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Npd view2

Manufactured by Hamamatsu Photonics
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Sourced in Japan, China

The NPD.view2 software is a data visualization and analysis tool developed by Hamamatsu Photonics. It is designed to display and process data from various types of photodetectors and imaging devices.

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Lab products found in correlation

Ab16669, by Thermo Fisher Scientific (2 mentions) Arginase 1, by Cell Signaling Technology (2 mentions) Nanozoomer 2.0 ht, by Meyer Instruments (2 mentions) Deepfx handpiece, by Lumenis (2 mentions) Nanozoomer, by Hamamatsu Photonics (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Nanozoomer 2.0 ht slide scanner, by Hamamatsu Photonics (1 mentions) Xylene, by Chem-Supply (1 mentions) Citric acid monohydrate, by Merck Group (1 mentions) Ethanol, by Merck Group (1 mentions)

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View2 software (8 citations)

9 protocols using npd view2

1

Placental Glycogen Cell Analysis

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Formalin-fixed paraffin-embedded tissue sections (4μm) were cut and stained with hematoxylin and eosin for histological examination. Slides were digitized using the NanoZoomer 2.0-HT slide scanner (Hamamatsu Photonics, Boston, MA, USA) and analysed using the software NPDview2 (Hamamatsu Photonics). Number and area of clusters of glycogen cells were evaluated on two sections per placenta, and six placentas from different litters in each group.
Bibeau K., Sicotte B., Béland M., Bhat M., Gaboury L., Couture R., St-Louis J, & Brochu M. (2016). Placental Underperfusion in a Rat Model of Intrauterine Growth Restriction Induced by a Reduced Plasma Volume Expansion. PLoS ONE, 11(1), e0145982.
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2

Histological Evaluation of Glandular Structures

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Here, 4-μm-thick sections were obtained for histological examination. Samples were then stained with hematoxylin and eosin and evaluated according to previously reported data [27 (link)] through the NPD View 2 viewing software (Hamamatsu Photonics, Korea). The biopsy assessment included evaluation of the glandular density and diameter, height of the luminal epithelia, and white blood cell counts.
Glandular density was evaluated by counting the number of glands in 10 randomly selected fields at 400× magnification in both the stratum spongiosum and the stratum compactum. Glandular diameter was evaluated by considering the mean of two perpendicular diameters of each gland (from the basal lamina to the opposite one), measured in the stratum spongiosum. A total of 30 randomly selected glands were studied at 400× magnification. The height of the luminal epithelia was determined by measuring a total of 30 randomly selected cells from the basal lamina to the apical membrane, recorded at 400× magnification. Neutrophil counting was performed by counting in 10 randomly selected fields at 400× magnification. A mean for each variable was calculated for each sample.
Martí A., Serrano A., Pastor J., Rigau T., Petkevičiuté U., Calvo M.À., Arosemena E.L., Yuste A., Prandi D., Aguilar A, & Rivera del Alamo M.M. (2021). Endometrial Status in Queens Evaluated by Histopathology Findings and Two Cytological Techniques: Low-Volume Uterine Lavage and Uterine Swabbing. Animals : an Open Access Journal from MDPI, 11(1), 88.
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3

Immunohistochemical Analysis of Tumor Samples

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Hematoxylin staining and immunostaining were performed on paraffin sections of tumors. Antibodies used were against LILRB4 (lab produced, 1:100), CD3 (Abcam, ab16669, 1:100), PD-1 (Thermo Fisher, J116, 14–9989-82, 1:100) and Arginase-1 (Cell signaling, 9819S, 1:100). The images were visualized using the Hamamatsu NanoZoomer 2.0-HT (Meyer instruments Inc., Houston, TX) and viewed in NPDview2 software (Hamamatsu, Japan).
Deng M., Gui X., Kim J., Xie L., Chen W., Li Z., He L., Chen Y., Chen H., Luo W., Lu Z., Xie J., Churchill H., Xu Y., Zhou Z., Wu G., Yu C., John S., Hirayasu K., Nguyen N., Liu X., Huang F., Li L., Deng H., Tang H., Sadek A.H., Zhang L., Huang T., Zou Y., Chen B., Zhu H., Arase H., Xia N., Jiang Y., Collins R., You M.J., Homsi J., Unni N., Lewis C., Chen G.Q., Fu Y.X., Liao X.C., An Z., Zheng J., Zhang N, & Zhang C.C. (2018). LILRB4 signaling in leukemia cells mediates T cell suppression and tumor infiltration. Nature, 562(7728), 605-609.
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4

Histological Evaluation of Organ Tissues

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The organs were fixed in neutrally buffered 4% formalin before embedding in paraffin. Afterwards, the sections were stained with hematoxylin and eosin (HE) or naphthyl acetate (chloro-)esterase (NACE). Histological figures and quantitative evaluation of lung specimen were done using NPD.view2 software (Hamamatsu) by measuring maximum extend of bronchial epithelia or smooth muscle cells of arterial vessels at three positions in the lung, three measurements each. Blood and bone marrow smears were prepared and Pappenheim stained for the differentiation of the hematopoietic cells (100 cells in the blood smear and 200 in the bone marrow).
Schubert C., Chatain N., Braunschweig T., Schemionek M., Feldberg K., Hoffmann M., Dufva O., Mustjoki S., Brümmendorf T.H, & Koschmieder S. (2017). The SCLtTAxBCR-ABL transgenic mouse model closely reflects the differential effects of dasatinib on normal and malignant hematopoiesis in chronic phase-CML patients. Oncotarget, 8(21), 34736-34749.
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5

