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18 protocols using scanscope scanner

1

Quantitative Analysis of S-100 Immunostaining

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High-resolution whole-slide digital scans of S-100 immunostained sections were created with a ScanScope scanner (Aperio Technologies, Inc.). The digital slide images were then viewed and analysed using the viewing and image analysis tools of Aperio ImageScope software (Aperio Technologies, Inc.). Five areas, each with the fixed size of 137,000 µm 2 , were randomly selected per section. To quantify the immunopositive reactions, the colour deconvolution (colour separation) algorithm (Aperio Technologies, Inc.) was set up (by colour calibration) to detect and quantify only the brown colour of DAB positive staining. The algorithm was then run on the selected area to measure the percentage of immunopositive reactions relative to the measured areas. The analysis output results were finally exported to Excel sheets and subjected to statistical analysis to be compared between neonatal and adult rats.
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2

Quantifying Alveolar Lung Microvascular Density

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Total number of MALLs was estimated as follows: Density of MALL on section (N, per cm2) was calculated as a mean value for 11 sections of 4-μm thickness (T = 0.0004 cm) collected at 100-μm intervals. The number and area of MALL and the area of alveolar region in each section were measured on whole section images using ScanScope scanner and ImageScope software (Aperio Technologies, Inc., Vista, CA, USA). Mean diameter of MALL (D, cm) was estimated as 0.005 cm. A hypothetical cubic tissue mass with a side of 1 cm can be sliced into 1/T sections. Therefore, the total number of MALL counts in all 1/T sections will be N/T. A single MALL is sliced into D/T pieces and counted D/T times. Dividing total MALL count (N/T) with this redundancy factor (D/T), three-dimensional density of MALL can be expressed as N/D per cm3. Using the following values (N = 4.3, D = 0.005, bilateral lung volume of 1.0 cm3) for a 37-week-old mouse, the total number of MALL in the lungs is calculated as N/D × lung volume = 4.3/0.005 × 1.0 = 860.
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3

Quantitative Analysis of Bone-Implant Interface

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Slides were digitized using high-resolution whole-slide digital ScanScope scanner (Aperio Technologies Inc.). The digital images from hematoxylin and eosin-stained slides were then viewed and quantified using the tools of ImageJ software. The whole implant is contoured to obtain the total implant area in pixels (TA). All areas of bone are selected to get a total bone area in pixels (BA). The BA/TA ratio was calculated and reported as percentage (n = 3 sections per implant and 4 implants/treatment). The digital images from Sirius red-stained slides were viewed and analyzed using Aperio's viewing and image analysis tools. In each slide, five rectangular fields of a fixed area of 1.18 mm2 were randomly selected. Color deconvolution (color separation) algorithm (Aperio Technologies Inc.) was then applied so as to detect and measure the area of red color of stained collagen and calculate its area relative to the total area.
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4

Quantifying Osteoid Tissue in Histological Sections

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High-resolution whole-slide digital scans of all histological sections were created with a ScanScope scanner (Aperio Technologies Inc., Buffalo Grove, IL, USA). Five images were captured for each section. The digital slide images were examined using the Aperio's ImageScope viewing software (Aperio Technologies Inc.). Random snapshots were taken from each section with × 10 objective magnification. Each snapshot measured 1 809 171.65 μm2 (~1.8 mm2). The images were then subjected to image analysis using the ImageJ software (National Institute of Health). Each image was color-thresholded so as to select only the pink color of osteoid tissue (as stained with hematoxylin and eosin) and measured its area percentage relative to the total area of the image. The analysis output results were then exported to Excel sheets and subjected to statistical analysis.
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5

Histological Analysis of Chick Femurs

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Chick femurs from each group were dehydrated through a series of graded alcohols and embedded in low-melting point paraffin using an automated Shandon Citadel 2000. Six micrometers tissue sections were cut and stained with Weigert’s hematoxylin, followed by staining with 0.5% Alcian blue for proteoglycan-rich cartilage matrix and 1% Sirius red for collagenous matrix.
To identify human endothelial cells, tissue sections were stained for human CD31 using human specific antibody (GeneTex). In brief, after quenching endogenous peroxidase activity with 3% H2O2 and blocking with 1% bovine serum albumin (BSA) in 1X PBS, sections were incubated overnight at 4 °C with anti-CD31 primary antibody diluted appropriately in 1% BSA in PBS. Following primary antibody incubations, sections were incubated with biotin-conjugated secondary antibody anti-rabbit IgG (DAKO A/S; 1:100) diluted appropriately in 1% BSA in PBS. Visualization of the immune complex involved the avidin–biotin method linked to peroxidase and 3-amino-9-ethylcarbazole, resulting in a reddish brown reaction product. Sections were counterstained for light green and Alcian blue. Control staining was performed by omitting the primary antibody. Slides were digitized using high-resolution whole slides digital ScanScope scanner (Aperio Technologies, Inc.).
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6

