Scanscope software

Manufactured by Leica Biosystems

Sourced in United States, Germany

ScanScope software is a digital pathology imaging solution from Leica Biosystems that enables high-resolution scanning and management of glass slides. It provides a platform for capturing, viewing, and analyzing digital images of tissue samples.

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Lab products found in correlation

Ihc nuclear image analysis algorithm, by Leica Biosystems (2 mentions) Imagescope software, by Leica Biosystems (2 mentions) Scanscope xt system, by Leica Biosystems (1 mentions) Scanscope cs system, by Leica Biosystems (1 mentions) Imagescope, by Leica Microsystems (1 mentions) F4 80, by BioLegend (1 mentions) Aperio cs2 digital scanner, by Leica Biosystems (1 mentions) Autoscanner, by Leica camera (1 mentions) Aperio cs2, by Leica Biosystems (1 mentions)

10 protocols using scanscope software

Quantitative Evaluation of Myelofibrosis

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Morphologic review of the peripheral blood smears, bone marrow aspirates and core biopsies was performed for each case. Two hematopathologists (MS and NS), blinded to the original diagnosis, assessed and quantified key histomorphologic features (i.e. megakaryocyte clustering, size, and nuclear lobulation, marrow cellularity and composition, intrasinusoidal hematopoiesis). Histomorphologic criteria of megakaryocytes including size, nuclear features and clustering was considered present if noted in at least 10% of the cells.
Digital image analysis was used to objectively grade and quantitate the degree of myelofibrosis in the reticulin-stained bone marrow core biopsies. Additionally, traditional subjective grading of fibrosis was performed in the standard manner aided by reticulin.[4 (link)] The slides were digitally scanned with ScanScope®XT system and the reticulin fibroses was quantified using a color deconvolution algorithm provided in ScanScope® software (Aperio Technologies, Inc., Vista, CA, USA) as previously described.[3 (link)] The fibrosis quantification score was defined as the proportion of total hematopoietic area (excluding trabeculae) occupied by reticulin fibers. The objective quantification of fibrosis using digital image analysis was highly correlated with the subjective fibrosis score (Spearman correlation, R=0.79) (data not shown).

Sangle N., Cook J., Perkins S., Teman C.J., Bahler D., Hickman K., Wilson A., Prchal J, & Salama M. (2014). Myelofibrotic transformations of polycythemia vera and essential thrombocythemia are morphologically, biologically and prognostically indistinguishable from primary myelofibrosis. Applied immunohistochemistry & molecular morphology : AIMM / official publication of the Society for Applied Immunohistochemistry, 22(9), 663-668.

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Histological Analysis of Adipose Tissue

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Adipose tissues were fixed in 10% buffered formalin for a minimum of 48 h, and then tissues were transferred into 70% ethanol until processing. Samples were paraffin-embedded, sectioned at 4 μm thickness, slide-mounted, and stained with hematoxylin and eosin. Sections were scanned using the ScanScope CS System (Aperio Tehcnologies, Sausalito, CA) and digital images captured at 100 μM using ScanScope Software (Aperio Technologies).

Beaudry J.L., Kaur K.D., Varin E.M., Baggio L.L., Cao X., Mulvihill E.E., Stern J.H., Campbell J.E., Scherer P.E, & Drucker D.J. (2019). The brown adipose tissue glucagon receptor is functional but not essential for control of energy homeostasis in mice. Molecular Metabolism, 22, 37-48.

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Pancreatic β-cell Mass Quantification

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At the end of the 9-week study, following killing of mice, pancreata and epididymal fat pads were rapidly excised and weighed. Pancreatic tissue was fixed in 10% neutral buffered formalin for 48 h and stored in 70% ethanol until further processing and embedding in paraffin. For assessment of β-cell mass, pancreatic sections were immunostained for insulin (using a guinea pig anti-insulin primary antibody, 1:100 dilution) as previously described.^{29 (link)} Two sections (separated by 100 μm) from each pancreas were analyzed. Slides were scanned using the ScanScope CS system (Aperio Technologies, Vista, CA, USA) at × 40 magnification. Digital images were analyzed with the ScanScope software (Aperio Technologies). β-Cell mass was calculated as the product of pancreas weight before fixation and the ratio of insulin positive/total pancreas cross-sectional area.

Lamont B.J., Waters M.F, & Andrikopoulos S. (2016). A low-carbohydrate high-fat diet increases weight gain and does not improve glucose tolerance, insulin secretion or β-cell mass in NZO mice. Nutrition & Diabetes, 6(2), e194-.

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Quantification of Myocardial Fibrosis

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Formalin (10 %) fixed and paraffin embedded myocardium from LV was sectioned into 5 µm thick slices and stained with H&E and Masson’s trichrome. For analysis, four transmural areas from each circumferential LV-section (one from each rat) were extracted using Scanscope software (Aperio Technologies inc.: Vista, CA, USA). For fibrosis quantification FRIDA (FRamework for Image Dataset Analysis: The Johns Hopkins University, Baltimore, MD, USA) was used. This is a custom open-source image analysis software package for color image datasets. Epicardium, pericardium and larger vessels were excluded from this analysis.

