Ndp scan software v3

Manufactured by Hamamatsu Photonics

NDP.scan software v3.2.4 is a digital imaging software designed to operate with Hamamatsu's NanoZoomer digital slide scanners. The software enables the user to capture, view, and manage digital images of microscopic samples.

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Lab products found in correlation

Autostainer link 48, by Agilent Technologies (8 mentions) 3 3 diaminobenzidine tetrahydrochloride, by Agilent Technologies (7 mentions) Envision flex target retrieval solution high ph, by Agilent Technologies (5 mentions) Envision flex, by Agilent Technologies (3 mentions) Envision flex target retrieval solution high, by Agilent Technologies (2 mentions)

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8 protocols using ndp scan software v3

SARS-CoV-2 Nucleoprotein Immunohistochemistry

Cited 2 times

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IHC (Figures 4C, S2A, and S4B) was performed as previously described (Saito et al., 2022 (link); Suzuki et al., 2022 (link)) using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 m at 97°C to activate, and mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX (Agilent) for 15 m and visualized by peroxidase-based enzymatic reaction with 3,3’-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 m. The N protein positivity (Figures 4D and 4E) was evaluated by certificated pathologists as previously described (Suzuki et al., 2022 (link)). Images were incorporated as virtual slide by NDP.scan software v3.2.4 (Hamamatsu Photonics). The N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Yamasoba D., Kimura I., Nasser H., Morioka Y., Nao N., Ito J., Uriu K., Tsuda M., Zahradnik J., Shirakawa K., Suzuki R., Kishimoto M., Kosugi Y., Kobiyama K., Hara T., Toyoda M., Tanaka Y.L., Butlertanaka E.P., Shimizu R., Ito H., Wang L., Oda Y., Orba Y., Sasaki M., Nagata K., Yoshimatsu K., Asakura H., Nagashima M., Sadamasu K., Yoshimura K., Kuramochi J., Seki M., Fujiki R., Kaneda A., Shimada T., Nakada T.A., Sakao S., Suzuki T., Ueno T., Takaori-Kondo A., Ishii K.J., Schreiber G., Sawa H., Saito A., Irie T., Tanaka S., Matsuno K., Fukuhara T., Ikeda T, & Sato K. (2022). Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell, 185(12), 2103-2115.e19.

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SARS-CoV-2 Nucleoprotein Immunohistochemistry

Cited 4 times

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Immunohistochemical (IHC) analysis (Fig. 6c and Supplementary Fig. 6) was performed as previously described^{2 ,5 (link),10 (link),25 (link)–27 (link)} using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 min at 97 °C for activation, and a mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D Systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX for 15 min and visualized by peroxidase-based enzymatic reaction with 3,3’-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 min. The N protein positivity was evaluated by certificated pathologists as previously described^{2 ,5 (link),10 (link),25 (link)–27 (link)}. Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). The N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Tamura T., Ito J., Uriu K., Zahradnik J., Kida I., Anraku Y., Nasser H., Shofa M., Oda Y., Lytras S., Nao N., Itakura Y., Deguchi S., Suzuki R., Wang L., Begum M.M., Kita S., Yajima H., Sasaki J., Sasaki-Tabata K., Shimizu R., Tsuda M., Kosugi Y., Fujita S., Pan L., Sauter D., Yoshimatsu K., Suzuki S., Asakura H., Nagashima M., Sadamasu K., Yoshimura K., Yamamoto Y., Nagamoto T., Schreiber G., Maenaka K., Hashiguchi T., Ikeda T., Fukuhara T., Saito A., Tanaka S., Matsuno K., Takayama K, & Sato K. (2023). Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nature Communications, 14, 2800.

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SARS-CoV-2 N Protein Immunohistochemistry

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Immunohistochemistry (IHC) (Figs. 5C and 7D) was performed as previously described using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 minutes at 97 °C for activation, and a mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D Systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX for 15 minutes and visualized by peroxidase-based enzymatic reaction with 3,3′-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 minutes. The N-protein positivity was evaluated by certificated pathologists as previously described. Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). The area of N-protein positivity was measured using Fiji software v2.2.0 (ImageJ).

