Mirax viewer

Manufactured by Zeiss

Sourced in Germany

The Mirax Viewer is a digital slide viewing software developed by Zeiss. It allows for the display and analysis of high-resolution digital microscope images.

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Lab products found in correlation

Mirax desk, by Zeiss (3 mentions) Mirax desk digital slide scanner, by Zeiss (2 mentions) Roti histol, by Carl Roth (2 mentions) Mirax scanner, by Zeiss (2 mentions) Entellan, by Avantor (2 mentions) Axiovision 4, by Zeiss (2 mentions) Mouse anti α sma antibody, by Bioss Antibodies (1 mentions) Axiocam 5, by Zeiss (1 mentions) Axioskop, by Zeiss (1 mentions) Biotinylated secondary antibody, by Agilent Technologies (1 mentions) Biotinylated rabbit anti mouse, by Agilent Technologies (1 mentions) Mirax microscope, by Zeiss (1 mentions) Anti human ki 67 clone mib 1, by Agilent Technologies (1 mentions) Vectastain abc kit, by Vector Laboratories (1 mentions) Mirax digital slide scanner, by Zeiss (1 mentions) K3468, by Agilent Technologies (1 mentions) Protein block, by Agilent Technologies (1 mentions) E0431, by Agilent Technologies (1 mentions) Ab5694, by Abcam (1 mentions) Mach 3 mouse ap polymer, by Biocare Medical (1 mentions)

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MIRAX Viewer software Mirax

13 protocols using mirax viewer

Quantifying Pancreatic β-Cell and α-Cell Area

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To quantify fractional β-cell area (BCA), the entire pancreatic section was imaged at the original magnification of ×200 (×20 objective) using a Mirax Scan and Mirax Viewer (Carl Zeiss MicroImaging GmbH). The ratio of BCA to total pancreas area was digitally measured using Image Pro Plus software (Media Cybernetics), as previously reported (7 (link), 8 (link)). Likewise, the ratio of α-cell area to total pancreas area (ACA) was also digitally measured, and the ratio of ACA to BCA was determined in each case. All measurements were conducted by a single investigator (J.I.), and the intraobserver coefficient of variance was 7%. All measurements were conducted twice, and the mean of the two measurements was used. At the time of measurement, the investigator was blinded to both the glycemic and obesity status for each specimen.
To conduct further morphometric analysis, size and density of islets, density of scattered β-cells, and insulin-positive duct cells were quantified in randomly selected areas of the pancreas that contained approximately 100 islets in each case (106 ± 6 islets, total 10 491 islets) using a Mirax Viewer (Carl Zeiss MicroImaging GmbH) (7 (link), 8 (link)). Scattered β-cells were defined as a cluster of three or fewer β-cells in acinar tissue. In addition, β-cell replication and apoptosis were quantified and expressed as percentage of islets.

Inaishi J., Saisho Y., Sato S., Kou K., Murakami R., Watanabe Y., Kitago M., Kitagawa Y., Yamada T, & Itoh H. (2016). Effects of Obesity and Diabetes on α- and β-Cell Mass in Surgically Resected Human Pancreas. The Journal of Clinical Endocrinology and Metabolism, 101(7), 2874-2882.

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Immunohistochemistry for α-SMA in Lung Tissue

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Immunohistochemistry (IHC) for the detection of α‐SMA in formalin‐fixed paraffin‐embedded lung tissue was performed with an Elivision plus Polyer HRP IHC Kit (Cat. #: 9901; MXB, Nanjing, China) according to the manufacturer's instructions. The sections were incubated with a mouse anti‐α‐SMA antibody (Cat. #: bs‐0189R; Bioss, Beijing, China). The stained sections were viewed under the microscope (Zeiss Axioskop and Axiocam 5) at 100–400× magnification. The slides were scanned by a MIRAX Desk Digital Slide Scanner (Zeiss, Gottingen, Germany) and analysed by MIRAX Viewer (Zeiss).

Sun H., Chen J., Qian W., Kang J., Wang J., Jiang L., Qiao L., Chen W, & Zhang J. (2016). Integrated long non‐coding RNA analyses identify novel regulators of epithelial‐mesenchymal transition in the mouse model of pulmonary fibrosis. Journal of Cellular and Molecular Medicine, 20(7), 1234-1246.

