Aperio scanscope xt

Manufactured by Leica Biosystems

Sourced in Germany, United States, Australia, Canada

The Aperio ScanScope XT is a high-performance digital slide scanner designed for use in pathology laboratories. It is capable of scanning glass slides and capturing digital images of tissue samples at high resolutions. The scanner utilizes advanced optics and imaging technology to produce detailed, high-quality digital slides for analysis and review.

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Lab products found in correlation

115 protocols using aperio scanscope xt

Automated Quantification of IHC Stained Cells

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CD4 and CD8 IHC stained sections were scanned with an Aperio ScanScope XT (Aperio Technologies, Inc., Vista, CA) and analyzed using the ImageScope Positive Pixel Count algorithm (version 9.1). The default parameters of the Positive Pixel Count (hue of 0.1 and width of 0.5) detected antigen adequately.

Hasenkrug K.J., Feldmann F., Myers L., Santiago M.L., Guo K., Barrett B.S., Mickens K.L., Carmody A., Okumura A., Rao D., Collins M.M., Messer R.J., Lovaglio J., Shaia C., Rosenke R., van Doremalen N., Clancy C., Saturday G., Hanley P., Smith B., Meade-White K., Shupert W.L., Hawman D.W, & Feldmann H. (2021). Recovery from acute SARS-CoV-2 infection and development of anamnestic immune responses in T cell-depleted rhesus macaques. bioRxiv.

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Breast Tumor FOXA1 Protein Expression Analysis

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TMAs containing breast tumor samples from 190 of the 383 AA cases, and 156 of the 350 EA cases, were stained using the monoclonal primary antibody HNF-3α (FOXA1) from Santa Cruz Biotechnology (Catalog No. sc-101058). Stained slides were digitally imaged at ×20 magnification using the Aperio ScanScope XT (Aperio Technologies, Vista, CA); automated image analysis of IHC staining was performed using a Genie classifier. Tumor cores on TMAs were collapsed into case-level data using a cellularity-weighted approach, as previously described [23 ]. With the weighted average of percent positivity values, an H-score was calculated, which reflects the extent of nuclear immunoreactivity, ranging from 0 to 300 [24 (link)]. The Spearman correlation between DNA methylation at the indicated 450K probe and FOXA1 protein expression (H-score) was computed.

Espinal A.C., Buas M.F., Wang D., Cheng D.T., Sucheston-Campbell L., Hu Q., Yan L., Payne-Ondracek R., Cortes E., Tang L., Gong Z., Zirpoli G., Khoury T., Yao S., Omilian A., Demissie K., Bandera E.V., Liu S., Ambrosone C.B, & Higgins M.J. (2017). FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?. Breast cancer research and treatment, 166(2), 559-568.

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Automated Scoring of IHC Biomarkers

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Two pathologists evaluated all the stained slides. They were blinded to the clinical information. All MCM-2-, Ki-67-, and EGFR-stained slides were digitally imaged using the Aperio ScanScope XT (Aperio Technologies, Vista, CA). The immunostaining intensities were automatically scored using the Aperio ImageScope (v.12.1.0.5029) with commercially available Nuclear v.9 algorithm for scoring MCM-2 and Ki-67, and Membrane v.9 algorithm for scoring EGFR expressions. The semi-quantitative definition of grading category of nuclei or membranes is as follows; 0 (negative), 1+ (weak staining), 2+ (moderate) and 3+ (strong). Scores were given as numbers between 0 and 100 in each category^{24 (link)}. The total expression scores of MCM-2, Ki-67 and EGFR were calculated according to the following formula.

\begin{matrix} Expression score & = (% of 3 + nuclei / membranes \times 3) + (% of 2 + nuclei / membranes \times 2) + (%) \\ (of 1 + nuclei / membranes \times 1) \end{matrix}

Vivatvakin S., Ratchataswan T., Leesutipornchai T., Ruangritchankul K., Keelawat S., Mahattanasakul P, & Bongsebandhu-phubhakdi S. (2021). MCM-2, Ki-67, and EGFR downregulated expression levels in advanced stage laryngeal squamous cell carcinoma. Scientific Reports, 11, 14607.

