Where appropriate, a sample with no primary antibody was used as a negative control. Whole-slide images were generated using a Panoramic SCAN (3D Histech) and ImageDx was used to generate AI-powered quantitative data. CD45+ cells were identified and quantitated within stained tissue sections as the number of positive cells within the total image analysis area for each sample. An algorithm using automated identification of tissue areas on whole-slide images followed by segmentation of cell nuclei and classification of positive cells was visualized by overlaid masks. The number of positive cells was counted and measured as the total amount of positive cells, total positive cell area, and percentage of positive cells within the total image analysis area for each sample. The intensity measurement was a mean intensity value of all positive cells. Data are reported per tissue.
Panoramic scan
Manufactured by 3DHISTECH
Sourced in Hungary
The Panoramic SCAN is a high-resolution digital slide scanner capable of scanning whole microscope slides. It is designed to digitize pathological samples and produce high-quality digital images for various applications, such as digital pathology and telemedicine.
Automatically generated - may contain errors
Lab products found in correlation
Panoramic viewer software, by 3DHISTECH (2 mentions)
Hematoxylin and eosin, by Merck Group (1 mentions)
Picrosirius red stain, by Polysciences (1 mentions)
Caseviewer software version 2.3, by 3DHISTECH (1 mentions)
Picrosirius red, by Leica (1 mentions)
Benchmark xt, by Roche (1 mentions)
F4 80, by Abcam (1 mentions)
Panoramic viewer program, by 3DHISTECH (1 mentions)
Caseviewer program, by 3DHISTECH (1 mentions)
Caseviewer 2, by 3DHISTECH (1 mentions)
Dab kit, by Vector Laboratories (1 mentions)
Caseviewer, by 3DHISTECH (1 mentions)
Caseviewer software, by 3DHISTECH (1 mentions)
Rnalater solution, by Thermo Fisher Scientific (1 mentions)
Neutral buffered formalin, by Thermo Fisher Scientific (1 mentions)
Densitoquant, by 3DHISTECH (1 mentions)
Pannoramic viewer software, by 3DHISTECH (1 mentions)
Ht7700, by Hitachi (1 mentions)
Image pro plus 6, by Media Cybernetics (1 mentions)
Paraformaldehyde (pfa), by Beyotime (1 mentions)
23 protocols using panoramic scan
1
Quantifying CD45+ Cells in Tissue
2
Histological Analysis of Lung Tissue
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After 2 hours of ventilation, ventilatory settings were switched back to baseline, animals underwent heparinization (1000 IU IV) to avoid postmortem blood clotting, and were euthanized by sectioning the inferior vena cava and abdominal aorta, which led to a massive hemorrhage. The trachea was clamped at end-expiration, and the lungs were extracted en bloc. The left lung was fixed in buffered 10% formaldehyde (Millonig's phosphate buffer, 100 mL HCHO, 900 mL H 2 O, 18.6 g NaH 2 PO4, and 4.2 NaOH) and subsequently embedded in paraffin. Next, 4-μm-thick frontal slices from the apex to the base were cut and stained with hematoxylin and eosin.
The histologic lung slices were then digitized (3DHistech Panoramic Scan, Budapest, Hungary), and images were processed using a routine written in MATLAB to quantify the fraction of air in each specimen. The total specimen area was computed, and the relative proportions of parenchyma, edema, or infiltration (presented in white color), and air (presented in black) were determined in each specimen. Qualitative analysis of parenchyma was performed with different magnifications (100×, 200×, and 400×) in a randomly picked square area.
The histologic lung slices were then digitized (3DHistech Panoramic Scan, Budapest, Hungary), and images were processed using a routine written in MATLAB to quantify the fraction of air in each specimen. The total specimen area was computed, and the relative proportions of parenchyma, edema, or infiltration (presented in white color), and air (presented in black) were determined in each specimen. Qualitative analysis of parenchyma was performed with different magnifications (100×, 200×, and 400×) in a randomly picked square area.
3
Histological Analysis of Repaired Skin
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The tissue sections were stained with hematoxylin and eosin, and images were collected using a Panoramic SCAN (3DHISTECH Ltd., Hungary) at the Kaohsiung Chang Gung Memorial Hospital. For different tattoos, variations in the average epidermal and dermal thickness were measured using CaseViewer software version 2.3 (3DHISTECH Ltd. Hungary).
For the histological study of repaired tissues at 2 and 6 months post-wound creation, a scalpel was used to excise a long rectangular piece of tissue from the center of each wound or normal skin. The samples were immersed and fixed in 10% formalin buffer for 24 h, dehydrated, and embedded in paraffin. Samples were sectioned at a 5-µm thickness and stained with hematoxylin and eosin (Merck, Germany) to observe the skin structure; picrosirius red stain (Polysciences Inc., USA) was used to identify the types and distribution of collagen fibrils, Masson’s trichrome stain HT-15 (Sigma-Aldrich Co., Switzerland) was used to determine the architecture and biosynthesis of collagen, and Verhoeff’s stain (Polysciences Inc., USA) was used to clarify the distribution and maturation of elastin fibrils. The stained tissue sections were analyzed under a light microscope (Leica, Germany) or with a polarizer when picrosirius red images were observed.
