Slide scanner

Manufactured by Zeiss

Sourced in Germany, France

The Zeiss Slide Scanner is a high-performance digital imaging system designed for scanning and digitizing glass microscope slides. It captures high-resolution images of slide specimens with exceptional clarity and detail.

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Lab products found in correlation

Axioplan 2 microscope, by Zeiss (5 mentions) Axioimager z2 apotome, by Zeiss (4 mentions) Zen software blue edition, by ZenBio (2 mentions) Alizarin red stain solution, by Merck Group (1 mentions) Hematoxylin, by Merck Group (1 mentions) Alcian blue solution, by Merck Group (1 mentions) Ec plan neofluar 10 0, by Zeiss (1 mentions) Axio imager z1 microscope, by Zeiss (1 mentions) Axiocam hrm, by Zeiss (1 mentions) Metamorph microscopy automation image analysis software, by Molecular Devices (1 mentions) A1r confocal microscope, by Nikon (1 mentions) Observer z1, by Zeiss (1 mentions) Hematoxylin, by Agilent Technologies (1 mentions) 3 3 diaminobenzidine (dab), by Avantor (1 mentions) Il 1β, by Santa Cruz Biotechnology (1 mentions) Coolsnap es camera, by Olympus (1 mentions) Alexa 488, by Thermo Fisher Scientific (1 mentions) 4 6 diamidino 2 phenylindole (dapi), by Thermo Fisher Scientific (1 mentions) Lsm 710, by Zeiss (1 mentions) Guinea pig anti insulin, by Agilent Technologies (1 mentions)

Spelling variants of this product

Axioscan slide scanner (50 citations) Axio Scan.Z1 Slide Scanner microscope (10 citations) Slide Scanner Axio Scan (6 citations) Axioscan 7 Slide Scanner (6 citations) MIRAX Desk Digital Slide Scanner (4 citations) Axio slide scanner (4 citations) AxioZoom Z.1 slide scanner (2 citations) Zeiss Axio Scan Z1 slide scanner fluorescence microscope (2 citations) Mirax Desk slide scanner (2 citations) Axio Scan Z1 Brightfield/Fluorescence Slide Scanner (2 citations)

20 protocols using slide scanner

Histological Analysis of Decalcified Tissue Samples

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The specimens were decalcified in 10% disodium ethylenediamine tetra-acetic acid (pH 7.4) solution for 4 weeks. Then, the specimens were casted by paraffin wax. The microtome was used to slice sample into 4 μm continuous sections in the horizontal direction and mounted on glass slides to be used for further staining.
For staining, the slides were rinsed in distilled water and stained in hematoxylin (Merck, Germany). Slides were counterstained in eosin (Sigma-Aldrich, USA) and dehydrated, cleared, and mounted. Slides were viewed with slide scanner (Zeiss, Germany).
Also, alizarin red was used to identify calcium in tissue sections such as the bone, and the Alcian Blue was used to identify mucosubstances of connective tissues. The first step for staining is deparaffinization then rehydration and staining with Alcian Blue solution (Sigma-Aldrich, USA). Slides were washed and stained in alizarin red stain solution (Sigma-Aldrich, USA). Slides were dehydrated, cleared, and mounted. Slides were viewed with slide scanner (Zeiss, Germany).

Alazzawi M.M., Husein A., Alam M.K., Hassan R., Shaari R., Azlina A, & Salzihan M.S. (2018). Effect of low level laser and low intensity pulsed ultrasound therapy on bone remodeling during orthodontic tooth movement in rats. Progress in Orthodontics, 19, 10.

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Limit of Detection for AFB Imaging

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In order to determine the limit of detection of AFB by using the Zeiss Slide Scanner, two AFB-negative sputum specimens were inoculated with either Mycobacterium bovis BCG strain Pasteur (Collection de l’Institut Pasteur, Paris, France) or with Mycobacterium tuberculosis H37Rv (Collection de l’Institut Pasteur) at inoculum concentration of 0, 10⁰, 10¹,10², 10³, 10⁴, 10⁵ mycobacteria/mL; then stained as described above and read by the Zeiss Slide Scanner without immersion oil.