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Immunohistochemical Analysis of Tumor Markers

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Immunohistochemistry using sections of paraffin-imbedded tumors was carried out as previously described [30] (link). Briefly, after antigen retrieval (microwave, citrate buffer, ph = 6), mouse anti-YKL-40 or corresponding isotype control (see above) was used as first antibody, respectively, followed by incubation with biotinylated rabbit anti-mouse (Dako, Glostrup, Denmark) and visualization using the streptavidin-alkaline-phosphatase based Vectastain ABC kit (Vector, Burlingame, CA, USA). Slides were scanned by a Mirax microscope (Zeiss, Jena Germany) and the Mirax Viewer (Zeiss) software was used to take images. Other antibodies used for immunohistochemistry (with corresponding biotinylated secondary antibodies (all Dako)) were: Anti murine EDG-1 (S1P1) (Santa Cruz, Heidelberg, Germany), anti-murine CD45 (clone 30-F11, BD) and anti-human Ki-67 (clone MIB-1, Dako). Images of four randomly chosen fields of vision (not containing necrotic areas) were taken with the viewer software. Human Ki-67 or murine CD45 positive cells were counted and murine S1P1 positive areas quantified using the ImageJ software (Wayne Rasband, NIH, USA). Positive cells or percent positive area per field of vision were calculated for each tumor.
Histochemical Masson-Goldner staining of paraffin-imbedded tumors was performed as described [33] .

Salamon J., Hoffmann T., Elies E., Peldschus K., Johansen J.S., Lüers G., Schumacher U, & Wicklein D. (2014). Antibody Directed against Human YKL-40 Increases Tumor Volume in a Human Melanoma Xenograft Model in Scid Mice. PLoS ONE, 9(4), e95822.

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Histological Analysis of Mycobacterial Lung Infection

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For histological analysis lungs from M. bovis BCG and M. tuberculosis infected mice were fixed in 4% phosphate buffered formalin, paraffin-embedded, and 4 μm sections (for M. bovis BCG) and 3 μm sections (for M. tuberculosis) stained with haematoxylin and eosin and a modified Ziehl-Neelsen method. The latter involved staining in a prewarmed (60°C) carbol-fuchsin solution for 10 min followed by destaining in 20% sulphuric acid and 90% ethanol before counterstaining with methylene blue. Histopathological analyses were done by quantification of lung tissue and lung free of lesions on tissue sections comprising a lung surface of 45 ± 20 mm² corresponding to one or two lobe sections per animal. Percentage of free alveolar space corresponds to % lung lesion free /lung tissue. Scorings were determined by a pathologist using digital microscopic images acquired by Mirax Digital Slide Scanner and Mirax Viewer (Carl Zeiss).

Segueni N., Vigne S., Palmer G., Bourigault M.L., Olleros M.L., Vesin D., Garcia I., Ryffel B., Quesniaux V.F, & Gabay C. (2015). Limited Contribution of IL-36 versus IL-1 and TNF Pathways in Host Response to Mycobacterial Infection. PLoS ONE, 10(5), e0126058.

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Immunohistochemical Analysis of Hepatic α-SMA

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Five-µm-thick hepatic tissue sections were deparaffinized in xylene and rehydrated serially with alcohol and water, followed by microwave antigen retrieval for 20 min at 98 °C in 10 mM sodium citrate buffer (0.05% tween 20, pH 6.0). Endogenous peroxidase was blocked with fresh 0.3% hydrogen peroxide in phosphate buffered saline (PBS) for ten minutes at room temperature. Sections were blocked 2 h with protein block (DAKO, Belgium) in PBS containing 0.5% triton and were incubated overnight at 4 °C in the presence of a specific alpha-smooth muscle actin antibody (α-SMA, 1/200, ab5694, Abcam, UK). After being washed three times in PBS, sections were incubated with biotinylated secondary swine anti-rabbit antibody (E0431, DAKO, Belgium) for 1 h and with streptavidine-HRP (1/800, P0397, DAKO, Belgium) for 30 min. α-SMA was visualized using DAB (K3468, DAKO, Belgium) and sections were counterstained with hematoxylin. Sections were observed at 20X magnification Mirax Desk and Mirax viewer, Carl Zeiss MicroImaging, Germany).

Cops J., Mullens W., Verbrugge F.H., Swennen Q., De Moor B., Reynders C., Penders J., Achten R., Driessen A., Dendooven A., Rigo J.M, & Hansen D. (2018). Selective abdominal venous congestion induces adverse renal and hepatic morphological and functional alterations despite a preserved cardiac function. Scientific Reports, 8, 17757.

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Quantifying Adipose Tissue Macrophages

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Paired subcutaneous and visceral adipose tissue specimens were fixed in phosphate-buffered formalin, dehydrated, embedded in paraffin and sectioned at 4 μm. After hydration and heat-induced antigen retrieval, a monoclonal antibody targeted at human CD68 was added to detect macrophages (Anti-Human CD68 clone PG-M1, DakoCytomation, Denmark). MACH 3 Mouse AP-Polymer and Warp Red was used as secondary and detection reagents (Biocare Medical Concord, CA). The sections were counter stained with hematoxylin and mounted. Slides were digitalized (Mirax Desk Digital Slide Scanner, Zeiss, Göttingen, Germany) and macrophages were counted and normalized for analyzed section area (Mirax Viewer, Zeiss). Origin of the tissue was unknown to the observer.