Fractional CO2 Laser Skin Irradiation

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AFL irradiation was performed using an Ultrapulse CO2 laser with a DeepFx handpiece (10,600 nm; Lumenis). Laser‐induced channels were generated using a single pulse at 15 mJ/microbeam (mJ/mb), 5% density (196 microscopic ablation zone [MAZ]/cm2), 0.12 mm spot size, and pulse duration of ~250 µs without overlap. Laser‐channel dimensions were measured in representative histological images of vertical skin sections originating from four 6‐mm punch biopsies immediately after irradiation. Distinct laser channel dimensions (n = 10) were measured using NPD.view2 software (Hamamatsu Photonics) as previously described (Figure 1).21
Wenande E., Gundavarapu S.C., Tam J., Bhayana B., Thomas C.N., Farinelli W.A., Vakoc B.J., Anderson R.R, & Haedersdal M. (2022). Local vasoregulative interventions impact drug concentrations in the skin after topical laser‐assisted delivery. Lasers in Surgery and Medicine, 54(10), 1288-1297.
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6

Laser-Induced Skin Channels Characterization

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AFL irradiation was performed using an Ultrapulse CO2 laser with a DeepFx handpiece (10,600 nm; Lumenis). Laser-induced channels were generated using a single pulse at 15 mJ/microbeam (mJ/mb), 5% density (196 microscopic ablation zone [MAZ]/cm2), 0.12 mm spot size, and pulse duration of ~250 μs without overlap. Laser-channel dimensions were measured in representative histological images of vertical skin sections originating from four 6-mm punch biopsies immediately after irradiation. Distinct laser channel dimensions (n = 10) were measured using NPD.view2 software (Hamamatsu Photonics) as previously described (Figure 1).21 (link)
Wenande E., Gundavarapu S.C., Tam J., Bhayana B., Thomas C.N., Farinelli W.A., Vakoc B.J., Anderson R.R, & Haedersdal M. (2022). Local vasoregulative interventions impact drug concentrations in the skin after topical laser‐assisted delivery. Lasers in Surgery and Medicine, 54(10), 1288-1297.
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7

Immunohistochemical Analysis of Tumor Samples

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Hematoxylin staining and immunostaining were performed on paraffin sections of tumors. Antibodies used were against LILRB4 (lab produced, 1:100), CD3 (Abcam, ab16669, 1:100), PD-1 (Thermo Fisher, J116, 14–9989-82, 1:100) and Arginase-1 (Cell signaling, 9819S, 1:100). The images were visualized using the Hamamatsu NanoZoomer 2.0-HT (Meyer instruments Inc., Houston, TX) and viewed in NPDview2 software (Hamamatsu, Japan).
Deng M., Gui X., Kim J., Xie L., Chen W., Li Z., He L., Chen Y., Chen H., Luo W., Lu Z., Xie J., Churchill H., Xu Y., Zhou Z., Wu G., Yu C., John S., Hirayasu K., Nguyen N., Liu X., Huang F., Li L., Deng H., Tang H., Sadek A.H., Zhang L., Huang T., Zou Y., Chen B., Zhu H., Arase H., Xia N., Jiang Y., Collins R., You M.J., Homsi J., Unni N., Lewis C., Chen G.Q., Fu Y.X., Liao X.C., An Z., Zheng J., Zhang N, & Zhang C.C. (2018). LILRB4 signaling in leukemia cells mediates T cell suppression and tumor infiltration. Nature, 562(7728), 605-609.
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8

FFPE Tissue Microdissection and Protein Extraction

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FFPE tissue blocks (n = 6 chemo-responsive and n = 6 non-responsive tissues) were water-bath-mounted onto PEN membrane slides (MicroDissect, Herborn, Germany) at 4 µm, as previously described [20 (link),21 (link)]. Briefly, the slides were deparaffinized by heating at 60 °C for 1 h, followed by rehydration using xylene (Chem-Supply, Gillman, Australia) for 90 s and then rinsed for 60 s with 100% ethanol (Merck, Bayswater, Australia). Slides were hematoxylin-stained and scanned using a NanoZoomer (Hamamatsu, Japan) at 43 × resolution (0.23 µm/pixel), and the tissues were annotated by an experienced pathologist using NPD.view 2.6.13 (Hamamatsu, Beijing, China). Approximately 1 mm2 per region of each tumor tissue was excised by laser capture microdissection (LCM) using a Leica microscope (Leica Microsystems, Wetzlar, Germany) into individual centrifuge tubes. Excised tissues were lysed using 2% SDS (GE Healthcare, Parramata, Australia) in 10 mM citric acid, pH 6 (citric acid monohydrate, Sigma-Aldrich, Japan), followed by antigen retrieval at 98 °C for 90 min. The total protein concentration of each sample was estimated using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA) at 280 nm.
Arentz G., Mittal P., Klingler-Hoffmann M., Condina M.R., Ricciardelli C., Lokman N.A., Kaur G., Oehler M.K, & Hoffmann P. (2023). Label-Free Quantification Mass Spectrometry Identifies Protein Markers of Chemotherapy Response in High-Grade Serous Ovarian Cancer. Cancers, 15(7), 2172.
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9

Tissue Imaging and Annotation Protocol

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Following data acquisition, matrix was removed using 50% ethanol (v/v, Merck) for 5 min and H&E stained for pathological examination. Slides were scanned using a nanozoomer (Hamamatsu, China) at 43 × resolution (0.23 µm/pixel), annotated by one experienced pathologist using NPD.view 2.6.13 (Hamamatsu, China) and co- registered to MALDI MSI data using flexImaging software.
Mittal P., Condina M.R., Klingler-Hoffmann M., Kaur G., Oehler M.K., Sieber O.M., Palmieri M., Kommoss S., Brucker S., McDonnell M.D, & Hoffmann P. (2021). Cancer Tissue Classification Using Supervised Machine Learning Applied to MALDI Mass Spectrometry Imaging. Cancers, 13(21), 5388.
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