Tamura T., Irie T., Deguchi S., Yajima H., Tsuda M., Nasser H., Mizuma K., Plianchaisuk A., Suzuki S., Uriu K., Begum M.M., Shimizu R., Jonathan M., Suzuki R., Kondo T., Ito H., Kamiyama A., Yoshimatsu K., Shofa M., Hashimoto R., Anraku Y., Kimura K.T., Kita S., Sasaki J., Sasaki-Tabata K., Maenaka K., Nao N., Wang L., Oda Y., Ikeda T., Saito A., Matsuno K., Ito J., Tanaka S., Sato K., Hashiguchi T., Takayama K, & Fukuhara T. (2024). Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant. Nature Communications, 15, 1176.

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SARS-CoV-2 N Protein Immunohistochemistry

Cited 3 times

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IHC (Figures 5D, S3A, and S3B) was performed as previously described (Saito et al., 2022 (link); Suzuki et al., 2022 (link); Yamasoba et al., 2022b (link)) using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 minutes at 97°C to activate, and mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX (Agilent) for 15 minutes and visualized by peroxidase-based enzymatic reaction with 3,3’-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 minutes. The N protein positivity (Figures 5D, S3A, and S3B) was evaluated by certificated pathologists as previously described (Suzuki et al., 2022 (link); Yamasoba et al., 2022b (link)). Images were incorporated as virtual slide by NDP.scan software v3.2.4 (Hamamatsu Photonics). The N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Kimura I., Yamasoba D., Tamura T., Nao N., Suzuki T., Oda Y., Mitoma S., Ito J., Nasser H., Zahradnik J., Uriu K., Fujita S., Kosugi Y., Wang L., Tsuda M., Kishimoto M., Ito H., Suzuki R., Shimizu R., Begum M.M., Yoshimatsu K., Kimura K.T., Sasaki J., Sasaki-Tabata K., Yamamoto Y., Nagamoto T., Kanamune J., Kobiyama K., Asakura H., Nagashima M., Sadamasu K., Yoshimura K., Shirakawa K., Takaori-Kondo A., Kuramochi J., Schreiber G., Ishii K.J., Hashiguchi T., Ikeda T., Saito A., Fukuhara T., Tanaka S., Matsuno K, & Sato K. (2022). Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell, 185(21), 3992-4007.e16.

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Immunohistochemical Analysis of SARS-CoV-2 N Protein in Hamster Tissues

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IHC was performed using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 min at 97 °C for activation, and mouse anti-SARS-CoV-2 N monoclonal antibody (R&D Systems, Clone 1035111, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX (Agilent) for 15 min and visualized by peroxidase-based enzymatic reaction with 3,3′-diaminobenzidine tetrahydrochloride as a substrate for 5 min.
For the evaluation of N protein positivity in the tracheae at 2 d.p.i. and the lung specimens of infected hamsters at 2 and 5 d.p.i. (B1.1, BA.1, BA.2, and BA.5, n = 4 each), staining was performed with mouse anti-SARS-CoV-2 N monoclonal antibody (1:400). N-protein positivity was evaluated by certified pathologists as previously described^{9 (link),11 (link)}. Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Tamura T., Yamasoba D., Oda Y., Ito J., Kamasaki T., Nao N., Hashimoto R., Fujioka Y., Suzuki R., Wang L., Ito H., Kashima Y., Kimura I., Kishimoto M., Tsuda M., Sawa H., Yoshimatsu K., Yamamoto Y., Nagamoto T., Kanamune J., Suzuki Y., Ohba Y., Yokota I., Matsuno K., Takayama K., Tanaka S., Sato K, & Fukuhara T. (2023). Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5. Communications Biology, 6, 772.