Svensson H., Odén B., Edén S, & Lönn M. (2014). Adiponectin, chemerin, cytokines, and dipeptidyl peptidase 4 are released from human adipose tissue in a depot-dependent manner: an in vitro system including human serum albumin. BMC Endocrine Disorders, 14, 7.

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Hot Spot Analysis of Immune Cells

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A computer assisted hot spot analysis was performed on whole block sections. Images were acquired with a standard light microscope and a CCD camera or a Mirax Midi system (Zeiss, Jena, Germany) for digital slide scanning and Mirax viewer software (Zeiss). Positive cells were manually selected by a pathologist. Numbers of positive cells per mm² in the area with the densest infiltration were evaluated using the image analysis software “Count” (Biomas, Erlangen, Germany). In CD83 stains positive cells showing the morphology of neoplastic HRS cells were excluded from the analysis. For evaluation of CD123 only cells with plasmacytoid morphology were counted.

Tudor C.S., Bruns H., Daniel C., Distel L.V., Hartmann A., Gerbitz A, & Buettner M.J. (2014). Macrophages and Dendritic Cells as Actors in the Immune Reaction of Classical Hodgkin Lymphoma. PLoS ONE, 9(12), e114345.

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Histomorphometric Analysis of Femoral Bone

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Bone histomorphometric analyses were performed using a semiautomatic image analyzing system (Leica Q600 Qwin; Leica Microsystems, Cambridge, UK). The pictures were taken with the Mirax Viewer imaging system (Carl Zeiss MicroImaging GmbH). Each value of trabecular and hypertrophic zone length is the average of three measurements on the same femoral section per mouse. GLS positively stained capillaries were counted in three independent high-power fields (HPF) per mouse. The lengths of the nestin-positive trabecular zone and periostin-positive bone marrow areas were measured in femur sections from 8-day-old mice using the ImageJ program.

Tuorto F., Herbst F., Alerasool N., Bender S., Popp O., Federico G., Reitter S., Liebers R., Stoecklin G., Gröne H.J., Dittmar G., Glimm H, & Lyko F. (2015). The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. The EMBO Journal, 34(18), 2350-2362.

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Immunohistochemical Analysis of Paraffin-Embedded Cardiac Tissue

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Paraffin sections (2 µm) were processed for immunohistochemistry [28 (link)]. Sections were deparaffinized with Roti^®-Histol (Carl Roth, Karlsruhe, Germany 6640) and hydrated by ethanol gradient (100–40%). H&E staining was performed by firstly adding hematoxylin solution (Sigma-Aldrich, GHS316) for 45 s followed by 10 s tap water and incubation of Eosin (Sigma-Aldrich, HT110232) for 1 min. After staining, samples were mounted with Entellan^® (VWR, Radnor, PA, USA 1079610500). Whole heart sections were scanned using MIRAX Scanner from Zeiss (Oberkochen, Germany). Quantification of stained area (cell size) was performed using software MIRAX Viewer and ZEN 2 (blue edition) both from Zeiss.

Ott C., Jung T., Brix S., John C., Betz I.R., Foryst-Ludwig A., Deubel S., Kuebler W.M., Grune T., Kintscher U, & Grune J. (2021). Hypertrophy-Reduced Autophagy Causes Cardiac Dysfunction by Directly Impacting Cardiomyocyte Contractility. Cells, 10(4), 805.

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Histological Analyses of Tissue Samples

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For histological analyses routinely used safranin O, alcian blue, toluidine blue and Masson’s trichrome staining were performed (See Supplemental Materials and Methods).
All samples were dehydrated in ethanol and xylene (ethanol: 70%, 80%, 95%, 100%, 100%, 100% xylene, 100% xylene, 2 min each) and mounted using DPX (Merck, Darmstadt, Germany). Slides were visualised with the Mirax slide scanner (Carl Zeiss NV-SA, Zaventem, Belgium) using the Mirax scan software. Photos of scanned slides were made with the Mirax viewer (Carl Zeiss NV-SA) or images were taken with a Leica DM2000 LED Microscope.

Lo Monaco M., Gervois P., Beaumont J., Clegg P., Bronckaers A., Vandeweerd J.M, & Lambrichts I. (2020). Therapeutic Potential of Dental Pulp Stem Cells and Leukocyte- and Platelet-Rich Fibrin for Osteoarthritis. Cells, 9(4), 980.

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