Slide scanner

Manufactured by Hamamatsu Photonics

Sourced in Japan, Germany

The slide scanner is a device designed to capture high-resolution digital images of microscope slides. It functions by automatically scanning the contents of a slide and converting the visual information into a digital file format. The device is capable of producing detailed, reproducible images that can be used for various scientific and medical applications.

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Lab products found in correlation

Nanozoomer software, by Hamamatsu Photonics (5 mentions) Nanozoomer program, by Hamamatsu Photonics (2 mentions) Ndp2 viewer software, by Hamamatsu Photonics (2 mentions) α amylase, by Merck Group (2 mentions) Biotinylated goat anti rabbit igg, by Agilent Technologies (1 mentions) Streptavidin peroxidase, by R&D Systems (1 mentions) 3 3 diaminobenzidine (dab), by Agilent Technologies (1 mentions) Cell d, by Olympus (1 mentions) Periodic acid, by Avantor (1 mentions) Hematoxylin, by Avantor (1 mentions) Alcian blue, by Thermo Fisher Scientific (1 mentions) Schiffs, by Merck Group (1 mentions) Nuclear fast red, by Vector Laboratories (1 mentions) Ab64883, by Abcam (1 mentions) Ab13970, by Rockland Immunochemicals (1 mentions) Ab7778, by Abcam (1 mentions) Elastin, by Abcam (1 mentions) Collagen 3, by Abcam (1 mentions) A1 upright confocal microscope, by Nikon (1 mentions) Click it edu imaging kit, by Thermo Fisher Scientific (1 mentions)

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39 protocols using slide scanner

Comprehensive Tumor Characterization in Mice

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Mouse tumors were fixed in 10 % formalin, embedded in paraffin, and 5 μm slides were cut. Routine hematoxylin and eosin (H&E) staining was performed and assessed by a pathologist. For immunohistochemistry, slides were probed with primary antibodies against Ki67 (Novus Biologicals Ltd.) and CD31 (Abcam) to assess proliferation and blood vessel density and diameter, respectively. Biotinylated goat anti-rabbit IgG (Dako) was used as secondary antibody, and detection was performed with streptavidin–peroxidase (R&D Systems) and 3,3′-diaminobenzidine (Dako). Hematoxylin served as counterstain. Slides were scanned using a slide scanner (Hamamatsu Photonics). To measure proliferation, the percentage of Ki67-positive cells per tumor area was determined by using Cell^d (Olympus Life Science Europe GmbH). Apoptosis levels were determined by counting the number of apoptotic cells in proliferating tumor areas (×20) in H&E-stained slides. To determine vascular density, CD31-positive blood vessels were counted in 20 representative fields (×40) for each tumor. The vascular diameter of 30 vessels for each tumor was measured in ×63 high power fields.

Braks J.A., Spiegelberg L., Koljenovic S., Ridwan Y., Keereweer S., Kanaar R., Wolvius E.B, & Essers J. (2015). Optical Imaging of Tumor Response to Hyperbaric Oxygen Treatment and Irradiation in an Orthotopic Mouse Model of Head and Neck Squamous Cell Carcinoma. Molecular Imaging and Biology, 17(5), 633-642.

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Histological Analysis of Fish Skin

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At trial end, skin samples were taken from 3 fish per tank to evaluate general structure and mucous cell density. Tissue samples were stored in 10% formalin pots (CellStore™ 20 mL Pots, CellPath). Embedding, sectioning, and staining of the tissue samples were done at the Norwegian Veterinary Institute in Harstad, Norway. In brief, the tissue sections were hydrated in water and stained with 1% Alcian blue (Alfa Aesar), 3% acetic acid for 15 min, transferred to 1% periodic acid (VWR) for 10 min, followed by Schiffs (Sigma-Aldrich^®) reagent for 15 min, 30 s in hematoxylin (VWR) before dehydration and mounting. The stained tissue sections were scanned with a Hamamatsu slide scanner (Hamamatsu) and uploaded to the Aiforia^® platform and analysed according to Sveen et al. (2021) (link).

