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17 protocols using panoramic scanner

1

Histological Analysis of Lung Fibrosis

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For histological analysis, whole lungs were fixed for 24 h in 4% phosphate-buffered formalin (PFA), dehydrated and embedded in paraffin, and 5 μM sections were stained using a Masson trichrome staining kit (G1340, Solarbio, Beijing, China) following the manufacturer’s protocols. To develop a modified Ashcroft score, 5 fields in each lung section were randomly selected under 100× magnification to obtain the mean score by two pathologists in a blinded fashion [45 (link)]. For immunohistochemical staining of a-SMA and collagen I, tissue slides were dewaxed by dimethyl benzene, polarized with descending concentrations of alcohol, and rinsed with deionized water. Endogenous peroxidase activity was blocked by incubating sections in 3% hydrogen peroxide solution at room temperature for 30 min after antigen retrieval. The 10% normal goat serum was used to block the slides for 1 h. Primary antibodies were incubated overnight at 4 °C followed by incubation of secondary antibody for 60 min at room temperature. The slides were visualized by DAB staining, and counterstaining was performed with hematoxylin. Images of the stained sections were obtained with a panoramic scanner (3DHISTECH, Budapest, Hungar).
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2

Quantifying Hepatic Lipid Accumulation

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The histology of the liver tissues was examined using Oil-O-Red (Abcam, #ab223796, USA) staining techniques. The Oil O Red stains lipid droplets bright red and is routinely used to determine lipid accumulation in the tissues [48 (link)]. The frozen tissues were cut into 5-μm thick sections, fixed with 4% paraformaldehyde at 4 °C for 30 min, and then washed with phosphate buffer saline and 60% isopropanol. The liver sections were stained with Oil Red O stain for 1 h at room temperature and then washed with 60% isopropanol, followed by PBS. The tissue slides were cleared with xylene and were mounted with a coverslip using a DPX mounting medium (histological grade, # 06522, Sigma Aldrich, Saint Louis, MO, USA). The histology of the tissue sections was observed under Nikon Eclipse 80i Microscope (magnification, ×400). The results were analyzed in three randomly selected fields of view in each section using the panoramic scanner (3DHISTECH Ltd., Hungary). The average densities of collagen fibres (Masson’s trichome staining) and fat droplets (Oil O Red staining) were calculated. Oil O Red staining was carried out in the dark.
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3

Histological Evaluation of Joints and Spleens

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All mice were sacrificed under anesthesia on day 55. The left rear ankle joint and spleen were collected after treatment. The thymus was weighed to calculate the thymus index by comparing the thymus weight (g) to body weight (g). The ankle joints were collected from indicated mice and fixed in formalin for 24 h, then were subjected to decalcification in 10% EDTA. 4 μm slices of paraffin-embedded joints and spleens were stained for H&E were imaged with a 3D HISTECH panoramic scanner and analyzed with caseviewer software 2.4.0.119028 (3DHISTECH Ltd., Budapest, Hungary). The evaluation criteria for histology images, as well as for the grades of joints and spleens, have been previously reported [26 (link)]. The severity of joint destruction was classified from grade 0 to grade 4 for the intensity of the lining layer hyperplasia, mononuclear cell infiltration, and pannus formation. Five parameters were applied for the pathological evaluation of the spleen: the amount of red pulp, the total number of GCs, cellularity of the periarteriolar lymphoid sheath (PALS), lymphoid follicles, and marginal zone. The inflammation was ranked on a numerical scale from 0–4 (severe change) [26 (link)].
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4

Immunohistochemical Analysis of SCARB2 and HS

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Paraffin-embedded sections of brain, liver, lung and intestine tissues from BALB/c mice were immunostained to evaluate the expression and distribution of HS and SCARB2. Sections were heated, deparaffinized with xylene and then cleared with alcohol. Following antigen retrieval, slides were blocked with 3% normal goat serum in PBS for 1 h. Subsequently, a rabbit anti-SCARB2 antibody (ProteinTech; 1:200 dilution) and a mouse anti-HS IgM (Amsbio, Abingdon, UK; 1:200 dilution) antibody, which can detect various kinds of HS, were incubated with the sections overnight at 4 °C. FITC-conjugated goat anti-rabbit IgG (ServiceBio, Hubei, China) and Cy3-conjugated goat anti-mouse IgM (ServiceBio, Hubei, China) antibodies were subsequently incubated with sections for 1 h at 37 °C. Images were acquired using a Panoramic scanner (3D-Histech, Hungary).
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5

