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Pannoramic viewer 1

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The Pannoramic Viewer 1.15.4 is a digital slide viewer software developed by 3DHISTECH. It is designed to enable the visualization and analysis of high-resolution digital pathology images.

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Lab products found in correlation

Pannoramic scan, by 3DHISTECH (8 mentions) Pannoramic scan 250 flash, by 3DHISTECH (6 mentions) Secondary anti rabbit igg, by ZSGB-BIO (2 mentions) Pannoramic scan 250, by 3DHISTECH (2 mentions) 3 3 diaminobenzidine (dab), by ZSGB-BIO (2 mentions) Cleaved caspase 3 asp175, by Cell Signaling Technology (2 mentions) Cd3 a0452, by Agilent Technologies (2 mentions) Axioimager z2 system, by Zeiss (2 mentions) Ki67 vp k451, by Vector Laboratories (2 mentions) Mib 1 monoclonal antibody, by Agilent Technologies (2 mentions) Mirax midi, by 3DHISTECH (2 mentions) Caseviewer 3, by 3DHISTECH (2 mentions) Histoquant software, by 3DHISTECH (2 mentions) Pannoramic midi whole slide scanner, by 3DHISTECH (2 mentions) Pannoramic midi bf fl, by 3DHISTECH (2 mentions) Pannoramic 250 flash scanner, by 3DHISTECH (1 mentions) Mirax midi slide scanner, by Zeiss (1 mentions) Anti ng2, by Merck Group (1 mentions) Anti cd31, by BioLegend (1 mentions) Anti rabbit af568, by Thermo Fisher Scientific (1 mentions)

41 protocols using pannoramic viewer 1

1

Immunohistochemical Analysis of Tumor Samples

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Tumor tissue samples were fixed in 4% paraformaldehyde and embedded in paraffin according to standard procedures. Sections were incubated with the indicated primary antibodies overnight at 4 °C. Subsequently, the slides were incubated with a secondary anti-rabbit or anti-mouse IgG (ZSGB-BIO, Beijing, China) and visualized using 3,3′-diaminobenzidine (ZSGB-BIO). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system and images were acquired using Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary). Images were analyzed using Image Pro Plus software.
Li D., Yao Y., Rao Y., Huang X., Wei L., You Z., Zheng G., Hou X., Su Y., Varghese Z., Moorhead J.F., Chen Y, & Ruan X.Z. (2022). Cholesterol sensor SCAP contributes to sorafenib resistance by regulating autophagy in hepatocellular carcinoma. Journal of Experimental & Clinical Cancer Research : CR, 41, 116.
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2

Histopathological Analysis of Rete Pegs

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Samples fixed in 4% paraformaldehyde were dehydrated through graded ethanol baths (100–70%), cleared in xylene and then embedded in paraffin wax. The paraffin blocks were serially sectioned at 5 μm thickness, using a Leica RM2125 rotary microtome (RM2125 RTS; Leica, Wetzlar, Germany). The sections were stained with hematoxylin–eosin, scanned using the Pannoramic 250 FLASH scanner and evaluated using the Pannoramic viewer 1.15.2 software (3D HISTECH, Budapest, Hungary). The length and density of rete pegs were analyzed in five random areas per slice using Image J software (National Institutes of Health, Bethesda, MA, USA).
Li Y., Du Z., Xie X., Zhang Y., Liu H., Zhou Z., Zhao J., Lee R.S., Xiao Y., Ivanoviski S, & Yan F. (2021). Epigenetic changes caused by diabetes and their potential role in the development of periodontitis. Journal of Diabetes Investigation, 12(8), 1326-1335.
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3

Histological Analysis of Liver Samples

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Liver samples were fixed in fresh 4% paraformaldehyde and subjected to routine histological procedures for embedding in paraffin. Then, the samples were cut in 4.5 μm-thick sections that were processed for hematoxylin and eosin (HE) or IHC staining with antibodies targeting PCK1 (1:500), pAMPK (1:200), or p27Kip1 (1:500). For IHC assays, the sections were incubated with secondary anti-rabbit IgG (ZSGB-BIO, Beijing, China) and stained with 3,3′-diaminobenzidine (ZSGB-BIO). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system and images were acquired using Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary).
Tuo L., Xiang J., Pan X., Hu J., Tang H., Liang L., Xia J., Hu Y., Zhang W., Huang A., Wang K, & Tang N. (2019). PCK1 negatively regulates cell cycle progression and hepatoma cell proliferation via the AMPK/p27Kip1 axis. Journal of Experimental & Clinical Cancer Research : CR, 38, 50.
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4