Kokkali M., Sveen L., Larsson T., Krasnov A., Giakovakis A., Sweetman J., Lyons P, & Kousoulaki K. (2023). Optimisation of trace mineral supplementation in diets for Atlantic salmon smolt with reference to holistic fish performance in terms of growth, health, welfare, and potential environmental impacts. Frontiers in Physiology, 14, 1214987.

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In situ Hybridization of miRNAs in CRC Tumors

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For in situ hybridization of miRNAs, 13 CRC tumours were used. Sections (5 µm) were cut in RNAse free water, deparaffinized, incubated with Proteinase-K (10 µg/ml) for 15 min at 37 °C, dehydrated and air-dried. Double-DIG-labelled miRNA probes (Exiqon, Denmark): miR-210 (40 nM) and scrambled (60 nM). Incubation was at 56 °C for 2 h with 25 µL of probe followed by washing with saline–sodium citrate. Slides were incubated with blocking buffer for 15 min, then with anti-DIG-Alkaline phophatase reagent (1:600, Exiqon, Denmark) at RT. Slides were washed with PBS–Tween and incubated with anti-AP substrate (NCT-BCIP, Roche, UK) for 2 h at RT, washed in water before counterstaining with Nuclear Fast Red (Vector, UK). Slides were rinsed in running tap water for 10 min, dehydrated, mounted with Eukkitt mounting medium (Sigma, UK) and then scanned using a Hamamatsu slide scanner.

Nijhuis A., Thompson H., Adam J., Parker A., Gammon L., Lewis A., Bundy J.G., Soga T., Jalaly A., Propper D., Jeffery R., Suraweera N., McDonald S., Thaha M.A., Feakins R., Lowe R., Bishop C.L, & Silver A. (2017). Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance. Human Molecular Genetics, 26(8), 1552-1564.

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Immunostaining of Skin Sections

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Paraffin- or optimal cutting temperature compound-embedded tissues were sectioned and stained6 (link)7 (link) using the following primary antibodies (all diluted 1:100 unless stated otherwise) for immunofluorescence labelling: Lrig: R&D Systems, FAB3688G; CD26: R&D Systems, AF954; Sca1: R&D Systems, AF1226; PDGFRa: R&D Systems, AF1062; Collagen III: Abcam, ab7778, Collagen11a1: Abcam, ab64883; Elastin: Abcam, ab21610; Caveolin: Cell Signaling Technology, 3267; phospho-Histone H3 (Ser10) antibody: Cell Signalling Technology, 970; Active Caspase-3: RnD Systems, AF835; K14: Covance, PRB-155P, 1:500; GFP: Abcam, ab13970, 1:500; RFP: Rockland, 600-401-379, 1:300. EdU staining was performed with a Click-it EdU imaging kit (Invitrogen) according to the manufacturer's recommendations. Images were acquired with a Nikon A1 Upright Confocal microscope. Images of H&E- and Herovici-stained sections were acquired with a Hamamatsu slide scanner. Representative images of skin from two to three independent experiments with at least three biological replicates per group are shown.

Lichtenberger B.M., Mastrogiannaki M, & Watt F.M. (2016). Epidermal β-catenin activation remodels the dermis via paracrine signalling to distinct fibroblast lineages. Nature Communications, 7, 10537.

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Aortic Morphometric Analysis in Animals

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For each animal, an aortic segment of 3 mm length was taken between the diaphragm and the hepatic artery, fixed in 4% PFA, embedded in paraffin, and cut into 6 µm serial cross-sections with a microtome. Sections were stained with Verhoeff’s solution, the first step in Van Gieson staining which highlights elastic laminae. Optical bright-field images acquired with a slide scanner (Nanozoomer, Hamamatsu, Japan) were digitally analyzed with simple image software (Fiji-ImageJ V1.8.0_172) (ImageJ, NIH, Bethesda, MD, USA) for morphometric analysis and elastin quantification. The morphometric analysis consisted of the measurement of internal and external perimeters of the tunica intima-media and then the inference of the internal and external diameters and media thickness. The values were averaged over 3 measurements for each vessel.

