Dataset 2 contained 1,518 images of colorectal glandular structures in 165 Hematoxylin and Eosin (H&E) stained slides. The slides were digitally scanned at 20 × magnification, with a resolution of 0.62005 μm/pixel, using a Zeiss MIRAX MIDI Slide Scanner. The image dimensions were 520 × 775 pixels for 151 slide scans, and 430 × 575 pixels for 14 slides. 934 gland structures in 74 slides were classified as benign and 584 structures in 91 slides as malignant. The luminance, calculated from the RGB slides were used in the analysis. The images were dithered using uniform noise, to reduce quantization errors.
Mirax midi slide scanner
Manufactured by Zeiss
Sourced in Germany, Hungary
The MIRAX MIDI Slide Scanner is a high-performance digital slide scanning system designed for efficient and accurate digitization of microscope slides. It captures high-resolution images of tissue samples or other specimens mounted on standard glass slides.
Automatically generated - may contain errors
Lab products found in correlation
3 3 diaminobenzidine (dab), by Agilent Technologies (3 mentions)
Pannoramic scanner, by 3DHISTECH (2 mentions)
Glyat primary antibody, by Abcam (2 mentions)
3 3 diaminobenzidine tetrachoric acid, by Merck Group (2 mentions)
Panoramic audience, by 3DHISTECH (2 mentions)
Vector hematoxylin qs, by Vector Laboratories (2 mentions)
Bond max, by Leica (2 mentions)
Extraavidin peroxidase, by Merck Group (1 mentions)
Anti neun clone a60, by Merck Group (1 mentions)
Anti ubiquitin clone ubi 1, by Merck Group (1 mentions)
Hemalum, by Merck Group (1 mentions)
Biotinylated anti rat secondary antibody, by Vector Laboratories (1 mentions)
Bx40 microscope, by Zeiss (1 mentions)
Pannoramic viewer software, by 3DHISTECH (1 mentions)
3 3 diaminobenzidine tetrahydrochloride, by Merck Group (1 mentions)
Harris hematoxylin counterstain, by Merck Group (1 mentions)
Biotinylated goat anti rabbit antibody, by Agilent Technologies (1 mentions)
Vectastain elite abc kit reagent, by Vector Laboratories (1 mentions)
Dpx mountant, by Merck Group (1 mentions)
Anti ng2, by Merck Group (1 mentions)
28 protocols using mirax midi slide scanner
1
Colorectal Glandular Structure Analysis
2
Immunohistochemistry of Mouse Tissues
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Mouse tissues were fixed in 4% paraformaldehyde and embedded in paraffin. Sections were then processed for immunohistochemistry as follows: endogenous peroxidases were inactivated by PBS supplemented with 3% hydrogen peroxide and slides were incubated with PBS containing 10% fetal calf serum to reduce non-specific binding. The sections were then incubated with the following primary antibodies: rat anti-human CD3 (clone CD3-12, known to cross-react with murine CD3 on mouse T cells, AbD Serotec, Kidlington, UK) or anti-iNOS (Assay Designs, Ann Arbor, MI, USA) or anti-LCMV-NP (VL-4, [18 (link)]). Then, sections were stained with biotinylated secondary antibodies specific for rat (DakoCytomation, Glostrup, Denmark). For detection, ExtraAvidin-Peroxidase (Sigma Aldrich, St. Louis, MO, USA) was used. Bound secondary antibody was revealed with 3,3′-diaminobenzidine as chromogen (DakoCytomation, Glostrup, Denmark) to visualize with brightfield microscopy. Slides were scanned using a MIRAX Midi slide scanner (ZEISS, Oberkochen, Germany) at 200× magnification.
