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Sigmascan pro

Manufactured by IBM
Sourced in United States

SigmaScan Pro is a versatile and advanced image analysis software developed by IBM. It is designed to provide users with powerful tools for analyzing and quantifying various types of digital images. The software offers a range of features and functionalities that allow users to extract critical information from their data.

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17 protocols using sigmascan pro

1

Quantifying Benthic Community Structure

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At Stations 1–10, three 25 × 25 cm quadrats were placed haphazardly every 5 m along the 50 m transect, and the quadrats were photographed (Σn = 33). Counts were made of the number of mobile individuals inside the quadrat based on the photograph although these may be underestimated because some moved when the quadrats were placed). The percentage of coverage of sessile species was scored using Sigma Scan Pro image software (version 5.0, SPSS). The average abundance of each species was calculated from the 33 quadrats of each station. Identifications of crustaceans, molluscs, algae and other invertebrates were based on Segawa [15 ], Miyake [16 , 17 ], Okutani [18 ] and Dai and Horng [19 , 20 ].
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2

Quantifying Aortic Atherosclerosis and Lipid Accumulation

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After mouse euthanasia, the distal portions of ascending aortas, aortic arches, and the distal parts from descending aortas down to the iliac bifurcations of mice in each group were extracted and laid flat on the white wax surface. Then, the samples were fixed with 10% (volume/volume) buffered formalin solution overnight, stained for 1 h with freshly-prepared filtered oil red O solution, and then rinsed twice with 78% methanol. The tissues were subsequently fixed on the slides and scanned with ScanScope slide scanning system (Nikon, Melville, NY, USA). Finally, the entire surface areas and oil red O-positive atherosclerotic lesion areas were scanned using Sigma Scan Pro software (SPSS Science, Chicago, IL, USA).
Well-grown cells at the logarithmic growth phase were cultured in the 6-well culture plates at 1 × 106 cells/well. When cell confluence reached 70%, the cells were rinsed thrice with PBS, fixed for 1 min with 50% isopropanol, and stained for 10 min with oil red O staining solution. Following 5-min hematoxylin staining, the red cells were observed and counted under the microscope to calculate the ratio of oil red O staining areas.
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3

Histological Analysis of Bone Regeneration

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After radiographic micro-CT analysis, each specimen underwent dehydration and embedding. Specimens were fixed in 10% neutral buffered formalin, dehydrated in ethanol, and decalcified using 5% formic acid (Fisher Diagnostics, Fair Lawn, NJ, USA) for 2 weeks. Two fragments were both embedded to show the sagittal section in the paraffin block. Tissue blocks were cut into at 4 μm, and staining was done using hematoxylin and eosin stain. Selective digital images of sections were taken using a digital camera (DP-20; Olympus, Tokyo, Japan; Figure 3). Sections from the center of each block were examined by light microscopy, and images were captured (ImageScope Version 9.1.19.1571; Aperio Technologies, CA, USA). The images were analyzed by SigmaScan Pro (SPSS, Chicago, IL). The amount of new bone as a percentage of the bone defect area was calculated.
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4

Histological Analysis of Calvarial Graft

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The calvarial samples were subjected to dehydration and embedding. The segments were embedded to show the sagittal sections in paraffin blocks. The paraffin blocks were sliced (5 μm) and stained with hematoxylin and eosin. The detailed staining procedure followed the standard method in the manufacturer’s manual. The selected sections were photographed with a digital camera (DP-73; Olympus, Tokyo, Japan). The images were analyzed with Sigma Scan Pro (SPSS, Chicago, IL). The ratio of the remaining graft was calculated based on the ratio of the remaining graft to the original size of the graft.
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5

Histological Analysis of Masseter Muscle Thickness

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The samples were harvested, decalcified in 5 % nitric acid for 5 days, and dehydrated in ethyl alcohol and xylene. After separation of the calvarial bones, the samples were embedded in paraffin blocks. The paraffin blocks were sliced into sections that were then stained with hematoxylin and eosin. The section with the occlusal plane area was selected.
The staining procedure for hematoxylin and eosin staining was as follows. First, de-wax and hydrate paraffin sections. The slide was stained in hematoxylin for 5 min. Overstained sections can easily be differentiated by agitating for a second in acid-alcohol then washing in tap water for 5 min. The slides were immersed in eosin for 30 s and then washed in running tap water for 1 min. The slides were dehydrated and cleared in xylene.
Digital images of the selected sections were captured with a digital camera (DP-73; Olympus, Tokyo, Japan). The images were analyzed by Sigma Scan pro (SPSS, Chicago, IL). The thickness of the masseter muscle was measured from the perpendicular line to the mandibular ramus.
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6

