Image sections were captured with the Aperio ScanScope XT Slide Scanner (Aperio Technologies, Vista, CA) system with a × 20 objective, and tumor burden was quantified with QuPath v0.1.2 software as described in the QuPath manual for H&E stain [33 (link)]. Briefly, the image file was opened as image type H&E stain. Random trees classifier was interactively trained to distinguish between healthy and hyperplasia at the cellular level. The same classifier was used for all the slides. The results from QuPath were comparable to the manual score using Spectrum WebScope (Spectrum version 10.1.5.2028). Percent tumor area (tumor burden) was calculated as the ratio of tumor area to total lung area per section, and all sections from a single mouse were averaged to get tumor area per mouse.
Scanscope xt slide scanner
Manufactured by Leica
Sourced in United States
The ScanScope XT Slide Scanner is a high-performance digital slide scanner designed for laboratory applications. It captures high-resolution digital images of microscope slides for various analytical and imaging purposes. The device features an automated slide loading system and advanced optics to generate detailed scans of specimen samples.
Automatically generated - may contain errors
Lab products found in correlation
Polymer hrp ihc detection system, by BioGenex (1 mentions)
Ar 10 solution, by BioGenex (1 mentions)
Spectrum analysis algorithm package, by Leica (1 mentions)
Color deconvolution algorithm, by Leica (1 mentions)
Imagescope analysis software, by Leica (1 mentions)
Matrigel, by Corning (1 mentions)
Bondrx immunostainer, by Leica (1 mentions)
H 7650, by Hitachi (1 mentions)
11 protocols using scanscope xt slide scanner
1
Quantitative Tumor Burden Analysis
2
Ovarian Follicle and Corpus Luteum Quantification
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Ovaries were collected from mice at the diestrus stage at the time of killing. Left and right ovaries were fixed in 4% paraformaldehyde for 24 h at 4°C, and then transferred to 30% sucrose and embedded in optimal cutting temperature compound (OCT). Ovaries were serially sectioned at 7 µm thickness along the longitudinal plane. Total 96 sections were collected and stained with hematoxylin and eosin (H&E). Sections were imaged with an Aperio ScanScope XT slide scanner (Aperio Technologies, Vista, CA, USA).
Follicles and corpora luteal were counted in every 4th ovary section. According to morphological criteria (Myers et al. 2004) , the follicles were classified as following: primordial follicles, secondary follicles, preantral follicles, antral follicles and preovulatory follicles. In our study, histological examination showed a morphologically undifferentiated appearance of primordial follicles and primary follicles. Consequently, follicles with one layer of cells surrounding the oocytes were counted as primary follicles. To avoid double counting, only follicles with an apparent nucleus of the oocyte were counted. Established and functional corpora luteal were counted in every 4th ovary section. Regressing and involuting corpora luteal were not counted.
Follicles and corpora luteal were counted in every 4th ovary section. According to morphological criteria (Myers et al. 2004) , the follicles were classified as following: primordial follicles, secondary follicles, preantral follicles, antral follicles and preovulatory follicles. In our study, histological examination showed a morphologically undifferentiated appearance of primordial follicles and primary follicles. Consequently, follicles with one layer of cells surrounding the oocytes were counted as primary follicles. To avoid double counting, only follicles with an apparent nucleus of the oocyte were counted. Established and functional corpora luteal were counted in every 4th ovary section. Regressing and involuting corpora luteal were not counted.
3
Quantifying Immune Cells in Breast Tissue
4
Quantifying Protein Expression in PDAC Tumors
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A TMA of treatment-naive PDAC tumours was constructed from 1 mm punch biopsies of well-demarcated tumours from paraffin-embedded tissue blocks by a pathologist. An Aperio Scan-Scope XT Slide Scanner (Aperio Technologies) was used to acquire 20× images. A previously validated tumour-specific nuclear algorithm (IHC-MARK) was used to quantify protein expression.14 22 (link) Positive staining was normalised to total tissue surface area and the mean intensity or cellular density per cm2 was used to classify samples into high, mid and low cohorts and overall survival following PDAC resection compared (online supplementary figure S1 ).
5
Automated Histopathology Image Acquisition
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Digital images were captured using the Aperio ScanScope XT Slide Scanner (Aperio Technologies, Vista, CA, USA) under 20x objective magnification (0.5 μm resolution). One TMA spot image per patient was used for the study.
