nacalai Tesque (1 mentions) Hcimage software, by Hamamatsu Photonics (1 mentions) Halo image analysis software, by Indica Labs (1 mentions) Ab16667, by Cell Signaling Technology (1 mentions) Ab48508, by Abcam (1 mentions) Cd163, by Leica Biosystems (1 mentions) Cleaved caspase 3, by Cell Signaling Technology (1 mentions)

15 protocols using nanozoomer digital pathology slide scanner

1

Automated Whole-Slide Quantification of Histological Markers

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Whole-section imaging was performed using a NanoZoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, NJ) at the University of Washington Histology and Imaging Core in Seattle, WA. Slides were scanned in bright-field at a 20× objective and the digital images imported for analysis using Visiopharm software (Hoersholm, Denmark), which provides automated quantification of stained areas and uniform systematic random sampling on whole-section bright-field images (26 (link)). The software labeled the marker (HA, IαI, versican, and TSG-6)-positive area vs. tissue area using a project-specific configuration based on a threshold of pixel values. The relative and total tissue areas stained by the markers were measured. All the images were processed together using this configuration to generate the desired outputs (stained and unstained tissue areas measured in square micrometers).
Bogdani M., Johnson P.Y., Potter-Perigo S., Nagy N., Day A.J., Bollyky P.L, & Wight T.N. (2014). Hyaluronan and Hyaluronan-Binding Proteins Accumulate in Both Human Type 1 Diabetic Islets and Lymphoid Tissues and Associate With Inflammatory Cells in Insulitis. Diabetes, 63(8), 2727-2743.
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2

Quantitative Analysis of HSV-1 in Orthotopic Tumors

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Mice harboring orthotopic TE8-luc tumors were treated and euthanized 34 days after the treatment as scheduled in Figure 3A. Orthotopic tumors were harvested, fixed in 10% formaldehyde neutral buffer solution (Sigma-Aldrich, St Louis, MOSA) for 72 h, and embedded in paraffin. Sections (5-μm thick) were rehydrated using an alcohol gradient and subjected to heat-mediated antigen retrieval using target retrieval solution S1700 (Dako, Santa Clara, CA).
Sections were mounted on silanized slides (Dako Cytomation, Glostrup, Denmark) and stained with HE. Sequential sections were subjected to immunohistochemical analysis to detect HSV-1. The sections were treated with peroxidase blocking solution (Dako) and Blocking One (Nacalai Tesque, Kyoto, Japan), incubated with a rabbit polyclonal anti-HSV-1 antibody (1:2,000 dilution, 3 μg/mL) (Dako Cytomation), rinsed, and incubated with an HRP-conjugated goat anti-rabbit IgG antibody (Nichirei Bioscience, Tokyo, Japan). The sections were developed with 3,3′-diaminobenzidine (DAB) Peroxidase Substrate kit (Vector laboratories, Burlingame, CA), and then counterstained with hematoxylin. A NanoZoomer Digital Pathology slide scanner (Hamamatsu Photonics K.K., Hamamatsu, Japan) was used to view slides.
Yajima S., Sugawara K., Iwai M., Tanaka M., Seto Y, & Todo T. (2021). Efficacy and safety of a third-generation oncolytic herpes virus G47Δ in models of human esophageal carcinoma. Molecular Therapy Oncolytics, 23, 402-411.
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3

Automated Image Analysis for Neuroinflammation

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Image analysis was performed using whole-slide digital images and automated image analysis. All slides were scanned in bright field with a 20× objective using a Nanozoomer Digital Pathology slide scanner (Hamamatsu, Bridgewater, NJ). Whole-slide digital images were imported into Visiopharm software (Hoersholm, Denmark) for analysis. The software converted the initial digital imaging into gray scale values using 2 features, RGB-R with a mean filter of 5 pixels by 5 pixels and an RGB-B feature. Visiopharm was then trained to identify positive labeling and the background tissue counterstain using a project-specific configuration based on threshold pixel values. Images were processed in batch mode using this configuration to generate the desired outputs (eg, area of Iba-1 and ratio of Iba-1 to total tissue area). Based on output for each brain analyzed, the mean value for each treatment group was calculated by averaging the results for the individual brains in each group.
For quantitative measurements of spinal cord, the Visiopharm Image Analysis module was used to define regions of interest by manually drawing around the spinal cord to exclude the vertebral body. As with the whole-slide analysis for brain, positively labeled versus unlabeled tissue was segmented using a project-specific configuration to generate the desired outputs.
Snyder J.M., Radaelli E., Goeken A., Businga T., Boyden A.W., Karandikar N.J, & Gibson-Corley K.N. (2022). Perfusion with 10% neutral-buffered formalin is equivalent to 4% paraformaldehyde for histopathology and immunohistochemistry in a mouse model of experimental autoimmune encephalomyelitis. Veterinary pathology, 59(3), 498-505.
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4