Eskesen K., Olsen N.T., Dimaano V.L., Fritz-Hansen T., Sogaard P., Chakir K., Steenbergen C., Kass D, & Abraham T.P. (2015). Sildenafil treatment attenuates ventricular remodeling in an experimental model of aortic regurgitation. SpringerPlus, 4, 592.

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Quantification of Tumor-Infiltrating Immune Cells

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The CD3, CD8, CD20, CD66b, CD163 and CD38 stained slides were digitalised using the Aperio CS2 digital scanner and ScanScope software (Aperio Technologies, Leica Biosystem, New Castle Ltd, UK) at 20× magnification and analysed using ImageScope (Leica Microsystems). Each scanned image was annotated manually, and IHC Nuclear Image Analysis algorithm or V9‐pixel count algorithm (Leica Biosystems, New Castle Ltd, UK) was chosen for the computerised whole slide analysis. From each case, we obtained the quantitative measure of immune cell density (number of cells mm⁻² or the relative frequency of the area positive for the biomarker) for the entire tumor area, including the invasive margin of the tumor, the latter considered to be an area 500 μm wide beneath the tumor nests. Examples of counted fields are provided in Supplementary table 1. For each section stained for CD20, these cells were also organised into aggregates also identifiable as tertiary lymphoid structures, based on the occurrence of BCL6⁺ germinal centre B cells and localisation in the same region of T cells, seen on the serial section stained for CD3 (CD20^TLS) or in form of diffuse stromal/intratumoral infiltrate (CD20^IT). The density of CD20^IT (number of CD20⁺ cells mm⁻²) was measured, excluding the aggregates of B cells and the TLS density (number of TLS mm⁻²).

Missale F., Bugatti M., Marchi F., Mandelli G.E., Bruni M., Palmerini G., Monti M., Bozzola A.M., Arena G., Guastini L., Boggio M., Parrinello G., Peretti G, & Vermi W. (2023). The prometastatic relevance of tumor‐infiltrating B lymphocytes in laryngeal squamous cell carcinoma. Clinical & Translational Immunology, 12(4), e1445.

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Histological and Immunohistochemical Analysis of Liver Sections

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Liver sections were fixed with 4% paraformaldehyde (PFA), embedded in paraffin, sectioned (3 μm), and stained with hematoxylin and eosin and were mounted and analyzed by light microscopy for histological evaluation. For IHC all reactions required antigen retrieval, 30 min at 95°C in 0,01 M Tris-1 mM EDTA pH 9. Incubations with primary antibodies at their optimal dilutions were performed overnight at 4°C. Primary antibodies used for the IHC were: F4/80 (BioLegend 123102, 1:400), cleaved Caspase-3 (activated Caspase-3 (a-Casp3)) (Cell Signaling 9661, 1:200). For HDAg analysis, patient serum with anti-HDAg reactivity was employed as primary antibody (1:10,000). After rinsing in TBS-T, the sections were incubated with the corresponding secondary antibodies for 30 min at RT. Peroxidase activity was revealed using DAB+ and sections were lightly counterstained with Harris hematoxylin. Finally, slides were dehydrated in graded series of ethanol, cleared in xylene and mounted with Eukitt (Labolan, 28500). Image acquisition was performed on an Aperio CS2 slide scanner using ScanScope Software (Leica Biosystems). All images were stored in uncompressed 24-bit color TIFF format and image analysis was performed using a plugin developed for Fiji, ImageJ (NIH, Bethesda, MD).

Camps G., Maestro S., Torella L., Herrero D., Usai C., Bilbao-Arribas M., Aldaz A., Olagüe C., Vales A., Suárez-Amarán L., Aldabe R, & Gonzalez-Aseguinolaza G. (2024). Protective role of RIPK1 scaffolding against HDV-induced hepatocyte cell death and the significance of cytokines in mice. PLOS Pathogens, 20(5), e1011749.

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Quantification of NOVA2-positive cells

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Stained slides were acquired using the Aperio CS2 digital scanner and ScanScope software (Leica Biosystems, Wetzlar, Germany). Images were viewed and organized using ImageScope software (Leica biosystems, Wetzlar, Germany). Region of interest consisted of the tumor area and normal colon; necrotic areas were excluded from the selection. IHC Nuclear Image Analysis algorithm (Leica biosystems, Wetzlar, Germany) was setup for the analysis to identify categories of strong and weak positive cells based on the signal intensity (Supplementary Fig. 18). Data are expressed as the absolute number of NOVA2-positive cells per mm² and as fractions of strong and weak positive cells.