Zingue D., Weber P., Soltani F., Raoult D, & Drancourt M. (2018). Automatic microscopic detection of mycobacteria in sputum: a proof-of-concept. Scientific Reports, 8, 11308.

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Quantifying Phospho-Tau Immunoreactivity

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Stained sections (3 per condition) were imaged using the slide scanner (Zeiss) at 20 × magnification and cropped into individual sections for analysis using the ImageJ software. Designated regions of interest (ROIs) were drawn for each brain region and phospho-tau immunoreactivity was quantified as a percentage area. The threshold for positive labelling was determined using the normal distribution of immunoreactivity from the control group and set at two standard deviations from the mean.

Baker S, & Götz J. (2016). A local insult of okadaic acid in wild-type mice induces tau phosphorylation and protein aggregation in anatomically distinct brain regions. Acta Neuropathologica Communications, 4, 32.

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Immunofluorescence Microscopy Imaging Protocol

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Images from immunoperoxidase stained sections were captured using a Leica slide scanner and Zeiss Axioplan 2 microscope; from immunofluorescent stained human sections with a Zeiss Axioimager Z2 apotome; from immunofluorescent stained marmoset sections with an Axio Imager Z1 microscope (Zeiss) equipped with a Zeiss Axiocam HRm digital camera using the Axiovision software (v 4.8.1.0) at a resolution of 1024 × 1024 pixels. The objectives used were Zeiss EC-Plan Neofluar 10×0.3, #420 340–9901. Filter sets used for visualizing fluorescently-labeled cells were Zeiss 49 Dapi #488 049-9901-000, and Zeiss HQ Texas Red #000 000-1114-462. Images were adjusted for brightness and sharpness using Adobe Photoshop CS6 software. Planes of sectioning are illustrated in Supplementary Figure S1.

Alzu’bi A., Homman-Ludiye J., Bourne J.A, & Clowry G.J. (2019). Thalamocortical Afferents Innervate the Cortical Subplate much Earlier in Development in Primate than in Rodent. Cerebral Cortex (New York, NY), 29(4), 1706-1718.

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Histopathological Analysis of Vascular Damage

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An expert in animal brain histopathology inspected all stained sections. For each animal, the H&E sections with the most evident effects were selected. These and the sections stained with GFAP and Von Kossa were digitized with a Zeiss slide scanner (Oberkochen, Germany). The H&E sections were inspected for signs and consequences of vascular damage. Fresh micro-hemorrhages produced during the last (sixth) session were evaluated separately from the consequences of small-vessel damage produced during the previous five sessions. The size of glial scars was measured. The GFAP sections were examined for activation of astroglial cells. The Von Kossa stained section was used to confirm the presence of mineralization.

Kobus T., Vykhodtseva N., Pilatou M., Zhang Y, & McDannold N. (2015). SAFETY VALIDATION OF REPEATED BLOOD–BRAIN BARRIER DISRUPTION USING FOCUSED ULTRASOUND. Ultrasound in medicine & biology, 42(2), 481-492.

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Automated AFB Detection Protocol

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The particular application of detecting AFB required a specific parameterization of the Zeiss Slide Scanner. MetaMorph® Microscopy Automation & Image Analysis Software (Molecular Devices Sunnyvale, California, USA) (https://www.moleculardevices.com/systems/metamorph-research-imaging/metamorph-microscopy-automation-and-image-analysis-software) were used for image treatment and AFB counting. Five fields were acquired per slide.

Zingue D., Weber P., Soltani F., Raoult D, & Drancourt M. (2018). Automatic microscopic detection of mycobacteria in sputum: a proof-of-concept. Scientific Reports, 8, 11308.