Desplanche E., Grillet P.E., Wynands Q., Bideaux P., Alburquerque L., Charrabi A., Bourdin A., Cazorla O., Gouzi F, & Virsolvy A. (2023). Elevated Blood Pressure Occurs without Endothelial Dysfunction in a Rat Model of Pulmonary Emphysema. International Journal of Molecular Sciences, 24(16), 12609.

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Immunohistochemical Analysis of ECM Proteins

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Immunohistochemical staining was performed using a standard protocol. Endogenous peroxidases were blocked using hydrogen peroxide.
Nonspecific binding was prevented by applying Dako Dual Endogenous Enzyme Block (Dako/Agilent; S2003). The following primary polyclonal rabbit antibodies were used: anti-mouse laminin (Dako/Agilent – Z009701-2; 1:1.000 dilution), anti-mouse elastin (Abcam – ab21610; 1:100 dilution), anti-mouse type I collagen (Abcam – ab34710; 1:500 dilution), and anti-mouse type IV collagen (Abcam – ab6586; 1:500 dilution).
The target antigens were visualized using a secondary anti-rabbit antibody labeled with a horseradish peroxidase polymer and DAB as the substrate (Dako Envision + System, HRP, labeled Polymer Anti-Rabbit). Hematoxylin was applied for 7 min as a counterstain for the detection of cell nuclei. Sections were digitalized using a Hamamatsu slide scanner.

Felgendreff P., Schindler C., Mussbach F., Xie C., Gremse F., Settmacher U, & Dahmen U. (2021). Identification of tissue sections from decellularized liver scaffolds for repopulation experiments. Heliyon, 7(2), e06129.

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Quantifying Extracellular Matrix Patterns

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All stained sections were scanned with a Slide Scanner (Hamamatsu Photonics K.K., Herrsching, Germany) at 20× magnification (Figure 1e). PSR fluorescent images (PSR-fluo) were generated with Zeiss LSM 780 CLSM confocal microscope (Carl Zeiss NTS GmbH, Oberkochen, Germany), λ_ex 561 nm/λ_em 566/670 nm at 40× magnification [38 (link)]. COL1A1, Elastin scans and PSR-fluo images were analyzed with TWOMBLI, an ImageJ/Fiji [39 (link)] plugin to quantify patterns in ECM [40 (link)]. Before analyzing the COL1A1 and Elastin, the Vector^® NovaRED™ color was isolated from the images using a color deconvolution plugin [41 (link)]. The images with only Vector^® NovaRED™ color were subsequently used for the analysis.
TWOMBLI was used to determine the number of fibers, end points, branching points, total fiber length and alignment, lacunarity (number and size of gaps in the matrix) and high-density matrix proportion (measure for compactness of matrix).

Martinez-Garcia F.D., de Hilster R.H., Sharma P.K., Borghuis T., Hylkema M.N., Burgess J.K, & Harmsen M.C. (2021). Architecture and Composition Dictate Viscoelastic Properties of Organ-Derived Extracellular Matrix Hydrogels. Polymers, 13(18), 3113.

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Establishment of Patient-Derived Xenograft Models

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PDCs were transferred to Oncotest as frozen vials. On site, the cells were thawed, the freezing medium was removed, and the cells were resuspended and transferred into T75 flasks. Cells were grown for 3 to 7 days in RPMI/10% FBS until the culture reached around 80% confluence. Cells were collected and counted, and 5 × 10⁶ cells were injected into the hind flanks of NOD scid gamma (NOG) mice (Taconic). Tumors developed within 25 to 85 days after injection; these tumors were explanted, and viable portions of the tumors were cut into pieces and implanted subcutaneously into female NMRI nu/nu mice (Harlan Laboratories). This process was repeated in order to serially passage the respective models. From each passage, formalin-fixed, paraffin-embedded (FFPE) blocks were prepared, and tumor slices were stained with hematoxylin and eosin (H&E). Slides were scanned with a Hamamatsu slide scanner, and images were extracted using the Nanozoomer program from Hamamatsu. All animal handling and experiments with animals were in accordance with the guidelines set by the Samsung Biological Research Institute.

