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162 protocols using caseviewer

1

Histomorphometric Analysis of Bone Augmentation

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The resected specimens were then decalcified, trimmed, and embedded in paraffin. The blocks were sectioned serially in 5 μm thickness perpendicular to the long axis of the socket. The central-most section was chosen for histological and histomorphometric analyses. Hematoxylin/eosin and Masson's trichrome staining were performed. The histological slides were scanned using digital slide scanner (Panoramic 250 Flash III, 3DHISTECH, Budapest, Hungary) and observed through CaseViewer (version 2.1, 3DHISTECH). The histomorphometric analysis was performed using CaseViewer (version 2.1, 3DHISTECH) and Photoshop CS6 (Adobe, CA, USA) by a single experienced investigator (H.C.L.) who was blinded to the group assignment.
The histomorphometric measurements were performed for both the entire augmented area and three rectangular regions of interest (ROIs) within the augmented area (each of size 2.0 mm2) set up by dividing the entire augmented area into three equal areas, defined as the coronal1/3, middle1/3, and apical1/3 areas. The following parameters were measured (Figure 2): (i) total augmented area including new bone, residual material, and nonmineralized tissue (TA), (ii) area of newly formed bone (NB), and (iii) area of residual bone substitute material (RM). The number of blood vessels (BV) was measured in each ROI.
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2

Histological Analysis of Rabbit Testes

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After fixation in 4% paraformaldehyde, testicular tissues were dehydrated with graded 75, 85, 95, and 100% alcohol, infiltrated in xylene, embedded in paraffin blocks, sectioned into 4 μm-thick sections, mounted onto slides, and stained with hematoxylin and eosin (HE). The section images were acquired on a Pannoramic MIDI scanner (3DHISTECH, Hungary). Perimeters and cross-sectional areas of seminiferous tubules (μm and μm2) were measured using the liner measurement annotation of Caseviewer (3DHISTECH, Hungary). Thicknesses of spermatogenic cell layers (μm) were measured using liner measurement annotation of Caseviewer (3DHISTECH, Hungary). The thicknesses of each seminiferous tubule were measured 4 times and then averaged. On average, 40–50 tubules were analysed per rabbit.
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3

Chromosome Counting with AZD1775

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Cells were treated with or without AZD1775 (1μM). Cytochalasin B (3 μg/mL) was added at the 20th hour to each culture and incubated at 37C. After 24hrs, the cells were centrifuged at 1000 rpm for 5 min. The supernatant was removed, and the pellet was treated with weak hypotonic solution (0.075 M KCl/0.9% Saline, 1:9) and incubated at 37C for 5 min. After this, the cells were centrifuged and the pellets were fixed in fresh fixative (methanol:acetic acid, 3:1). Cells were dropped onto glass slides prepared and stained with ProLong Gold Antifade Mountant with DAPI (CST) for scoring. The slides were scanned with a 20x/0.8NA plan-apochromat objective in a 3DHistech Pannoramic 250 Flash Scanner (3DHISTECH, Öv u. 3., Hungary). The scanned images were evaluated with Case Viewer (3DHISTECH) in the setting of 20x in Case Viewer. At least 10 areas following the standard specifications, were scored for each slide.
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4

Chromosome Counting with AZD1775

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Cells were treated with or without AZD1775 (1μM). Cytochalasin B (3 μg/mL) was added at the 20th hour to each culture and incubated at 37C. After 24hrs, the cells were centrifuged at 1000 rpm for 5 min. The supernatant was removed, and the pellet was treated with weak hypotonic solution (0.075 M KCl/0.9% Saline, 1:9) and incubated at 37C for 5 min. After this, the cells were centrifuged and the pellets were fixed in fresh fixative (methanol:acetic acid, 3:1). Cells were dropped onto glass slides prepared and stained with ProLong Gold Antifade Mountant with DAPI (CST) for scoring. The slides were scanned with a 20x/0.8NA plan-apochromat objective in a 3DHistech Pannoramic 250 Flash Scanner (3DHISTECH, Öv u. 3., Hungary). The scanned images were evaluated with Case Viewer (3DHISTECH) in the setting of 20x in Case Viewer. At least 10 areas following the standard specifications, were scored for each slide.
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5

Quantifying Interstitial Fibrosis in Tissue

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Tissue samples were sliced at 5-µm thickness and stained with hematoxylin-eosin (HE) and Masson’s stainings. The microscopic images were scanned into a personal computer and quantitatively analysed with Caseviewer (3DHISTECH, Budapest, Hungary). Interstitial fibrosis was quantified on the basis of a colour discrimination algorithm and expressed as a percentage of the reference tissue area. The mean value of the three fields in each section was used for the analysis. Histological examination was performed by the investigators who were blinded to treatment assignment.
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6