Histological Analysis of Organ Samples

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Organ samples were fixed in fresh 4% paraformaldehyde at 4 °C overnight and further subjected to routine histological procedures for embedding in paraffin. 5-μm sections of the samples from at least three different animals per group were placed on microscopic slides next to one another to enable cross-comparison within a slide after H&E staining or IHC staining with the antibodies indicated. Antibodies used were GFP (D5.1) XP, PTEN (D4.3), phospho (p)-AKT (S473) (D9E), p-ribosomal protein S6 (S235/236) (D57.2.2E), Cleaved Caspase-3 (Asp175) (all: Cell Signaling Technologies, Danvers, MA), Ki67 (VP-K451, Vector Laboratories, Burlingame, CA), and CD3 (A0452) (DAKO, Glostrup, Denmark). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system and images acquired using Pannoramic Viewer 1.15.2 (both: 3DHistech, Budapest, Hungary). Additional images were taken on a Zeiss Axio Imager.Z2 system.
Miething C., Scuoppo C., Bosbach B., Appelmann I., Nakitandwe J., Ma J., Wu G., Lintault L., Auer M., Premsrirut P.K., Teruya-Feldstein J., Hicks J., Benveniste H., Speicher M.R., Downing J.R, & Lowe S.W. (2014). PTEN action in leukemia dictated by the tissue microenvironment. Nature, 510(7505), 402-406.
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5

Hypoxia and Vascular Perfusion Imaging in Tumors

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Mice were i.v. injected with 1.5 mg pimonidazole (Hypoxyprobe) one hour before termination. For determination of tissue perfusion, mice were i.v. injected with 100 µg FITC-labeled Lycopersicon esculentum (tomato) lectin (Vector Labs) 5 min prior to whole body perfusion with PBS followed by tumor dissection and embedding in OCT (TissueTek). Tissue sections (5 µm) were fixed for 10 min in ice-cold acetone, rehydrated in PBS and blocked with 1%BSA in PBST (PBS/0.1% Tween 20) for one hour at room temperature (RT). Sections were then incubated with anti-pimonidazole (Omni Kit Hypoxyprobe) and anti-CD31 (Biolegend) antibodies overnight at 4 °C in blocking buffer. After washing with PBST (3×), antibodies: anti-rabbit-AF568, anti-rat-AF647 (Life Technologies) were incubated for 1 h at RT, counterstained with DAPI (Sigma) and mounted in Prolong Gold (Life Technologies). Pericytes were stained with anti-NG2 (Millipore). pimonidazole, CD31 or NG2 staining was determined using MIRAX MIDI Slide Scanner (Zeiss). Images were acquired with a CLSM SP5 Resonant APD Confocal Microscope (Leica) and analyzed with the Imaris software (Bitplane). Vessel area was calculated using the software Pannoramic Viewer 1.15.2 (3D Histech).
Glaus Garzon J.F., Pastrello C., Jurisica I., Hottiger M.O., Wenger R.H, & Borsig L. (2020). Tumor cell endogenous HIF-1α activity induces aberrant angiogenesis and interacts with TRAF6 pathway required for colorectal cancer development. Neoplasia (New York, N.Y.), 22(12), 745-758.
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6

Immunohistochemical Analysis of Liver Tissue

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Liver tissue samples were fixed in 4% paraformaldehyde and embedded in paraffin according to standard procedures. Sections were incubated with the indicated primary antibodies overnight at 4 °C. Thereafter, the slides were incubated with a secondary anti-rabbit or anti-mouse IgG antibody (ZSGB-BIO, Beijing, China) and visualized using 3,3'-diaminobenzidine (ZSGB-BIO). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system, and images were acquired using Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary).
Hu J., Gao Q., Yang Y., Xia J., Zhang W., Chen Y., Zhou Z., Chang L., Hu Y., Zhou H., Liang L., Li X., Long Q., Wang K., Huang A, & Tang N. (2021). Hexosamine biosynthetic pathway promotes the antiviral activity of SAMHD1 by enhancing O-GlcNAc transferase-mediated protein O-GlcNAcylation. Theranostics, 11(2), 805-823.
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7

Immunohistochemistry of Liver Tissues

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Immunohistochemistry was performed as described.14 (link) After fixation of liver tissues with 4% paraformaldehyde, paraffin-embedded sections were prepared according to the standard procedure and stored at room temperature. The tissue sections were incubated overnight with primary antibodies at 4 °C, followed by coating with biotin-labelled sheep anti-mouse/-rabbit IgG polymer (ZSGB-BIO, Beijing, China) at room temperature for 30 minutes. Diaminobenzidine solution (ZLI-9019, ZSGB-BIO, Beijing, China) was applied for colour development at the end. The Pannoramic Scan 250 Flash or MIDI system was used to scan the stained slides, and the Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary) was employed for image acquisition.
Chen S., Li B., Luo W., Rehman A.U., He M., Yang Q., Wang S., Guo J., Chen L, & Li X. (2024). Paclitaxel-induced Immune Dysfunction and Activation of Transcription Factor AP-1 Facilitate Hepatitis B Virus Replication. Journal of Clinical and Translational Hepatology, 12(5), 457-468.
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8