Calvarial Bone Defect Analysis

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The calvarial samples were harvested, decalcified in 5 % nitric acid for 5 days, and dehydrated in ethyl alcohol and xylene. After separation of the parietal bones through the midline sagittal suture, the calvarial samples were embedded in paraffin blocks. The paraffin blocks were sliced into sections that were then stained with hematoxylin and eosin. The section with the largest defect area was selected, along with sections 50 μm proximal and distal to the largest defect section.
The staining procedure for hematoxylin and eosin staining was as follows. First, de-wax and hydrate paraffin sections. The slide was stained in hematoxylin for 5 min. Overstained sections can easily be differentiated by agitating for a second in acid-alcohol, then washing in tap water for 5 min. The slides were immersed in eosin for 30 s and then wash them in running tap water for 1 min. The slides were dehydrated and clear in xylene.
Digital images of the selected sections were captured with a digital camera (DP-73; Olympus, Tokyo, Japan). The images were analyzed by Sigma Scan pro (SPSS, Chicago, IL). The new bone formation was calculated as the percentage of newly formed bone in the calvarial defect area.
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7

Histologic Analysis of Bone Graft

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After the μ-CT analysis, the samples were decalcified in 5% nitric acid for 2 weeks and dehydrated in ethyl alcohol and xylene. The samples were separated through the midline sagittal suture and embedded in paraffin blocks. The paraffin blocks were sliced into sections that were then stained with hematoxylin and eosin. The sections that showed the sagittal image of the parietal bone and bone grafted area were selected for histologic analysis. Digital images of the selected sections were taken with a digital camera (DP-73; Olympus, Tokyo, Japan). The images were analyzed by Sigma Scan pro (SPSS, Chicago, IL, USA). The amount of newly formed bone was calculated as the percentage of the total region of the bone graft area.
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8

Organoid Analysis via Histological Imaging

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In separate experiments, after 8 d of bioreactor culture, organoids were gently removed using a wide-mouthed transfer pipet, and fixed overnight at 4°C in HistoChoice MB (Electron Microscopy Sciences, Hatfield, PA). After fixation, the organoids were embedded in Cytoblock kit cassettes (ThermoFisher, Pittsburgh, PA) and histoprocessed to paraffin. The paraffin/Cytoblock polymer disks containing the organoids were embedded in paraffin, sectioned (4 μm), and stained with hematoxylin and eosin. Microscopic images were captured using IPLab (Scanalytics, Rockville, MD) and analyzed. For each cell line, ten organoids from two separate experiments were randomly selected for analysis. Images were imported into image analysis software (SigmaScan Pro, SPSS Science, Chicago, IL); organoids were manually traced; and maximum cross-sectional areas, perimeters, and shape factors (see below) were calculated by the software.
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9

Stroke Infarct Volume Measurement

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As previously described (Takahashi et al., 1996 (link)), we anesthetized animals deeply at 48 h after stroke induction and collected the brains (N = 8 for mice; N = 12 for rats). Brains were perfused, fixed, sliced coronally, and stained with 1% triphenyltetrazolium chloride (TTC; Sigma) in saline at 37 °C for 30 min. The area of infarcted brain, identified by the lack of TTC staining, was measured on the rostral and caudal surfaces of each slice and numerically integrated across the thickness of the slice to obtain an estimate of infarct volume in each slice (SigmaScan Pro, SPSS Inc., San Jose, CA). The infarct volumes were derived for the cortex, caudoputamenal complex, and entire hemisphere and expressed as a percent of the contralateral uninjured structure. Infarct volume was corrected for swelling by comparing the volumes in the ipsilateral and contralateral hemispheres. The corrected infarct volume was calculated as: volume of contralateral hemisphere – (volume of ipsilateral hemisphere – volume of infarct) (Swanson et al., 1990 (link); Lin et al., 1993 (link)).
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10

TTC Staining for Infarct Quantification

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Freshly cut brain slices were stained with 2% 2,5-triphenyltetrazolium chloride (TTC; T8877, Sigma-Aldrich, St. Louis, MO, USA) in PBS at 37°C for 7.5 minutes and then fixed overnight in 10% buffered formalin (Merck KGaA). The red live and white infarct areas on the posterior side of brain slices were measured using SigmaScan Pro (SPSS Inc., Chicago, IL, USA) by a researcher who was blinded to the genotypes of each mouse. Infarct areas and volume were estimated indirectly to minimize inaccuracy due to swelling (Swanson et al., 1990), and hemispheric swelling was estimated using the following equation: (ipsilateral volume − contralateral volume)/contralateral volume × 100%. Hemorrhagic transformations, identified as dark-brown areas on the posterior side of brain slice number three (at approximately bregma –0.34 mm), were presented as percentages of infarct and contralateral areas.
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