6
Quantification of Tumor Angiogenesis
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Xenografted tumors were first fixed with zinc solution (550,523, BD Pharmingen) for 24 h. Tumors were embedded and dissected into 5 μm thick sections, followed by de‐waxing and blocking with 3% H2O2. The blood vessels in tumor sections were stained by purified rat antimouse CD3121 antibody (1:20, 550,274, BD Pharmingen) overnight at 4 °C. The detection was followed by polymer‐HRP IHC system and sections were counterstained with methyl green (1%). Digital images were captured by an Aperio ScanScope XT Slide Scanner (Aperio Technologies, Vista, CA) under 20‐fold magnification. The DAB‐positive areas were quantified using MetaMorph 4.6 software (Puchheim, Germany).22
7
Globo H Expression in Breast Cancer
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Human clinical breast cancer specimens were obtained from patients at the time of initial surgery and were fully encoded to protect patient confidentiality. Clinical specimens were utilized under a protocol approved by the Institutional Review Board of the Human Subjects Research Ethics Committee of Chang Gung Memorial Hospital. For GHCer staining, tissue sections were deparaffinized followed by antigen retrieval by autoclaving at 121 °C for 5 min in AR-10 solution (Biogenex, Fremont, CA, USA). Slides were incubated with mAb VK9 (1:100 antibody dilution buffer) (Ventana Medical Systems, Inc., Oro Valley, AZ, USA) overnight at 4 °C, followed by antibody detection using a polymer-HRP IHC detection system (Biogenex). The slides were counter stained with hematoxylin and mounted. Digital images were captured using an Aperio ScanScope XT Slide Scanner (Aperio Technologies, Vista, CA, USA) under 20× magnification. The expression of Globo H and the morphology of tumor blood vessels were confirmed by pathologists.
8
Pancreatic Tumor Microarray Analysis
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After obtaining IRB approval, tissue microarray (TMA) studies were conducted on a cohort of 60 previously untreated patients with pancreatic ductal adenocarcinoma who underwent pancreaticoduodenectomy at Barnes-Jewish Hospital. Patients did not receive neo-adjuvant therapy and were typically treated with adjuvant chemotherapy. To construct the TMA, well-defined areas of tumor were demarcated and punched (1 mm diameter) from paraffin-embedded tumor blocks. An Aperio Scan-Scope XT Slide Scanner (Aperio Technologies) system was used to acquire digital images using a 20× objective. A tumor-specific nuclear algorithm (IHC-MARK) developed in-house [15 (link)] was modified to quantify CD14, CD8, and ALDH1 expression.
9
Quantifying Immunohistochemical Staining
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Slides were scanned at 20X magnification using a ScanScope XT slide scanner (Aperio Technologies, Vista, CA, USA). The Spectrum Analysis algorithm package, ImageScope analysis software and Color Deconvolution algorithm (version 9; Aperio Technologies.) were applied to quantify immunohistochemical (IHC) staining. These algorithms were used to calculate the average positive intensity (API), as well as the area of positive staining, and the percentage of weak (1+), medium (2+), and strong (3+) positive staining. The final API was subtracted from 255, as these intensity ranges on an 8-bit scale of 0 to 255 (black to white, respectively). The maximum value from both cores for each patient was used for statistical analysis.
10
Xenograft Tumor Growth Assay
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A549-WT and KI clones 1 and 2 (obtained from two independent nucleotransfection rounds) were thawed and kept in culture for two passages in DMEM 10% FCS 1% L-Glutamine. Cells with 50% Matrigel (Corning) were s.c. injected in the right flank of 6–11 nude mice per group (specified in the legend of Fig. 3 ) at 2Mi cells per inoculation. Tumor growth was measured bi-weekly for 36–50 days using a caliper. After termination, tumors were collected, weighed, placed into 10% v/v neutral phosphate buffered formalin solution (Avantor) for 24 h for histology prior to tissue processing or snap-frozen in liquid nitrogen for further analysis. Formalin-fixed tumors were rinsed for 5 min under running tap water, dehydrated with graded ethanol concentrations (50% to 100%), cleared with xylene and infiltrated with paraffin overnight using a vacuum infiltration tissue processor (Leica Biosystems). Tumor tissues were then embedded in paraffin blocks. Paraffin sections were stained with haematoxylin and eosin (H&E). Staining for Ki67 was performed on a Ventana Discovery XT immunostainer (Roche Diagnostics), staining for msCD31 and SMA on a BondRX immunostainer (Leica Biosystems). Slides were digitalized using a ScanScope XT slide scanner (Leica Biosystems) with objective x20.
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