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22 protocols using dmrx microscope

1

Analyzing Spherulitic Superstructure in Extruded Strands

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POM served
for analysis of the spherulitic superstructure of the extruded strands
and for the possible identification of phase separation of PBS and
DEET. We used a DMRX microscope (Leica, Wetzlar, Germany) in transmission
mode, with samples located between crossed polarizers. For the preparation
of sections with a thickness of about 10 μm, a rotary microtome
CUT 5062 (Slee, Mainz, Germany) equipped with a tungsten carbide knife
was used. In addition, samples were heated using a hotstage THMS 600
(Linkam, Tadworth, UK), for confirmation that the initial micrometer-scale
structure of the strands is preserved on heating to 100 °C, being
the maximum evaporation temperature in TGA.
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2

Quantitative Immunohistochemical Analysis of Mucosal Tissues

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The immunohistochemically stained sections were examined using a DMR-X microscope (Leica, Wetzlar, Germany). Digital images were transferred from the microscope (Leica) to the Quantimet, Q 550 IW computerized image analysis system (Leica Imaging Systems, Cambridge, U.K.) (45 (link)). The epithelium and the submucosa were analyzed separately, including the total area of the epithelium and a submucosal area measured from the basal membrane to ~400 μm (355–415 μm) depth into the mucosa. For each tissue section, about eight fields of the epithelium and seven fields of the submucosa were scanned at ×20 magnification. Each field represents an average area of 1.4 ×105 μm2 epithelium and 1.8 ×105 μm2 submucosa; thus, a total area of 1.1 × 106 μm2 epithelium and 1.2 × 106 μm2 sub-mucosal tissue was analyzed. The percentage of cells within the total tissue area was calculated by measuring the hematoxylin-stained cellular area in the total tissue area. The frequency of positively stained cells (CD3+, CD8+, and HLA-DR+ cells) was expressed as the percentage of stained area of the total tissue area. All imaging analyses were performed by a blinded investigator.
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3

Spatial Analysis of Immune Cell Subsets in Tissues

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In situ staining was performed on 8‐μm‐thick sections of frozen biopsies, as previously described 22. Sections were fixed in 2% formaldehyde and stained sequentially. Antibody reagents used for tissue staining are listed in Supporting Information Table 3. The tissue sections stained for Vα7.2 in combination with IL‐18Rα were scanned into digital images using a Pannoramic 250 Flash Slide Scanner (3DHistech, Budapest, Hungary). The distance measurement was performed using the digital microscope application CaseViewer (3DHistech), where the distance from the surface of the double‐positive cells to the basal membrane was measured. The tissue sections stained for HLA‐DR in combination with MR1, and Vα7.2 in combination with CD3 were visualized using DMR‐X microscope (Leica, Weitzlar, Germany) and images were acquired with a Retiga 2000 R camera (Qimaging, Surrey, Canada).
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4

Postnatal Cerebellar Development Analysis

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Analysis of the EGL was performed in 4 predefined regions: the inner and outer portion of lobule V, and the inner and outer portion of lobule IX, respectively (Fig. 1). These regions were chosen as the regions with possible maturational differences in EGL proliferation and in subsequent width. Measurement of the width of the proliferative EGL, as constituted by Ki67-positive cells, was performed by using the ×40 objective lens on the Leica DMRX microscope. The average of the 4 respective measured widths was calculated for each pup. Ki67-negative cells were regarded as differentiated, and were counted over an area of 100 µm. Qualitative evaluation was performed of Purkinje cell (calbindin immunoreactivity) and Bergmann glia morphology (GFAP immunoreactivity) at repeated postnatal ages in both the PT and T groups. Distribution and the presence of immunoreactivity for cleaved caspase-3 and Shh were described qualitatively.
Using the Leica Q500 image analysis system of the microscope, the area of calbindin-positive-stained cells was determined in relation to the area of the molecular layer. Thus, calbindin staining was expressed as percentage positive area in relation to a standardized area of the molecular layer. Nonspecific background staining was taken into consideration.
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5

Histological Characterization of Experimental Gliomas

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Experimental gliomas from CAM and mouse/mice tumors were fixed with formol 10% and embedded in paraffin (Pathology department, CHU Limoges). Tumors were cut into 4 μm sections and stained with hematoxylin-erythrosin-safran. To characterize mouse/mice vessels, an immunohistochemistry with CD31 (1/30, Histonova) was performed. Ki-67 (1/50, Dako) immunostaining was processed with automated immunohistochemistry using the BenchMark technology (Ventana medical Systems). The sections were observed using a DMRX microscope (Leica). Negative controls were obtained by using an isotypic control, mouse IgG (Santa Cruz Biotechnology), or by omitting the primary antibody.
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6