3
Automated Immunostaining and Quantification
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At least three mice from all nine genotypes and ages were taken into analysis. Mice were decapitated with a guillotine and the brains isolated. Brain hemispheres were post-fixed for at least 24 hours in buffered, 4% PFA. Paraffin- embedded, 4-μm-thick coronal sections were stained using a BondMax™ (Leica Microsystems GmbH/Menarini, Germany) automated immunostaining system. Analysis was conducted on 5–10 sections per mouse. Sections were pretreated with Citrate, EDTA or Enzyme 1 pretreatment solutions (Menarini, Germany) and immunostained using anti-IBA1 (EDTA pretreatment 20 min, 1:1,000 for 15 min, Wako GmbH, Germany), anti-GFAP (Enzyme 1 pretreatment, 1:500 for 15 min, DAKO, Germany), anti-NeuN (clone A60, Citrate pretreatment 20min, 1:500 for 15 min, Chemicon, Germany), anti-Ubiquitin (clone Ubi-1, EDTA pretreatment 20 min, 1:10,000 for 15 min, Millipore, Germany) and the Bond™ Polymer Refine Detection kit (Menarini, Germany) as described in (Scheffler et al., 2012). Whole tissue sections were fully digitized at a resolution of 230nm using a Mirax Midi slide scanner (Zeiss, Germany) as described in (Krohn et al., 2011) and 10 fields of view (FOV) at a natural magnification (1:1, 230nm per pixel, 53,3 fold on a 24” screen) were analyzed semi-automatically using the BX Analysis software package and a custom programmed macro (Keyence, Germany).
4
Immunohistochemical Analysis of LCMV Nucleoprotein
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Mouse tissues were fixed in cold 4% paraformaldehyde overnight and then embedded in paraffin. Sections were processed for immunohistochemistry as follows. Tissue sections were first incubated in PBS containing 3% hydrogen peroxide to inactivate endogenous peroxidases. Then, sections were blocked with PBS containing 10% FCS to reduce unspecific binding. The sections were then incubated with primary anti-LCMV nucleoprotein sera as described previously (Bergthaler et al., 2007 (link)). Bound primary antibody was stained with biotinylated secondary anti-rat antibody (Vectorlabs) and detected with streptavidin peroxidase (DakiCytomation). Bound secondary antibody was revealed with 3.3’-diaminobenzidine as chromogen (DakoCytomation). Hemalum (Merck) was used to counterstain nuclei. Slides were scanned by using a MIRAX Midi slide scanner (ZEISS, Germany) at 200X magnification.
5
Quantitative Analysis of rnf38 mRNA Expression
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Section images were scanned and captured with a MIRAX MIDI slide scanner (Carl Zeiss, Oberkochen, Germany) and computer software (Pannoramic Scanner; 3DHISTECH, Budapest, Hungary). The staining density of rnf38 mRNA was subjectively scored on a four-point scale as follows: + + + (high), + + (moderate), + (low), and - (absent). Nomenclature for the brain area was adopted from Parhar (1990 ); Soga et al. (2005 (link)), and Ogawa et al. (2016 (link)).
6
Fabrication and Characterization of EPC-Seeded 3D Scaffolds
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Three milliliters of EPC spheroids (6×106 cells/mL; ~150 μm in diameter) was seeded on the electrospun scaffolds, and the cells were monitored using light microscopy during the cell culture. After 3 days of cell culture, the aluminum foil frames were removed from the scaffold using scissors. The fiber structure was mechanically stable because of the colonized cells around the fibers, which formed a hybrid structure of cells and fibers inside the scaffold. Thus, the 3D scaffold structure remained intact without the fibers collapsing during the 3D cell culture, even after the aluminum foil frames were removed from the scaffold.24 As previously described,24 the colonized EPCs on the 3D scaffold were fixed using 3.7% formaldehyde, dried through an ethanol gradient, embedded in paraffin, stained with hematoxylin and eosin (H&E), and examined using a MIRAX MIDI slide scanner (Carl Zeiss, Jena, Germany). Also, cell morphology was confirmed using SEM after EPCs on the 2D or 3D scaffolds were fixed using 3.7% formaldehyde and dried through an ethanol gradient.