Kim H.K., Kim S.Y., Lee S.J., Kang M., Kim S.T., Jang J., Rath O., Schueler J., Lee D.W., Park W.Y., Kim S.J., Park S.H, & Lee J. (2016). BEZ235 (PIK3/mTOR inhibitor) Overcomes Pazopanib Resistance in Patient-Derived Refractory Soft Tissue Sarcoma Cells. Translational Oncology, 9(3), 197-202.

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Quantifying B16F10 Melanoma Metastasis

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B16F10 melanoma cells growing in log phase were harvested and suspended in PBS. 2 × 10⁵, or 10⁶ cells were injected into mice through the retro-orbital or tail vein. Fourteen days later post-injection, the recipient mice were euthanized, 10 ml PBS was used for a right ventricular flush, and the lungs were excised. Each set of lungs were photographed, and the lung nodules were counted. For early B16F10 metastasis formation, 10⁶ cells were injected, and the lungs were analyzed on day 7 of post-injection. For optimal metastasis, 2 × 10⁵ B16F10 cells were injected, and the lungs were analyzed on day 14 of post-injection. Tumor nodules in the lung were counted in a blinded manner. Lungs were fixed in 10% (v/v) neutral buffered formalin for 24–72 h. After fixing, tissues were dehydrated through graded ethanol, cleared with xylene, paraffin infiltrated (Sakura VIP5 automated tissue processor) and embedded into tissue blocks. Tissue blocks were cut at 4 μm and mounted on poly-L-lysine coated slides. Sections were deparaffinized with xylene, rehydrated, and stained with Hematoxylin and Eosin on an automated staining platform (Sakura Prisma). Stained slides were scanned using a Hamamatsu Slide scanner and viewed using NDPiView software.

Nanbakhsh A., Mani A., Holzhauer S., Riese M., Zheng Y., Wang D., Burns R., Reimer M.H., Rao S., Lemke A., Tsaih S.W., Flister M.J., Dahl R., Lao S., Thakar M.S, & Malarkannan S. (2019). MicroRNA Mirc11 optimizes the inflammatory responses by silencing ubiquitin modifiers and altering K63 and K48 ubiquitylation of TRAF6. Cancer immunology research, 7(10), 1647-1662.

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Liver Regeneration Histological Analysis

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Livers from C57/Bl6N mice (Charles River, Sulzfeld, Germany) were explanted before, 24 hr after, and 48 hr after 70% liver resection following the technique described in previous work.⁶⁷ (link) All procedures and housing of the animals were strictly carried out according to the German animal welfare legislation (reference numbers 02-123-10, 02-123-10, 02-122-12). After formalin fixation and paraffin embedding the whole livers were subjected to serial sectioning (4 μm) followed by repeated serial staining. Every 25 sections, 2 serial sections were stained with H&E and GS. Sections were scanned using a Hamamatsu slide scanner at 400-fold magnification resulting in a resolution of 227 nm per pixel. From the total of 92 H&E and GS pairs, we randomly chose a subset of 30 pairs of neighboring H&E and GS for further processing.

Budelmann D., Laue H., Weiss N., Dahmen U., D’Alessandro L.A., Biermayer I., Klingmüller U., Ghallab A., Hassan R., Begher-Tibbe B., Hengstler J.G, & Schwen L.O. (2022). Automated Detection of Portal Fields and Central Veins in Whole-Slide Images of Liver Tissue. Journal of Pathology Informatics, 13, 100001.

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