Histological Analysis of Grafts

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Grafts were recovered at the end of the observation period. Samples were fixed in 7.5% formalin overnight and embedded in paraffin within 24h. Paraffin blocks were subsequently sectioned and stained with hematoxylin and eosin (H&E). Slides were scanned using an Aperio ScanScope scanner (Aperio Technologies, Inc., Vista, CA). Grading was performed according to the International Society for Heart and Lung Transplantation (ISHLT) 2004 guidelines (29 (link)) for cellular rejection score by an experienced pathologist (H.R.) blinded to the experimental background of tissue samples.
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7

Quantification of Myocardial Fibrosis and Immunostaining

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High-resolution whole-slide digital scans of all stained sections were created with a ScanScope scanner (Aperio Technologies, Inc.). The digital slide images were then viewed and analysed using the viewing and image analysis tools of Aperio's Ima-geScope software (Aperio Technologies, Inc.). To quantify the immunopositive reaction and the extent of fibrosis, five areas, each with the fixed size of 0.264 mm 2 , were randomly selected per section, and the colour deconvolution (colour separation) algorithm (Aperio Technologies, Inc.) was set up (by colour calibration) to detect and quantify only the brown colour of DAB positive immunostaining or only the green colour of fibrous tissue (as stained by Masson's trichrome). The algorithm was then run on the selected areas to measure the percentage of the colour of interest relative to the total area of analysis. The thickness of the wall of the left ventricle (LV) was measured on the digital scans of H&E-stained slides, using the linear measurement tool of Aperio's ImageScope software (Aperio technologies, Inc.). To minimise error, thickness was measured at 5 randomly chosen points per heart section and averages were calculated. All image analysis output results were finally exported to Excel sheets and subjected to statistical analysis.
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8

Left Ventricular Wall Thickness Measurement

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The excised hearts were fixed in 10% buffered formalin at 4°C for 24 hours and processed to prepare transverse, mid-ventricular, 5-μm-thick paraffin sections. These sections were stained with hematoxylin and eosin (H&E) and Masson’s Trichrome stains. The thickness of the wall of the left ventricle was measured using image analysis by scanning H&E-stained slides. High-resolution, whole-slide digital scans of all stained slides were created with a ScanScope scanner (Aperio Technologies, Vista, CA, USA). The digital slide images were viewed and analyzed using Aperio’s viewing and image analysis tools. Left ventricular thickness was measured at ×20 magnification using the linear measurement tool of Aperio’s Image Scope software (Aperio Technologies). To minimize error, thickness was measured at five randomly chosen points per heart section and averages were calculated.
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9

Quantitative Immunohistochemical Analysis of Bone Regeneration

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High-resolution full-slide optical scans of the anti-osteopontin immunostained parts were produced using the ScanScope scanner (Aperio Technologies, Inc.). Later the digital slide images were seen and analyzed utilising the viewing and image processing methods of Aperio’s ImageScope program (Aperio Technologies, Inc.). Each section was divided into three regions: centre of defect, interface, and newly mineralised bone (either at the centre or at the border). Random selection of five regions, each with a fixed size of 19,200 µm2 per zone was done. Colour deconvolution (colour separation) programme (Aperio Technologies, Inc.) was fabricated (by colour calibration) to measure the immunopositive response and to identify and evaluate only the brown colour of DAB-positive staining. The programme was then applied to the chosen region to calculate the proportion of immunopositive reactions compared to the overall area of study. The thickness (µm) of newly formed bone in the centre of the deformity was measured. The results obtained from the image analysis were sent for statistical analysis.
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10

Histological Analysis of Excised Hearts

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Histological processing was prepared as described previously.30 The excised hearts were cleaned and fixed in 10% buffered formalin for 24 hours. The fixed samples were processed to prepare 5-μm thick paraffin sections, which were then stained with hematoxylin and eosin (H&E) and Masson’s trichrome stains. High-resolution digital scans of all stained slides were created with a ScanScope scanner (Aperio Technologies, Vista, CA, USA) and were viewed and analyzed using Aperio’s viewing and image analysis tools.
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