7
Quantifying Liver Apoptosis via TUNEL
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Liver samples were fixed in a 10% solution of neutral buffered formalin, dehydrated in graded alcohols, embedded in paraffin wax, and stained with hematoxylin and eosin (H&E). Histological sections were evaluated qualitatively for morphological differences and quantitatively for apoptosis (by TUNEL immunohistochemical assays). TUNEL staining (Research Histology Services, University of Pittsburgh) was performed on the formalin-fixed, paraffin-embedded tissue sections. Apoptotic Kupffer cells and hepatocytes were counted in 10 high-power fields (HPFs) for each mouse. Stained slides were viewed under an Olympus (Tokyo, Japan) BX40 microscope and were scanned using a Mirax MIDI slide scanner (Carl Zeiss Microscopy, Jena, Germany); images were captured using Pannoramic Viewer software (3DHistech, Budapest, Hungary).
8
Immunohistochemical Localization of PSPC1 and IMPα2
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Immunohistochemistry with anti-PSPC1 (Kuwahara et al., 2006 (link)) and anti‑IMPα2 (cat. no. ab84440; Abcam) antibodies was performed as previously described (Loveland et al., 1999 (link)) using 50 mM glycine for antigen retrieval (pH 3.5; >90°C for 8 min), and diluted primary antibodies (0.1% BSA/TBS) for O/N incubation at RT. Control sections lacked primary antibody. Secondary antibody incubations (1:500 in 0.1% BSA/TBS, 1 h), either biotinylated rabbit anti-mouse antibody (cat. no. E0354; DAKO, North Sydney, Australia) or biotinylated goat anti-rabbit antibody (cat. no. 656140; Invitrogen), were followed by Vectastain Elite ABC kit reagent (Vector Laboratories, distributed by Abacus Als, Waterford, Australia). Antibody binding was detected as a brown precipitate following development with 0.20 mg/ml 3,3′-diaminobenzidine tetrahydrochloride (Sigma-Aldrich). Harris hematoxylin counterstain (Sigma-Aldrich) and DPX mountant (Sigma-Aldrich) were applied. Germ and somatic cell types were identified based on nuclear morphology and position within the developing gonad (Byskov, 1986 (link); Russell, 1990 ). Slides were imaged using a Mirax Midi slide scanner (Carl Zeiss, Sydney, Australia) with a 20× objective.
9
Quantitative RNF38 Peptide Staining
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Section images were scanned and captured with a MIRAX MIDI slide scanner (Carl Zeiss) with an appropriate excitation filter for Alexa Fluor 488 and computer software (Pannoramic Scanner). RNF38 peptide staining density was subjectively scored on a four-point scale as follows: + + + (high), + + (moderate), + (low), and – (absent). Nomenclature for the brain area was adopted from Parhar (1990 ); Soga et al. (2005 (link)), and Ogawa et al. (2016 (link)).
10
Hypoxia and Vascular Perfusion Imaging in Tumors
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Mice were i.v. injected with 1.5 mg pimonidazole (Hypoxyprobe) one hour before termination. For determination of tissue perfusion, mice were i.v. injected with 100 µg FITC-labeled Lycopersicon esculentum (tomato) lectin (Vector Labs) 5 min prior to whole body perfusion with PBS followed by tumor dissection and embedding in OCT (TissueTek). Tissue sections (5 µm) were fixed for 10 min in ice-cold acetone, rehydrated in PBS and blocked with 1%BSA in PBST (PBS/0.1% Tween 20) for one hour at room temperature (RT). Sections were then incubated with anti-pimonidazole (Omni Kit Hypoxyprobe) and anti-CD31 (Biolegend) antibodies overnight at 4 °C in blocking buffer. After washing with PBST (3×), antibodies: anti-rabbit-AF568, anti-rat-AF647 (Life Technologies) were incubated for 1 h at RT, counterstained with DAPI (Sigma) and mounted in Prolong Gold (Life Technologies). Pericytes were stained with anti-NG2 (Millipore). pimonidazole, CD31 or NG2 staining was determined using MIRAX MIDI Slide Scanner (Zeiss). Images were acquired with a CLSM SP5 Resonant APD Confocal Microscope (Leica) and analyzed with the Imaris software (Bitplane). Vessel area was calculated using the software Pannoramic Viewer 1.15.2 (3D Histech).
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