Fluorescent Immunohistochemistry Imaging

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Zeiss LSM-Meta confocal microscope and ZEN 2009 software (Zeiss) was used to image slides from fluorescent immunohistochemical assays. Brightfield imaging of H&E stained slides was performed at 20X magnification using a Nanozoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, New Jersey). Apart from minor adjustments of contrast and brightness to the entire image, there was no additional image alteration. Figures were prepared on Adobe Illustrator.
Haldipur P., Bernardo S., Aldinger K.A., Sivakumar T., Millman J., Sjoboen A.H., Dang D., Dubocanin D., Deng M., Timms A.E., Davis B.D., Plummer J.T., Mankad K., Oztekin O., Manganaro L., Guimiot F., Adle-Biassette H., Russo R., Siebert J.R., Kidron D., Petrilli G., Roux N., Razavi F., Glass I.A., Di Gioia C., Silvestri E, & Millen K.J. (2021). Evidence of disrupted rhombic lip development in the pathogenesis of Dandy-Walker malformation. Acta neuropathologica, 142(4), 761-776.
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5

Dorsal Skin Histology Protocol

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To collect the dorsal skin, we used CO2 gas to euthanize all the mice. Portions of the dorsal skin biopsies were fixed in 4% paraformaldehyde and then moved to a 70% ethyl alcohol solution at 20–22 °C for 24 h. The samples were embedded in paraffin wax and sectioned into 4 µm slices. The skin sections were stained with hematoxylin and eosin (H&E) and toluidine blue. Stained slides were observed using a NanoZoomer Digital Pathology slide scanner and HCImage software (Hamamatsu Photonics, Milan, Italy).
Yun H.R., Ahn S.W., Seol B., Vasileva E.A., Mishchenko N.P., Fedoreyev S.A., Stonik V.A., Han J., Ko K.S., Rhee B.D., Seol J.E, & Kim H.K. (2021). Echinochrome A Treatment Alleviates Atopic Dermatitis-like Skin Lesions in NC/Nga Mice via IL-4 and IL-13 Suppression. Marine Drugs, 19(11), 622.
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6

Comprehensive Immunohistochemical and In Situ Hybridization Analysis

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Fixation, tissue processing, and immunohistochemistry were performed as previously described50 (link) using the following primary antibodies: Calbindin (Swant, CB38, rabbit, 1:3000), PAX6 (Biolegend, 901301, rabbit, 1:300), SKOR2 (Novus, NBP2–14565, rabbit, 1:100), and NEUN (Millipore, MAB377, mouse, 1:100). All sections were counterstained using Vectashield DAPI (H1000, Vector labs) which marks all nuclei.
In situ hybridization was performed using commercially available probes from Advanced Cell Diagnostics. Manufacturer recommended protocols available on the ACD webpage were used without modification. Probes used include: LMX1A (#540661), MKI67 (#591771), ATOH1 (#417861), OTX2 (#484581), and HOXB3 (custom-made). All sections were counterstained using Fast Green.
Slides processed for fluorescent IHC were imaged using Zeiss LSM Meta confocal microscope and ZEN 2009 software (Zeiss). Brightfield imaging was performed using a Nanozoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, New Jersey). Barring minor adjustments limited to contrast and brightness to the entire image, no additional image alteration was performed.
Aldinger K.A., Thomson Z., Phelps I.G., Haldipur P., Deng M., Timms A.E., Hirano M., Santpere G., Roco C., Rosenberg A.B., Lorente-Galdos B., Gulden F.O., O’Day D., Overman L.M., Lisgo S.N., Alexandre P., Sestan N., Doherty D., Dobyns W.B., Seelig G., Glass I.A, & Millen K.J. (2021). Spatial and cell-type transcriptional landscape of human cerebellar development. Nature neuroscience, 24(8), 1163-1175.
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7

