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Zen 2 pro

Manufactured by Zeiss
Sourced in Germany, United States

The Zen 2 Pro is a powerful and versatile microscope imaging software developed by Zeiss. It provides advanced image acquisition, processing, and analysis capabilities for a wide range of microscopy applications. The software offers a user-friendly interface and a comprehensive set of tools to enable efficient and streamlined workflows for researchers and scientists.

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28 protocols using zen 2 pro

1

Fluorescent Imaging of Cerebellar Tissue

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Fluorescent images were digitized using a cooled color CCD camera (AxioCam1Cm1, Zeiss, Oberkochen, Germany) attached to a fluorescent microscope (AxioImager.Z2, Zeiss) in 12-bit gray-scale with appropriate filter sets. To digitize a section of the cerebellum, 2.5X objective and tiling function of the software to control digitizing (Zen 2 Pro, Zeiss) was used. Images of all serial sections of a brain were obtained with the same exposure and gain parameters. Images were adjusted in contrast and brightness and assembled using a software (Zen 2 Pro, Zeiss and Photoshop 7, Adobe, San Jose, CA, USA). High magnification confocal images were taken with a 63X objective lens and appropriate filters and laser light sources attached to the confocal microscope (TCS SP8, Leica, Wetzlar, Germany). Images were adjusted in contrast and brightness and assembled using software (Las X, Leica). A combination of pseudo-colors was applied to fluorescent and confocal images in figures. Photographs were assembled using Photoshop and Illustrator software (Adobe). Digital enhancements were applied to entire images and no manipulations were applied other than contrast or brightness.
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2

Immunofluorescence Staining of Cultured Cells

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Cells were seeded on coverslips for 12–24 h, washed once in Dulbecco’s Phosphate Buffer Saline (DPBS, Lonza) containing Calcium and Manganese and fixed with 4% paraformaldehyde (PAF) in PBS (Phosphate Buffer Saline) pH 7.3, for 30 min at room temperature. Coverslips were subsequently washed three times with PBS. Cells were permeabilized with 0.5% Triton X-100 in PBS for 15 min then washed three times with PBS. Coverslips were then saturated for 1 h in blocking buffer [0.2% gelatin, 2% Bovine Serum Albumin (BSA), 2% FBS (Lonza) in PBS], followed by the incubation for 1 h with primary antibody diluted at 1:100 in blocking buffer, except for GPP130 that was diluted at 1:300. After washing with PBS, cells were incubated for 1 h with Alexa 488- or Alexa 568- secondary antibody (Life Technologies) diluted at 1:600 in blocking buffer. After three washes with PBS, nuclei were labeled with DAPI 1:300 for 15 min and then coverslips were mounted on glass slides with Mowiol. Fluorescence was detected through an inverted Zeiss LSM700 confocal microscope. Acquisitions were done with ZEN pro 2.1 software (Zeiss, Oberkochen, Germany).
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3

Immunofluorescence Staining Protocol for Cells

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Cells were seeded on coverslips for 12 to 24h, washed once in Dulbecco’s Phosphate Buffer Saline (DPBS, Lonza) and fixed either with 4% paraformaldehyde (PAF) in PBS pH 7.3, for 30 min at room temperature or with ice-cold methanol for 10 minutes at room temperature. Coverslips were then washed three times with PBS. Only if the fixation had been done with PAF, cells were permeabilized with 0.5% Triton X-100 in PBS for 15 min then washed three times with PBS. Coverslips were then put in saturation for 1h in blocking buffer [0.2% gelatin, 2% Bovin Serum Albumin (BSA), 2% Fetal Bovine Serum (FBS) (Lonza) in PBS], followed by the incubation for 1h with primary antibody diluted at 1:100 in blocking buffer. After washing with PBS, cells were incubated for 1h with Alexa 488-, Alexa 568- or Alexa 700-conjugated secondary antibody (Life Technologies) diluted at 1:600 in blocking buffer. After three washing with PBS, coverslips were mounted on glass slides with Mowiol. Fluorescence was detected through an inverted Zeiss LSM780 confocal microscope. Acquisition were done using the ZEN pro 2.1 software (Zeiss, Oberkochen, Germany). For selective membrane permeabilization, we have used digitonine. Stock solution was prepared at 5mg/mL in absolute ethanol, 0,3M sucrose, 0,1M KCl, 2,5 mM MgCl2, 1 mM EDTA, 10 mM HEPES, pH 6,9. Permeabilization was done at 4°C during 15min.
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4