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SARS-CoV-2 N Protein Immunohistochemistry

Cited 4 times

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Immunohistochemical (IHC) analysis (Fig. 6c and Supplementary Fig. 4) was performed as previously described^{2 (link),17 (link),26 (link),31 (link),35} using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 min at 97°C for activation, and a mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D Systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX for 15 min and visualized by peroxidase-based enzymatic reaction with 3,3’-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 min. The N protein positivity was evaluated by certificated pathologists as previously described^{2 (link),17 (link),26 (link),31 (link),35}. Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). The N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Ito J., Suzuki R., Uriu K., Itakura Y., Zahradnik J., Kimura K.T., Deguchi S., Wang L., Lytras S., Tamura T., Kida I., Nasser H., Shofa M., Begum M.M., Tsuda M., Oda Y., Suzuki T., Sasaki J., Sasaki-Tabata K., Fujita S., Yoshimatsu K., Ito H., Nao N., Asakura H., Nagashima M., Sadamasu K., Yoshimura K., Yamamoto Y., Nagamoto T., Kuramochi J., Schreiber G., Saito A., Matsuno K., Takayama K., Hashiguchi T., Tanaka S., Fukuhara T., Ikeda T, & Sato K. (2023). Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nature Communications, 14, 2671.

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SARS-CoV-2 Nucleoprotein Immunohistochemistry

Cited 3 times

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Immunohistochemistry (IHC) (Figures 5D and S5A–S5C) was performed as previously described (Kimura et al., 2022b (link), 2022c (link); Yamasoba et al., 2022a (link); Suzuki et al., 2022 (link); Saito et al., 2022 (link); Tamura et al., 2022 (link)) using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent, Cat# K8004) for 20 minutes at 97°C for activation, and a mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D Systems, Cat# MAB10474-SP, 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX for 15 minutes and visualized by peroxidase-based enzymatic reaction with 3,3’-diaminobenzidine tetrahydrochloride (Dako, Cat# DM827) as substrate for 5 minutes. The N protein positivity (Figures 5D and S5A–S5C) was evaluated by certificated pathologists as previously described (Kimura et al., 2022b (link), 2022c (link); Yamasoba et al., 2022a (link); Suzuki et al., 2022 (link); Saito et al., 2022 (link); Tamura et al., 2022 (link)). Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). The N-protein positivity was measured as the area using Fiji software v2.2.0 (ImageJ).

Saito A., Tamura T., Zahradnik J., Deguchi S., Tabata K., Anraku Y., Kimura I., Ito J., Yamasoba D., Nasser H., Toyoda M., Nagata K., Uriu K., Kosugi Y., Fujita S., Shofa M., Monira Begum M., Shimizu R., Oda Y., Suzuki R., Ito H., Nao N., Wang L., Tsuda M., Yoshimatsu K., Kuramochi J., Kita S., Sasaki-Tabata K., Fukuhara H., Maenaka K., Yamamoto Y., Nagamoto T., Asakura H., Nagashima M., Sadamasu K., Yoshimura K., Ueno T., Schreiber G., Takaori-Kondo A., Shirakawa K., Sawa H., Irie T., Hashiguchi T., Takayama K., Matsuno K., Tanaka S., Ikeda T., Fukuhara T, & Sato K. (2022). Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant. Cell Host & Microbe, 30(11), 1540-1555.e15.

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SARS-CoV-2 N Protein Immunohistochemistry

Cited 9 times

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IHC was performed as previously described²⁴ (link)^,²⁵ (link)^,²⁶ (link)^,²⁷ (link)^,²⁸ (link)^,²⁹ (link)^,³⁰ (link)^,³¹ (link)^,³² (link)^,³³ (link) using an Autostainer Link 48 (Dako). The deparaffinized sections were exposed to EnVision FLEX target retrieval solution high pH (Agilent) for 20 min at 97°C for activation, and a mouse anti-SARS-CoV-2 N monoclonal antibody (clone 1035111, R&D Systems, dilution 1:400) was used as a primary antibody. The sections were sensitized using EnVision FLEX for 15 min and visualized by peroxidase-based enzymatic reaction with 3,3′-diaminobenzidine tetrahydrochloride (Dako) as substrate for 5 min. Images were incorporated as virtual slides by NDP.scan software v3.2.4 (Hamamatsu Photonics). The area of N-protein positivity was measured using Fiji software v2.2.0 (ImageJ).

Tamura T., Ito H., Torii S., Wang L., Suzuki R., Tsujino S., Kamiyama A., Oda Y., Tsuda M., Morioka Y., Suzuki S., Shirakawa K., Sato K., Yoshimatsu K., Matsuura Y., Iwano S., Tanaka S, & Fukuhara T. (2024). Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection. iScience, 27(5), 109647.

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