For the histological study of repaired tissues at 2 and 6 months post-wound creation, a scalpel was used to excise a long rectangular piece of tissue from the center of each wound or normal skin. The samples were immersed and fixed in 10% formalin buffer for 24 h, dehydrated, and embedded in paraffin. Samples were sectioned at a 5-µm thickness and stained with hematoxylin and eosin (Merck, Germany) to observe the skin structure; picrosirius red stain (Polysciences Inc., USA) was used to identify the types and distribution of collagen fibrils, Masson’s trichrome stain HT-15 (Sigma-Aldrich Co., Switzerland) was used to determine the architecture and biosynthesis of collagen, and Verhoeff’s stain (Polysciences Inc., USA) was used to clarify the distribution and maturation of elastin fibrils. The stained tissue sections were analyzed under a light microscope (Leica, Germany) or with a polarizer when picrosirius red images were observed.
4
Immunostaining of Tumor-Infiltrating Cells
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Paraffin-embedded tissue sections of mouse ID-8 ovarian tumor specimens were obtained from mouse experiments. One slide with maximum tumor area per mouse was sent to pathology core laboratory (National Health Research Institutes, Taiwan) for further staining with F4/80 (Abcam) or GR-1 (BioLegend) antibody by using the automatic slide stainer BenchMark XT (Ventana Medical Systems, AZ). All immunostained slides were digitalized with Panoramic Scan (3DHISTECH Ltd., Budapest, Hungary). Each slide is from one individual tumor, and positively stained cells among the tumor areas in one single slide were counted and divided by the tumor area (mm2). Four or five mice, i.e. 4 to 5 slides, were analyzed per group. Student t test was used for the statistical test (*P<0.05).
5
Fibrosarcoma Tissue Array Aptamer Binding
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The slides of fibrosarcoma tissue array (SO2084) were purchased from Xi'an Elina Biotechnology Co., Ltd. These slides were preheated at 60 °C for 30 min and then immersed in xylene for 30 min. They were sequentially immersed in a gradually decreasing ethanol solution for rehydration (100%, 95%, 90%, 80%, and 70%) at 5 min intervals. They were washed with WB, and placed in 0.01 M citrate (pH 6.0), heat for 20 min. After naturally cooled down at room temperature, they were treated with pre-cooled blocking buffer (BB, 20% FBS and 0.1 mg/mL salmon sperm DNA) for 1 h. They were then incubated with 250 nM Cy5-labeled aptamer S11e and Library for 1 h at 4 °C, separately. Finally, the fluorescence images were captured by a Panoramic SCAN (3DHISTECH, Spain). Fluorescence intensity was calculated and marked as negative (–, <30,000), weak (+, 30,000–60000), moderate (++, 60,000–100000) or strong (+++, >100,000), respectively.
6
Liver Tumor Volume Quantification
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To determine the tumor volume of livers, HE stained sections were scanned by Panoramic Scan (3D Histech Ltd., Budapest, Hungary). The length and width of tumors in each section were determined with the help of Panoramic viewer program (3D Histech Ltd.) Tumor volume was calculated as V = (a2*b*π)/6 where ‘a’ refers to width (mm) and ‘b’ stands for length (mm).
7
Histopathological Analysis of Ubiquitinated H2A and Protamine 1
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The testes were sectioned into 3 μm-thick slices and fixed in paraffin. After deparaffinization and rehydration, the sections were prepared for immunohistochemistry (IHC) staining using primary antibodies against either ubiquitinated H2A (ubH2A) or protamine 1 (Prm1) following a blocking and antigen retrieval procedure. The histopathology slides were scanned at a magnification of 40× using Panoramic Scan (3DHISTECH Ltd., Budapest, Hungary). The staining intensity was scored on a scale of 0 to 3, where 0 indicates no staining, 1 indicates weak staining (light yellow), 2 indicates moderate staining (yellow–brown), and 3 indicates strong staining (brown). The percentage of positively stained cells was scored as follows: 1 (<10%), 2 (10–50%), 3 (50–75%), or 4 (>75%). The staining index was calculated by multiplying the staining intensity score by the percentage of positive cells. The index value ranges from 0 to 12.
8
Histomorphometric Analysis of Pancreatic and Adipose Tissues
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The tissues were fixed in 10% neutral formalin, embedded in paraffin, sectioned (thickness: 5 µm), and stained with H&E. Images of the tissues were captured using Panoramic SCAN (3DHISTECH, Budapest, Hungary), and the pancreatic islet area and the number of beta cells were measured using the CaseViewer program (3DHISTECH, version 2.2). The iWAT, eWAT, and BAT adipocyte areas were measured using the adipocyte tool plugin in ImageJ software 1.52a (NIH, Bethesda, MD, USA).
9
Histopathological Analysis of Tissue Samples
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Tissue samples collected at 3 and 5 dpi were fixed in 10% neutral buffered formalin, processed by a standard histological procedure. Sections with a thickness of 5 µm were cut and stained with haematoxylin and eosin [31 (link)]. The slides were scanned and digitalized with Panoramic SCAN (3DHISTECH Ltd., Hungary), and histopathological lesions were evaluated with CaseViewer 2.2 (3DHISTECH Ltd.).
10
Immunohistochemical Analysis of HK2 Expression
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The immunohistochemistry (IHC) was performed on 5 µm tissue sections using the antibodies of HK2 (Cell Signaling Technology). Briefly, after incubation with primary antibody (1 : 100 diluted with 10 % goat serum in PBS) overnight at 4°C, the slides were washed three times with PBS and incubated with biotin conjugated second antibody (1 : 100, #14708, Cell Signaling Technology) for an additional hour at room temperature. The final image of IHC was developed using a DAB kit (Vector, Burlingame, CA, USA) as described by the manufacturer. The results of the IHC analysis were taken with a digital slide scanning system (Panoramic Scan, 3DHISTECH Ltd.). The results were quantified as mean density (IOD/area) by Image J software.
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