Striatal TH-positive Fiber Density Analysis

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TH-positive fiber density in the striata of 3-month-old mice was determined using immunostained coronal striatal sections at approximately A/P +1.32 mm, 0.7 mm, and 0.35 mm relative to bregma. Immunostained sections were scanned with a Pannoramic 250 Flash II scanner (3DHISTECH, Budapest, Hungary) at the service provided at the Institute of Biotechnology, University of Helsinki. Images were taken with the CaseViewer (3DHISTECH) software and analyzed using Image-Pro Analyzer 7.0 (Media Cybernetics). The contralateral side of each striatal section was used as a control, the corpus callosum was used to eliminate unspecific background staining, and all analyses were done by the experimenter who was blind to the treatments.
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7

Multinational Thyroid Pathology Consensus

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This study was initially opened to all members of the Asian Working Group in Thyroid Pathology [19 (link),20 (link)], enrolling volunteers who had a special interest and expertise in thyroid pathology. Twelve thyroid pathologists with 8 to 40 years of experience from 12 centers located in Japan (n=4), Korea (n=3), China (n=2), India (n=1), Taiwan (n=1), and Thailand (n=1) were asked to perform a review of 16 whole slide images using a web browser-based image viewer or CaseViewer (3DHistech) installed on a personal computer. Observers were blinded to clinicopathologic data and molecular status. They were asked to interpret histologic features of 16 cases.
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8

Multicolor Immunofluorescence Staining of Spleen

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Spleen samples embedded in optimal cutting tissue reagent (Sakura) were sliced to sections of 6 to 10μm thickness and stained with appropriate primary and secondary antibodies. Primary antibodies: IgD (Southern Biotech), GL7 (clone GL7; eBioscience), B220 (clone RA3–6B2; abcam), Ki-67 (abcam) and cleaved caspase-3 (clone D175; Cell Signaling). Secondary reagents: Alexa Fluor 488-conjugated anti-rat pAb, Alexa Fluor 546-conjugated anti-rat pAb, and cyanine 5-conjugated streptavidin (Jackson ImmunoResearch Laboratories). Nuclei were visualized with DAPI (Boehringer Mannheim), and sections mounted with FluorSave (Calbiochem). Manufacturer instructions (TACS2 TdT-Fluor, Trevigen) were followed for in situ apoptosis detection. Slides were scanned with Pannoramic Flash (3DHistech, Hungary) using 20x/0.8NA objective, and regions of interest were drawn manually using CaseViewer (3DHistech, Hungary) and exported into TIFF files. Raw unedited images were then analyzed using ImageJ/FIJI where the area of the interest was automatically measured. Signals of interest were thresholded and the area and count were measured. Scoring of desired area was done manually with randomly shuffled pictures to reduce bias.
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9

Quantitative Analysis of Pancreatic Islet Morphology

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Stained sections were imaged using a Pannaromic MIDI II digital slide scanner and morphometrical parameters were examined as follows. For each animal, three H&E-stained sections were obtained at 100-µm intervals (n = 3–4 for 1-month-old mice, and n = 3–4 for 4-month-old mice). The total islet number, the size of each islet, and the pancreatic area were counted or analyzed using the software CaseViewer from 3DHISTECH. Briefly, in each section from WT and PAK4 KO groups, islet/pancreas area was the total islet area in a section divided by the total pancreas area of that section; the number of islet per mm2 pancreas area was determined by dividing total islet number by total pancreatic area (mm2). The average islet size was determined by averaging the size of each islet per section. In sections stained with anti-insulin or anti-glucagon antibodies (n = 3–4 for 1-month-old mice, and n = 3–4 for 4-month-old mice), the positive area and the size of each islet were measured using Image J software (version 1.48).
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10

Histopathological and Oxidative Stress Analysis of Myocardial Injury

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Heart tissues were fixed with 4% paraformaldehyde and embedded in paraffin blocks, as well as an optimal cutting temperature (OCT) compound. Then, 5 µm thick slices fixed on the slide were stained with H&E (Servicebio, China) and Masson’s trichrome solution (Servicebio, China) for pathological injury assessment, stained with dihydroethidium (DHE) for ROS fluorescent labeling. All slides were recorded through Pannoramic Digital Slide Scanner and analyzed by CaseViewer (3DHISTECH, Hungary) or Image J software (NIH, USA). Afterward, the myocardial injury was scored in light of the degrees and scope of histopathological lesions in the tissue sections [23 (link), 48 (link)]. The percentage of positive area and total tissue area in the full field was measured for semi-quantitative analysis of collagen hyperplasia and ROS accumulation.
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