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22 protocols using panoramic digital slide scanner

1

Immunohistochemical Analysis of Tumor Samples

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The IHC procedure was performed following the method described by Lopes et al (46 (link)). Tumor samples were embedded into paraffin blocks and cut into 3-µm sections. The samples were prepared on silanized glass slides prior to deparaffinization. The sections were rehydrated in an ascending range of alcohol concentrations and incubated with 3% hydrogen peroxide for 30 min. Antigen retrieval was performed by heating at 95°C in buffer for 35 min. The slides were incubated with bovine serum albumin (BSA). The slides were incubated at 4°C overnight with the primary antibodies (Table I). After being washed with phosphate-buffered saline (PBS) for 15 min, incubation was carried out with Starr Trek Universal HRP Detection kit (Medical Biocare, Concord, CA, USA), consisting of the secondary antibody ‘anti-mouse, rabbit and goat immunoglobulin with biotin’ for 1 h and ‘streptoavidin complex with peroxidase’ for 30 min, followed by washes with PBS for 15 min. Subsequently, 0.5% 3,3′-diaminobenzidine tetrahydrochloride was applied to the slides for 2–5 min at 20–22°C. The slides were counterstained with Harris' hematoxylin for 40 min. Negative controls were obtained by omitting the primary antibody.
The slides were scanned using the Panoramic Digital Slide Scanner (magnification, ×40; 3DHISTECH®) and Panoramic Viewer software (3DHISTECH®) (47 (link)).
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2

Digital Pathology Image Analysis Workflow

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Stained sections were digitalized with a Panoramic Digital Slide Scanner (3D Histech, Budapest, Hungary), stored as tiled tiff format, and imported into QuPath (version 2.0.0). QuPath is an open-source software tool for digital pathology image analysis [29 (link),30 (link),31 (link)]. Based on delineation of tissues by pathologist TB, tumor and premalignant borders were manually annotated in Qupath by BH and MC and copied to sequential sections. Within all these tissue annotations, cell detection, cell classification and staining quantification was conducted by a script (Script S1). After running the script, an export file of the results was automatically generated in MS excel. This export file included intensity thresholds for positive stained cells, divided in three categories: low (1+), medium (2+) or high (3+) intensity staining (examples of by QuPath processed image are shown in Figures S2 and S3).
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3

Constructing ngTMA from Digitized H&E Slides

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As discussed before, [32 (link)] the last histological Haematoxylin and Eosin (H&E) slide of each patient was retrieved. The H&E stained slides were scanned using panoramic Digital Slide Scanner (3DHISTECH). Using the free digital slide viewer software, the digital slides were evaluated and areas of interest for integration into the ngTMA were found. The annotation (600 μm) was thereafter moved to the desired histological structures for incorporation into the ngTMA. Then, a list of all cases with their corresponding annotations was created. The corresponding paraffin tissue blocks for all annotated digital slides were retrieved and sorted in the desired order for tissue microarraying. Next, the donor blocks were loaded up into the tissue microarrayer. Then the tissue microarrayer started to drill holes of 0.6 mm in diameter in the recipient block at the selected starting point. In the next step, using the punching tool, the instrument punched holes into the tissue from the selected donor block at the exact annotated and confirmed region. Cores (only one per patient) are then transferred from the donor to the recipient block. [32 (link)] (S1 Fig).
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4

Fluorescence Imaging of Tumor Sections

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Tumors were resected with surrounding normal tissue, embedded in paraffin, sectioned, and scanned for 800-nm fluorescence using the Odyssey. After scanning, sections were stained for hematoxylin and eosin and digitalized with the Panoramic Digital slide Scanner and CaseViewer 2.3 (both 3D Histech, Budapest, Hungary). Overlays were created with Adobe Photoshop CC 2018 (Adobe Systems, CA, USA).
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5

Automated Quantification of Immunohistochemistry

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The stained slides were scanned by panoramic Digital Slide Scanner (3DHISTECH). The scanned images were opened in the QuPath (Queen’s University Belfast) digital image analysis system. Then the tissue cores were automatically detected using ngTMA dearrayer. After modifications of the individual selected cores, unsuitable cores for analysis, were marked as “Missing data” and excluded. To perform automatic quantification of immunohistochemistry red stained tissue by measurement of optical density of red color—which is proportional to the expression extent of specific antigens, [33 (link)] Image J (NIH, Bethesda, MD, USA) macro runner was applied in QuPath (Queen’s University Belfast) to run the proper ImageJ macro (https://imagej.nih.gov/ij/docs/examples/stained-sections/index.html) based on extracting image regions from each ngTMA. In order to validate the full-automated image analysis, all 2975 stained cores were also evaluated by an experienced staff using a semi-quantitative scale, as followings: 0 = absent; 1 = very low expression; 2 = low expression; 3 = moderate expression; 4 = strong expression; 5 = very strong expression (Fig 1).
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6