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Automated Image Analysis of TMA Cores

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Stained slides were digitally scanned at 20× magnification using Aperio ScanScope‐XT (Aperio Technologies). Digital images were stored and analyzed within an Aperio eSlideManager Database. TMA images were segmented into individual cores using the Tissue Studio TMA portal (Tissue Studio version 2.7 with Tissue Studio Library v4.4.2; Definiens Inc, Munich, Germany). Epithelial cell‐enriched regions were digitally separated out for analysis using Tissue Studio Composer software (Definiens). Tissue Studio's Nuclear Algorithm was then used to detect and enumerate cells that expressed JPT1. The percentage of positive nuclei and an H‐score (formula = (% at 1+) * 1 + (% at 2+) * 2 + (% at 3+) * 3) were determined for each TMA core.

Bateman N.W., Teng P., Hope E., Hood B.L., Oliver J., Ao W., Zhou M., Wang G., Tommarello D., Wilson K., Litzy T., Conrads K.A., Hamilton C.A., Darcy K.M., Casablanca Y., Maxwell G.L., Bae‐Jump V, & Conrads T.P. (2019). Jupiter microtubule‐associated homolog 1 (JPT1): A predictive and pharmacodynamic biomarker of metformin response in endometrial cancers. Cancer Medicine, 9(3), 1092-1103.

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Quantifying Cardiac Fibrosis via Histology

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Hearts were harvested, fixed for 24 hours at 10% formaldehyde. Seven micrometer longitudinal or cross sections of paraffin-embedded specimens were subjected to H&E, PAS (Periodic Acid-Schiff), Masson’s Trichrome staining. Whole-field digital microscopy was performed using the Aperio ScanScope XT (Aperio Technologies) as previously described.^{27 (link)} A pixel count algorithm with optimized color hue and saturation values (ImageScope 10.0, Aperio Technologies, Inc.) was set to accurately identify blue colored collagen fibers versus red cardiomyocytes, thereby allowing for calculation of percent fibrosis. All histopathologic data was confirmed by a blinded pathologist.

Javan H., Szuscik A.M., Li L., Schaaf C.L., Salama M.E, & Selzman C.H. (2014). Cardiomyocyte p65 NF-κB Is Necessary for Compensatory Adaptation to Pressure-Overload: Javan et al: NF-κB and Pressure-Overload. Circulation. Heart failure, 8(1), 109-118.

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IHC Tissue Analysis with Aperio ScanScope

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IHC stained tissue slides were scanned with an Aperio ScanScope XT (Aperio Technologies, Inc.) and analyzed using the ImageScope Positive Pixel Count algorithm (version 9.1). The default parameters of the Positive Pixel Count (hue of 0.1 and width of 0.5) detected antigen adequately.

Port J.R., Adney D.R., Schwarz B., Schulz J.E., Sturdevant D.E., Smith B.J., Avanzato V.A., Holbrook M.G., Purushotham J.N., Stromberg K.A., Leighton I., Bosio C.M., Shaia C, & Munster V.J. (2021). Western diet increases COVID-19 disease severity in the Syrian hamster. bioRxiv.

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Histological Analysis of Marmoset Tissues

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Marmoset tissues were evaluated for pathology and the presence of viral antigen. All tissues were fixed for a minimum of 7 days in 10% neutral-buffered formalin and subsequently embedded in paraffin. Lungs were perfused with 10% formalin and processed for histologic review. The lung is divided into right upper, right lower, left upper, and left lower lobe. Each of these four sections are then sampled at the hilus, at mid-lobe and at the periphery of the lobe for a minimum of 12 sections per animal. This method is used for all non-human primate studies at Rocky Mountain Laboratories. Hereafter, tissue sections were stained with hematoxylin and eosin. For the detection of viral antigen immunohistochemistry was performed using an in-house produced rabbit polyclonal antiserum against HCoV-EMC/2012 (1:1000). Grading was done blinded by a board-certified veterinary pathologist. To obtain morphometrical data of immunohistochemistry staining, stained sections were scanned with an Aperio ScanScope XT (Aperio Technologies, Inc., Vista, CA) and analyzed using the ImageScope Positive Pixel Count algorithm (version 9.1). Between 30 and 105 mm squared were evaluated at 2× magnification. The default parameters of the Positive Pixel Count (hue of 0.1 and width of 0.5) detected antigen adequately.

van Doremalen N., Falzarano D., Ying T., de Wit E., Bushmaker T., Feldmann F., Okumura A., Wang Y., Scott D.P., Hanley P.W., Feldmann H., Dimitrov D.S, & Munster V.J. (2017). Efficacy of antibody-based therapies against Middle East respiratory syndrome coronavirus (MERS-CoV) in common marmosets. Antiviral Research, 143, 30-37.