Responsive Gelatin-Based Hydrogel Synthesis

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In a typical experiment, 50 g of gel stock was prepared by dissolving gelatin (2.5 g, 5 wt %) in hot water (47.5 mL, 65 C) and adding NH4OH ( 25%,22 μL ). Aliquots (roughly 1.5 mL) of this hot solution were then transferred to cylindrical glass tubes (60 × 0.6 mm) and allowed to cool down to RT, by which the gels had solidified. The mechanically responsive counterparts were produced by simply dissolving sodium alginate (0.25 g, 0.5 wt %) in water prior to the addition of gelatin. Precipitation was induced by mounting a syringe without a stopper onto these glass tubes that was subsequently filled with 20 mL of either AgNO3 (0.2 to 0.8 M) for SGs or a combination of AgNO3 (0.2 to 0.8 M) and Ca(NO3)2 (0.5 to 4.9 M) for MRGs. After precipitation in the entire gel column was complete, gels were cut into thin slices. These slices were analyzed under a Leica DMRX microscope (SI Appendix, Fig. S5).
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7

Immunohistochemistry Analysis of Tumor Ki67

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Tumors were immediately frozen and embedded in OCT compound. They were left at −80°C until sectioning. 7 μm-thick tumor sections were cut with a cryo-microtome (Leica CM 3050). Samples were fixed in 4% paraformaldehyde, and saturated in 1% BSA before incubation with Ki67 antibody (M7240, clone MIB-1, Dako). Detection was performed with the EnVision System-HRP-DAB (K4010) from Dako, according to the manufacturer's instructions. Finally, sections were counter-stained with hematoxylin (Merck) before mounting on slides with the Coverquick mounting medium (Labonord). The observation was done under the Leica DM-RX microscope.
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8

Image Analysis of H3R Expression

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Image analysis was performed using a DMR-X microscope coupled to a DC500 digital camera (Leica) and the image analysis system Quantimet Q550 (Leica). Nine randomly selected discontinuous fields (20×) per samples were evaluated. The positive area, total area and the integrated optical density of H3R were stained and quantified using the Image-Pro Plus software (Media Cybernetics). The PEA was measured as positive area/total area × 100%. The MD of H3R expression in a selected discontinuous fields was measured as the integrated optical density/total area × 1000. The average of PEA and MD form the above nine fields were calculated as the behalf of a sample for the further data analysis.
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9

Immunofluorescence Staining of Endometrial and Ectocervical Tissue

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Immunofluorescence staining was performed on 8 µm thick sections of cryopreserved endometrial and ectocervical biopsies as previously described (44 (link)). The tissue sections were pre-incubated with an Avidin/Biotin Blocking Kit (Vector Laboratories, Burlingame, CA) and stained sequentially. First, CD1d was detected by mouse anti-human CD1d mAb (clone 51.1) in combination with an Alexa Fluor-594-conjugated donkey anti-mouse IgG mAb (Molecular Probes). Second, HLA-DR was detected with biotinylated mouse anti-human HLA-DR mAb (clone L243) (BD Biosciences) and streptavidin-conjugated Alexa Fluor-488 (Molecular Probes). Finally, tissue sections were mounted with Vectashield containing Dapi (Vector Laboratories, Burlingame, CA), and images acquired on a DMR-X microscope (Leica, Wetzlar, Germany) with a Retiga 2000R camera (QImaging, Surrey, Canada) using Image-Pro Premier 9.1 software (Media Cybernetics, Rockville, USA), which was also used for image processing.
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10

Quantitative Immunohistochemical Analysis of Pancreatic Islets

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Consecutive 8 μm cryosections were prepared from 5 different levels of the pancreas and stained with optimal concentration of anti-CD4, anti-CD8 (both from Affymetrix; Santa Clara, Ca, USA), anti F4/80 and anti-FoxP3 (eBioscience, Nordic Biosite, Täby, Sweden). The slides were then incubated with polymer horseradish peroxidase-labeled secondary antibodies, and 3,3-Diaminobenzidine (DAB), respectively. The stained sections were analyzed in a Leica DMRX microscope. At least 40 islets were analyzed from each pancreas. The scoring of the extent of staining was performed as follows:
CD4/CD8: score 1, cells located peripherally, encircling the islet; score 2, cells infiltrating up to 1/3 of the islet; score 3, cells infiltrating 1/3 to 2/3 of the islet; score 4, cells infiltrating more than 2/3 of the islet.
F4/80: score 1, cells located peripherally, encircling the islet; score 2, discrete presence of cells in islet; score 3, moderate presence of cells in islet; score 4, marked presence of cells in islet.
FoxP3: score 1, only a few positive cells; score 2, low density of positive cells in islet; score 3, moderate density of cells in islet; score 4, high density of cells in islet.
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