Immunostaining of Formalin-Fixed Paraffin-Embedded Tissue

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Samples were fixed in 10% formalin (HT501128, Sigma-Aldrich) and paraffin embedded. Sections were dewaxed, dehydrated, and incubated in antigen unmasking solution (H-3300, Vector Laboratories) in a preheated pressure cooker for 20 minutes. Sections were incubated in 0.6% H2O2 in methanol for 20 minutes. Staining was performed using the SuperSensitive polymer-HRP kit (QD430-XAKE, Biogenex) according to manufacturer's protocol. Primary antibody [AlphaV 1:200 HPA004856, RRID:AB_1846316, Beta3 1:500 HPA027852, RRID:AB_10601760, POSTN 1:250 HPA012306, RRID:AB_1854827, TGFBI 1:750 HPA017019, RRID:AB_2669511 (Sigma), p53 1:100 IS616 Dako] was diluted (ZUC025, Zytomed Systems) and incubated 1 hour at room temperature. Sections were washed, incubated with Biogenex SuperEnhancer for 20 minutes, washed again, incubated with Biogenex ss label poly-HRP for 30 minutes. Sections were washed before addition of DAB chromogen and counterstaining with hematoxylin (C.I.75290, Merck). Sections were dehydrated, mounted in DPX (06522, Sigma-Aldrich), and examined with Panoramic digital slide scanner (3DHISTECH).
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7

Immunohistochemical Analysis of Skin Samples

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Immunohistochemical (IHC) studies were performed on 2‐μm‐thick paraffin‐embedded skin sections, which were rehydrated in xylene and increasing dilutions of ethanol. Antigen retrieval was performed using a TRIS‐EDTA buffer solution (pH 9.0). The following antibodies were used: CD3 (#RM9107‐S0, Thermo Fisher Scientific, USA), STAT3 (9D8; #MA1‐13042, Thermo Fisher Scientific), STAT5A (E289; #ab32043, Abcam, UK), STA5B (#ab235934, Abcam), and pY‐STAT5 (Tyr694/699; #9359, Cell Signaling Technologies/CST, USA). The stained slides were imaged/scanned by the Panoramic Digital Slide Scanner (3DHistech. Ltd, Hungary) and Aperio Digital Pathology Slide Scanners (Leica Biosystems, Germany). IHC images were analyzed with the CaseViewer software (3DHistech. Ltd) and QuPath (Bankhead et al, 2017 (link)).
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8

Quantitative Histological Analysis of Liver Cancer

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Liver tissues were fixed overnight at 4˚C in 4% (v/v) formaldehyde solution, dehydrated in an ascending series of ethanol (50, 70, 80, 90, 95 and 100%), cleared in xylene and embedded in paraffin. Specimens were sliced into sections that were 5 µm thick. The slides were stained with hematoxylin for 6 min and eosin for 1 min at room temperature and scanned with a panoramic digital slide scanner (3DHISTECH Ltd.). For each image, an area of 4,000x2,500 µm (10 mm2) was randomly selected to locate and calculate the cancer area characterized histopathologically by the presence of thick-cell cords (35 (link)) using the CaseViewer software (v1.3.0.41885; https://www.3dhistech.com/caseviewer). A total of 21 images of each animal group were sampled, in which three specialists in liver histopathology identified the thick-cell cords and located the cancer areas. The mean cancer area in each group was then calculated.
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9

Panoramic Scanning of Fascia Tissue

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Superficial fascia slides should be panoramically scanned to obtain the most complete histological information. A panoramic digital slide scanner (3DHISTECH, Budapest) was used to scan slides of whole-mounted fascia. A CaseViewer digital microscope application supplied by the manufacturers was used for picture display and processing.
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10

Quantitative Breast Tissue Analysis

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Stained sections were imaged using a 3DHISTECH Panoramic digital slide scanner and analysed using QuPath (version 0.2.3) open-source software48 (link). Immunohistochemical analysis was performed on a duct-by-duct basis. Ducts were numbered and identified as either; normal, benign or DCIS within each case, by an expert breast pathologist. For expression analysis; each duct was then scored as negative or positive for integrin β6, fibronectin and MMP13 in serial sections. For samples stained with fibronectin, periductal staining was measured, which was defined as a 50 µm region bordering DCIS lesions. For DCIS duct size analysis, only cross-sectional ducts were included. For cell and nuclear size analysis; myoepithelial cells positive for SMA or p63 were segmented by semi-automated detection, and cell and nuclear morphology features were extracted.
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