Quantification of Islet Insulin and HA

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Islet insulin-stained areas were measured using ImageJ supported by the National Institutes of Health (https://imagej.nih.gov/ij/index.html). The measurement of total and intra-islet HA-positive (HA+) areas was performed using whole-section imaging as described (16 (link), 18 (link)).
Whole-section imaging was performed using a NanoZoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, NJ, USA). Slides were scanned in bright field with a 20× objective and the digital images imported for analysis using HALO image analysis software (Indica Labs, Albuquerque, NM, USA). Islets were identified by their staining for synaptophysin (SYN). All the islets present in the rat pancreas sections were analyzed. The intra-islet HA+ area represents the HA located within islet area bordered by the endocrine side of the peri-islet capillaries. The total islet HA area is the sum of the intra-islet HA+ and the HA+ area measured around the islets at a 5-nm distance from the endocrine side of the peri-islet capillaries (16 (link)). The outer border of this area was delineated using the HALO annotation tool. The stained areas were measured using HALO software. The percent islet HA+ area is calculated as intra-islet HA+ area/islet area × 100.
Bogdani M., Faxius L., Fex M., Ramelius A., Wernersson A., Mordes J.P., Blankenhorn E.P, & Lernmark Å. (2021). The Vbeta13 T Cell Receptor Monoclonal Antibody Reduces Hyaluronan and CD68+, CD3+, and CD8+ Cell Infiltrations to Delay Diabetes in Congenic BB DRLyp/Lyp Rats. Frontiers in Endocrinology, 12, 629242.
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8

Placental Proliferation and Apoptosis Assessment

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To assess the effect of supplementation on placental proliferation, apoptosis and DNA damage, explants from first trimester placentas (n = 12) of 7–12 weeks’ gestation were cultured as mentioned above. Tissue sections of 5 µm were placed on microscope slides for immunohistochemical labelling for assessment of proliferation (Ki67; Abcam®; ab16667), apoptosis (cleaved caspase-3; Cell Signalling Technology®; CST.9661L) or DNA damage (8-hydroxy-2’-deoxyguanosine; Abcam®; ab48508) (Table 1). A Hamamatsu NanoZoomer Digital Pathology slide scanner was used to scan the stained sections. Eight areas per explant tissue, randomly chosen using NDP.view2 software, were used for quantification and statistical analyses. Positively stained cells per mm2/area were counted.
Habibi N., Labrinidis A., Leemaqz S.Y., Jankovic-Karasoulos T., McCullough D., Grieger J.A., Gilbert S., Ricciardelli C., Zhou S.J., Perkins A.V., Roberts C.T, & Bianco-Miotto T. (2021). Effect of Selenium and Iodine on Oxidative Stress in the First Trimester Human Placenta Explants. Nutrients, 13(3), 800.
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9

Quantifying Pancreatic Endocrine Cell Types

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Islets were defined as groups of >20 endocrine cells56 (link)–58 (link) and smaller groups were defined as clusters. Estimation of the relative pancreatic area occupied by SYN, INS, or CHYM cells was performed as described53 (link), using a Nanozoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, New Jersey) at the Cellular and Molecular Imaging Core, DRC University of Washington, and the Visiopharm software (Hoersholm, Denmark).
Bogdani M., Blackman S.M., Ridaura C., Bellocq J.P., Powers A.C, & Aguilar-Bryan L. (2017). Structural abnormalities in islets from very young children with cystic fibrosis may contribute to cystic fibrosis-related diabetes. Scientific Reports, 7, 17231.
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10

Histological analysis of tumor samples

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Tumors were fixed in 10% formalin for 48 hours and paraffin embedded. 4 μm sections were stained with hematoxylin and eosin (H&E), Masson’s trichrome, or Picrosirius red at the University of Washington Histology Core. Primary antibodies used recognized CD163 (Novocastra, 10D6, 1:200), cleaved caspase 3 (Cell Signaling, D175, 1:200), and Ki67 (Thermo Fisher, clone SolA15, 1:200). Slides were scanned using the Nanozoomer Digital Pathology slide scanner (Hamamatsu; Bridgewater, New Jersey), and Visiopharm software (Hoersholm, Denmark) was used to identify regions of interest (ROI, i.e. tumor tissue, excluding normal tissue) sampled at 100%. The software was trained to detect immunoreactivity using a project-specific configuration based on a threshold of pixel values as we previously reported (6 (link)). The number of positively stained cells was measured in 3–5 non-overlapping 20X fields using NIS-Element imaging software (Nikon’s universal software platform, n=3–5 mice per group). Collagen was quantified from 2 tumor sections stained with Picrosirius red, and intensity of the red staining was assessed in a blinded manner across 3–5 20X fields as follows: 0, no staining detected; 1, light staining; 2, moderate; 3, moderate-high staining intensity; 4, high staining, as we previously described (6 (link)) (n= 3–6 animals per cohort).
Stromnes I.M., Burrack A.L., Hulbert A., Bonson P., Black C., Brockenbrough J.S., Raynor J.F., Spartz E.J., Pierce R.H., Greenberg P.D, & Hingorani S.R. (2019). Differential effects of depleting versus programming tumor-associated macrophages on engineered T cells in pancreatic ductal adenocarcinoma. Cancer immunology research, 7(6), 977-989.
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