Pradella D., Deflorian G., Pezzotta A., Di Matteo A., Belloni E., Campolungo D., Paradisi A., Bugatti M., Vermi W., Campioni M., Chiapparino A., Scietti L., Forneris F., Giampietro C., Volf N., Rehman M., Zacchigna S., Paronetto M.P., Pistocchi A., Eichmann A., Mehlen P, & Ghigna C. (2021). A ligand-insensitive UNC5B splicing isoform regulates angiogenesis by promoting apoptosis. Nature Communications, 12, 4872.

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Histological and Immunohistochemical Analysis of Liver Tissue

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Hematoxylin & Eosin (H&E): Liver sections were fixed with 4% paraformaldehyde (PFA), embedded in paraffin, sectioned (3 μm), and stained with hematoxylin and eosin. Sections were mounted and analysed by light microscopy for histologic evaluation.
Immunohistochemistry (IHC): the first steps were the same as for the H&E staining. Then, a step of antigen retrieval was performed that consisted of incubation for 30 min at 95 °C in 0.01 M Tris-1 mM EDTA pH 9. Subsequently, primary antibodies were incubated overnight at 4 °C. After rinsing in TBS-T, the sections were incubated with the corresponding secondary antibodies for 30 min at RT. Peroxidase activity was revealed using DAB+ and sections were lightly counterstained with Harris hematoxylin. Finally, slides were dehydrated in graded series of ethanol, cleared in xylene and mounted with Eukitt (Labolan, #28500, Navarra, Spain). Image acquisition was performed on an Aperio CS2 slide scanner using ScanScope Software (Leica Biosystems, Vista, CA, USA). The image analysis was performed using a plugin developed for Fiji, ImageJ (NIH, Bethesda, MD, USA). The antibodies employed are summarized in Table 1.

Maestro S., Gómez-Echarte N., Camps G., Usai C., Suárez L., Vales Á., Olagüe C., Aldabe R, & González-Aseguinolaza G. (2021). AAV-HDV: An Attractive Platform for the In Vivo Study of HDV Biology and the Mechanism of Disease Pathogenesis †. Viruses, 13(5), 788.

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Quantitative Analysis of Immune Cells in Tumor

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Single stained sections were digitally scanned using a Leica autoscanner at 20x magnification. Positive cells/mm^{2 (link)} were analyzed using ScanScope software (Leica Biosystems), or Qupath.^{23 (link)} Whole tissue regions (1 section/patient) were selected for analysis by identifying tumor cells surrounded by clear desmoplastic stroma in consultation with a pathologist (C.B.) Adjacent normal and adipose tissue on the periphery was excluded from analysis. These analysis regions also included TLS when present. Hi vs. low cutoffs were determined by median cut-points. E-TLS positivity was determined by recognition of two or more lymphoid aggregates observed to contain both CD20⁺ B cells and CD3⁺T cells. For all patients, a range of 4–8 slides were examined/tissue block that were directly serial to the original H&E used for diagnosis and the sample extracted for RNA-sequencing. These sections were used for IHC and/or additional multiplex immunofluorescence where indicated. Additionally, 5 TLS⁻ patients were randomly selected to assess for the possible presence of TLS in 3 different tissue blocks with pathologically defined cancer whereby all of the available H&E slides cut from those blocks was examined for the presence or absence of a TLS (8–13 slides/block). None of these five patients was determined to contain a TLS.

Gunderson A.J., Rajamanickam V., Bui C., Bernard B., Pucilowska J., Ballesteros-Merino C., Schmidt M., McCarty K., Philips M., Piening B., Dubay C., Medler T., Newell P., Hansen P., Tran E., Tang E., Bifulco C., Crittenden M., Gough M, & Young K.H. (2021). Germinal center reactions in tertiary lymphoid structures associate with neoantigen burden, humoral immunity and long-term survivorship in pancreatic cancer. Oncoimmunology, 10(1), 1900635.

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Quantitative Immunohistochemical Analysis

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Stained slides were acquired using the Aperio CS2 digital scanner and ScanScope software (Leica Biosystems, Wetzlar, Germany). Images were viewed and organized using ImageScope software (Leica biosystems, Wetzlar, Germany). Each scanned image was annotated manually and IHC Nuclear Image Analysis algorithm was chosen for the analysis. The whole tumor area has been considered for the analysis, with the exclusion of necrotic areas. Data are expressed as absolute number of CD66b⁺ or CD3⁺ cells per mm².

Mandelli G.E., Missale F., Bresciani D., Benerini Gatta L., Scapini P., Caveggion E., Roca E., Bugatti M., Monti M., Cristinelli L., Belotti S., Simeone C., Calza S., Melocchi L, & Vermi W. (2020). Tumor Infiltrating Neutrophils Are Enriched in Basal-Type Urothelial Bladder Cancer. Cells, 9(2), 291.

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