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Identification of Triple-Negative Breast Tumor Cells

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For the identification of triple-negative subpopulations in 10 whole sections of luminal primary tumors we used standard immunofluorescence imaging. We combined unconjugated primary rabbit ER, PR, and HER2 antibodies into the same secondary channel (Cy7) and additionally imaged panCK (Cy3) and DAPI in order to reveal triple-negative tumor cells (Cy7-negative and Cy3-positive). Fluorescence images were acquired using a ZEISS slide scanner and segmented into approximately 6 million single cells, which were then classified into epithelial and non-epithelial cells based on a random forest object classifier using QuPATH (v.0.2.2).⁶⁶ (link) We applied a Gaussian mixture model to the log-transformed Cy7 single-cell expressions to distinguish cells positive for ER, PR, and HER2 from cells that did not express these markers (R package mclust v.5.4.6).⁵⁶ (link) We included a clinically triple-negative tumor as a true negative reference. Tumor cells with low expression of panCK were identified based on a Gaussian mixture model applied to the log-transformed Cy3 single-cell expressions (R package mclust v.5.4.6)⁵⁶ (link) and excluded from analysis to account for staining and tissue quality effects.

Fischer J.R., Jackson H.W., de Souza N., Varga Z., Schraml P., Moch H, & Bodenmiller B. (2023). Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers. Cell Reports Medicine, 4(3), 100977.

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Microscopy and Image Processing Protocol

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All immunoperoxidase staining figures presented in this study were captured using a Leica slide scanner and Zeiss Axioplan 2 microscope. The double immunofluorescent figures were obtained with a Zeiss Axioimager Z2 apotome and Triple Immunofluorescent images were obtained with a Nikon A1R confocal microscope. Processing of images, which included only adjustment of brightness and sharpness, was achieved using the Adobe Photoshop CS6 software.

Alzu’bi A., Lindsay S., Kerwin J., Looi S.J., Khalil F, & Clowry G.J. (2016). Distinct cortical and sub-cortical neurogenic domains for GABAergic interneuron precursor transcription factors NKX2.1, OLIG2 and COUP-TFII in early fetal human telencephalon. Brain Structure & Function, 222(5), 2309-2328.

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Quantifying Cell Populations in Developing Fetal Brain

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Images from immunoperoxidase‐stained sections were captured using a Leica slide scanner and Zeiss Axioplan 2 microscope; and from immunofluorescent‐stained sections with a Zeiss Axioimager Z2 apotome. Images were adjusted for brightness and sharpness using Adobe photoshop CS6 software. Cells were counted from five sections selected at intervals along the anterior–posterior axis of each fetal sample (12 PCW, n = 2 and 19 PCW, n = 2, therefore n = 10 for each age). Sections were observed under medium magnification; rectangular counting boxes 100 μm in width were placed over the ventricular/subventricular zones (VZ/SVZ) and intermediate zone/cortical plate (IZ/CP) delineated by the nuclear staining (DAPI).

Alzu'bi A, & Clowry G.J. (2019). Expression of ventral telencephalon transcription factors ASCL1 and DLX2 in the early fetal human cerebral cortex. Journal of Anatomy, 235(3), 555-568.

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Quantification of Fetal Brain Cell Types

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Images from immunoperoxidase stained sections were captured using a Leica slide scanner and Zeiss Axioplan 2 microscope; from immunofluorescent stained cells and sections with a Zeiss Axioimager Z2 apotome. Images were adjusted for brightness and sharpness using Adobe Photoshop CS6 software. Cells were counted from 5 sections from each fetal sample (8 PCW, n = 2 and 12 PCW, n = 2, therefore n = 10 for each age). Sections were observed under medium magnification, rectangular counting boxes of 100 μm width were placed over the ventricular/subventricular zones (VZ/SVZ) and intermediate zone/CP (IZ/CP) delineated by the nuclear staining (DAPI) on intact parts of the anterior and posterior cortex but otherwise without examining the section first. For quantification in dissociated culture, cells were cultured from 3 different fetal brains in 12-well plates, each staining combination made in duplicate. Photomicrographs were captured from 3 random fields of view from each well from which cell counts were made (therefore n = 18). Mean values with the standard error were calculated. Experimental groups were compared using a 2-tailed t-test.

Alzu'bi A., Lindsay S.J., Harkin L.F., McIntyre J., Lisgo S.N, & Clowry G.J. (2017). The Transcription Factors COUP-TFI and COUP-TFII have Distinct Roles in Arealisation and GABAergic Interneuron Specification in the Early Human Fetal Telencephalon. Cerebral Cortex (New York, NY), 27(10), 4971-4987.

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