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Histological and Immunohistochemical Analysis

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Preparation of slides and image analysis has been described previously [26 (link)]. In brief, for each block a single haematoxylin and eosin section was prepared, on which a pathologist examined the tissue to confirm normal histology. All IHC sections were scanned in an Aperio ScanScope XT slide scanning system (Aperio Technologies, USA) at × 40 magnification and blinded before manually read using the ImageScope viewing software. Digital images of the sections were captured using the ScanScope photo tool. Stromal, epithelial and adipose areas were manually selected using the Annotations tool. The total areas of analysis (comprising stromal, epithelial and adipose tissues) generated through the markup images were used to calculate the proportion of each tissue type. Calculations of epithelial and stromal protein expressions were done without knowledge of the different exposures of the study and have been described previously [26 (link)]. In brief, per cent epithelial nuclear expression of ER, PR and Ki-67 was assessed manually for each section separately. Likewise, stromal nuclear expression of ER, PR and Ki-67 was manually categorised as positive (≥ 1% positive cells) or negative for each section. Detailed information on tissue and protein characteristics of the cohort is found in Table 1.

Gabrielson M., Chiesa F., Behmer C., Rönnow K., Czene K, & Hall P. (2018). Association of reproductive history with breast tissue characteristics and receptor status in the normal breast. Breast Cancer Research and Treatment, 170(3), 487-497.

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Histological Evaluation of Intestinal Allografts

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Intestinal graft tissue biopsies were fixed with 10% neutral buffered formalin and submitted for processing into paraffin blocks. Paraffin blocks underwent serial sectioning (

5 μ m

) and staining with hematoxylin and eosin (H&E) for histological evaluation and rejection grading. Whole slides of graft samples were scanned with an Aperio ScanScope XT (Aperio Technologies, Inc., Vista, California). Allograft histology was evaluated in a blinded fashion by a trained transplant pathologist (A.B.F).

Jelly E.T., Kwun J., Schmitz R., Farris A.B., Steelman Z.A., Sudan D.L., Knechtle S.J, & Wax A. (2021). Optical coherence tomography of small intestine allograft biopsies using a handheld surgical probe. Journal of Biomedical Optics, 26(9), 096008.

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Histological Assessment of Skin and Eye Irradiation

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Eyes and irradiated dorsal trunk skin were removed from euthanized mice 24 h after the final irradiation. Where possible both eyes were removed but in some cases one eye was damaged during removal and was excluded from the study. The tissues were fixed in 10% neutral formalin (skin for 24 h, eyes for 48 h) before transfer into 70% ethanol, and left for at least 24 h before processing. Tissues were embedded in paraffin and sections (skin 5 µm, eye 4 µm) cut onto coated glass slides (Superfrost Plus, Lomb Scientific Pty Ltd. Sydney, Australia). Slides were dried overnight at 45°C. Hematoxylin and eosin stained sections (Surgipath Leica Biosystems, Richmond IL, USA) were scanned using the Aperio Scanscope XT (Aperio Technologies, Sandigo, USA). ImagePro viewing software was used for the measurement of epidermal and corneal epithelial thickness in 10 and 5 (respectively) randomly selected 200x magnification fields. Counts in the corneal epithelium were performed between limbus to limbus in transverse tissue sections. The observer was masked during analysis.

Hassan N.M., Painter N., Howlett C.R., Farrell A.W., Di Girolamo N., Lyons J.G, & Halliday G.M. (2014). Brm Inhibits the Proliferative Response of Keratinocytes and Corneal Epithelial Cells to Ultraviolet Radiation-Induced Damage. PLoS ONE, 9(9), e107931.

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