Histological Analysis of Midgut Tissue

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Midguts fixed with 4% paraformaldehyde that were in good condition were pruned, dehydrated, embedded, sliced, stained with hematoxylin and eosin, and sealed using the methods published by Sun et al. [12 ]. The midgut tissue morphology was observed using a panoramic scanner (3D HISTECH, Budapest, Hungary).
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6

Precise Neuroanatomy Mapping via Cryo-slicing

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The brains of 11 out of 15 fish were fixed in 4% paraformaldehyde overnight (Electron Microscopy Sciences, CAS #30525-89-4) and then were immersed in a 40% glucose solution for cryoprotection. After freezing, the brains were cryo-sliced (40 μm slices) and Nissl stained to reveal the position of the electrodes in the brain (i.e., the central area of the telencephalon). All slices were then scanned by automated microscope (Panoramic scanner, 3DHISTECH, Hungary) with a 20× (NA 0.8) and a 40× (NA 0.95) objective. The slices were compared to the neuroanatomical landmarks of [40 (link)] to confirm the recording region.
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7

Histological Analysis of Liver Tissue

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The liver tissues were embedded in paraffin after treatment with a 10% formaldehyde solution overnight. H&E staining of the tissue slides was performed for the examination of the tissue morphology. The Panoramic Scanner (3DHISTECH, Budapest, Hungary) was used to analyze the liver slices.
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8

Sirius Red Staining of Tumor Sections

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Sirius red staining was performed on fixed and paraffin-embedded tumor sections. The sections were first deparaffinized and rehydrated with a graded ethanol series. Hematoxylin was used to stain the nuclei for 8 min, followed by a wash with running tap water. The sections were then incubated with a 0.1% Sirius red–1.3% picric acid solution for 1 h. After that, the sections were rapidly washed with 0.5% acetic acid, dehydrated in three changes of 100% ethanol, and cleared in xylene. Finally, the sections were mounted with EUKITT mounting medium (Orsatech, London, UK). The stained sections were visualized with an Olympus LX2-KSP microscope or a panoramic scanner (3DHISTECH Ltd., Budapest, Hungary) and quantified using HistoQuant software (Quant Center 2.0 software).
Hematoxylin–eosin (H&E) staining was performed as described previously [23 ].
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9

Formalin-Fixed Paraffin-Embedded Tissue Sampling

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After identifying the most suitable formalin-fixed paraffin-embedded (FFPE) tissue blocks per case, fresh slides were sectioned, stained with H&E, and digitized with a Panoramic scanner (3DHISTECH, Budapest, Hungary). Annotations for the prepared TMA were marked on the digitized slides in the CaseViewer software (3DHISTECH) in accordance with the following principles: two cores from the middle of the tumor, two cores from the tumor border (invasive margin) and two cores from the non-tumor area. The blocks were cut into 3.5μm-thick sections. Tissue microarray (TMA) blocks were prepared with a TMA Master II tissue microarrayer (3DHISTECH), containing 0.6 mm-diameter cores.
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10

Quantitative Analysis of SIRT2 Expression in Breast Cancer

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The breast cancer tissue microarrays (TMAs) containing 192 cases of primary breast tumors with annotated receptor status were purchased from US Biomax (BR1921 and BR487). Each specimen consisted of a 5 µM thick core section which was immunostained with anti-SIRT2 antibodies (Sigma). Immunohistochemistry was performed using the avidin-biotin complex method (Vector Laboratories). Additional immunohistochemistry details are provided in the Supplemental Experimental Procedures. IHC staining was analyzed in a pathologist blinded fashion using automated quantitative imaging method (Panoramic scanner, 3D HISTECH). The two-tailed unpaired student’s t-test was used for statistical analysis of SIRT2 expression between patient cohorts.
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