Quantifying Tumor Immune Infiltration

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Among the 108 cases, formalin-fixed paraffin-embedded (FFPE) tissue samples were available for 55 cases, which were analyzed by IHC and mRNA expression. The FFPE tissue sections were stained using an automatic immunohistochemical staining device (Benchmark XT, Ventana Medical Systems, Tucson, AZ). The antibodies to CD3 (1:50, Novocastra Laboratories, Newcastle upon Tyne, UK), CD8 (1:400, Dako, Glostrup, Denmark), CD20 (1:500, Novocastra Laboratories), and MECA79 (1:200, Santa Cruz Biotechnology, Dallas, TX; recognizes sulfate-dependent carbohydrate epitopes of PNAd expressed in endothelial cells of HEVs), were used. The total number of MECA79-positive blood vessels in each slide were counted manually.
The immunostained slides were scanned using a digital microscopy scanner (Pannoramic 250 FLASH, 3DHISTECH Ltd., Budapest, Hungary). The entire tumor area was selected in whole slides. In each case, the images were then scanned using computer viewer software (Pannoramic Viewer 1.15.2, 3DHISTECH Ltd.) and the number of CD3-, CD8-, and CD20-positive lymphocytes were counted in the tumor area using the NuclearQuant module. The positive cell densities were calculated by dividing the immuno-positive cell numbers by the tumor area.
Song I.H., Heo S.H., Bang W.S., Park H.S., Park I.A., Kim Y.A., Park S.Y., Roh J., Gong G, & Lee H.J. (2016). Predictive Value of Tertiary Lymphoid Structures Assessed by High Endothelial Venule Counts in the Neoadjuvant Setting of Triple-Negative Breast Cancer. Cancer Research and Treatment : Official Journal of Korean Cancer Association, 49(2), 399-407.
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9

Histological Analysis of Organ Samples

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Organ samples were fixed in fresh 4% paraformaldehyde at 4 °C overnight and further subjected to routine histological procedures for embedding in paraffin. 5-μm sections of the samples from at least three different animals per group were placed on microscopic slides next to one another to enable cross-comparison within a slide after H&E staining or IHC staining with the antibodies indicated. Antibodies used were GFP (D5.1) XP, PTEN (D4.3), phospho (p)-AKT (S473) (D9E), p-ribosomal protein S6 (S235/236) (D57.2.2E), Cleaved Caspase-3 (Asp175) (all: Cell Signaling Technologies, Danvers, MA), Ki67 (VP-K451, Vector Laboratories, Burlingame, CA), and CD3 (A0452) (DAKO, Glostrup, Denmark). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system and images acquired using Pannoramic Viewer 1.15.2 (both: 3DHistech, Budapest, Hungary). Additional images were taken on a Zeiss Axio Imager.Z2 system.
Miething C., Scuoppo C., Bosbach B., Appelmann I., Nakitandwe J., Ma J., Wu G., Lintault L., Auer M., Premsrirut P.K., Teruya-Feldstein J., Hicks J., Benveniste H., Speicher M.R., Downing J.R, & Lowe S.W. (2014). PTEN action in leukemia dictated by the tissue microenvironment. Nature, 510(7505), 402-406.
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10

Immunohistochemical Analysis of Liver Samples

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Liver samples were fixed in fresh 4% paraformaldehyde and subjected to routine histological procedures for embedding in paraffin. Then, the samples were cut in to 4.5-μm sections, which were processed for hematoxylin and eosin (HE) staining or IHC staining with antibodies targeting PCK1(1:500), and β-catenin (1:500). For IHC assay, the sections were incubated with secondary anti-rabbit IgG (ZSGB-BIO, Beijing, China) and stained with 3,3′-diaminobenzidine (ZSGB-BIO). Stained slides were scanned with a Pannoramic Scan 250 Flash or MIDI system and images were acquired using Pannoramic Viewer 1.15.2 (3DHistech, Budapest, Hungary).
Xiang J., Zhang Y., Tuo L., Liu R., Gou D., Liang L., Chen C., Xia J., Tang N, & Wang K. (2019). Transcriptomic changes associated with PCK1 overexpression in hepatocellular carcinoma cells detected by RNA-seq. Genes & Diseases, 7(1), 150-159.
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