Immunofluorescence detection of HS3ST3B

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Microscopy experiments were performed essentially as described in [30 (link)]. For the detection of HS3ST3B, cells were seeded on glass coverslips, washed with PBS and fixed in 4% paraformaldehyde in PBS for 30 min. They were then permeabilized with 0.1% saponin in PBS, treated with a blocking solution containing 0.2% gelatin, 2% BSA and 2% FCS in PBS and incubated with the anti-HS3ST3B antibody (1:100) in the blocking buffer for 1 h After washing, cells were incubated for 1 h with Alexa 568-conjugated secondary antibodies (1:600) in blocking buffer. For the detection of 3-O-sulfated HS, recombinant HSV-1 gD (10 μg/mL) was first incubated with anti-HSV-1 gD antibody (1:100) in blocking buffer for 30 min at 4 °C. The complex was then incubated with the cells for 30 min at room temperature. After washing, cells were fixed and incubated with Alexa 488-conjugated secondary antibody, as above. In all experiments, cells were stained with 500 ng/mL DAPI (Sigma-Aldrich) for 10 min, in order to visualize cell nuclei. Immunofluorescence was analyzed with an inverted Zeiss LSM 780 microscope (Oberkochen, Germany) equipped with a 63 × oil immersion lens. Data were collected using the Zeiss Zen Pro 2.1 software and processed with Image J software (Bethesda, MD, USA).
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5

Immunofluorescence Labeling of Cellular Proteins

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Cells were seeded on coverslips for 24 h, washed twice in Dulbecco’s Phosphate Buffer Saline (DPBS, Lonza) and fixed with 4 % paraformaldehyde (PAF) in PBS (Phosphate Buffer Saline) pH 7.4 for 30 min at room temperature. Coverslips were then washed three times with PBS and cells were permeabilized with 0.5 % Triton X-100 in PBS for 10 min before being washed three times with PBS. Coverslips were then incubated either for 2 h in BSA-Block (Candor-Bioscience, Germany) (SPCA1 antibody) or for 1 h in blocking buffer (0.2 % gelatin, 2 % bovine serum albumin, 2 % fetal bovine serum in PBS) (GM130 and TMEM165 antibodies) and then for 2 h with primary antibody diluted either at 1:100 (anti-SPCA1 and anti-GM130) or 1:300 (anti-TMEM165) in BSA-Block or blocking buffer. After 3 washings with PBS, cells were incubated for 1 h with Alexa Fluor 488-, or Alexa Fluor 568- conjugated secondary antibody (Fisher Scientific) diluted at 1:600 in BSA-Block or blocking buffer. After 3 washings with PBS, nuclei were labelled with DAPI 1:200 for 10 min and then mounted on glass slides with Mowiol. Fluorescence was detected by an inverted Zeiss LSM700 confocal microscope. Acquisitions were done using ZEN Pro2.1 Software (Zeiss, Oberkochen, Germany).
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6

Cell Surface Glycan Profiling via Lectin Staining

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Cells were seeded on glass coverslips in 6-well plates and incubated in the above-described cell culture conditions for 24 h. Cells were then washed three times with Dulbecco’s Phosphate Buffer Saline containing magnesium and calcium (DPBS+/+) (Sigma Aldrich) and fixed with 4% paraformaldehyde (PAF) for 20 min at room temperature. PAF was neutralized by 50 mM NH4Cl [Sigma–Aldrich (St Louis, MO, United States)] for 10 min at room temperature. Neuraminidase from Vibrio Cholerae (Sigma Aldrich) was diluted at 1/60 in PBS (Euromedex) and incubated for 1 h on coverslips, at 37°C. VVL-fluorescein and PNA-Cy5 lectins (Vector Laboratories) were diluted at 2 μg/ml in PBS containing 0.1% bovine serum albumin (BSA) (Roche Diagnostics, Penzberg, Germany) and added on coverslips for 1 h in a humid atmosphere in the dark. Coverslips were then washed three times with PBS and stained with 5 μg/ml DAPI in PBS for 10 min. After one wash with PBS, coverslips were rinsed in deionized water before being mounted on glass slides with Mowiol. Fluorescence was detected through an inverted Zeiss LSM780 confocal microscope. Acquisitions were performed using the ZEN pro 2.1 software (Zeiss, Oberkochen, Germany).
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7

Histological Analysis of Adipose Tissues

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Thoracic aorta (PVAT intact), abdominal aorta (PVAT intact), WAT (renal and gonadal) and BAT (inter-scapular) were harvested, fixed in 70% v/v ethanol and processed through to paraffin wax blocks. Adipose tissue sections were stained with H&E, visualized using light microscopy and analyzed using Zen Pro 2 computer package (ZEISS, UK). Areas of interest were selected, covering 70% of each tissue type per section respectively (PVAT, blood vessel wall, WAT and BAT) and the cell counter Plugin (Image J) was used to calculate average cells per mm2. The thickness (lumen to adventitia) of the blood vessel wall was measured across 12 equidistant regions that covered the entire vessel. Subtle fatty changes were expressed numerically by calculating pixels contained in lipid droplets versus total per region of interest (expressed as percentage) using Adobe Photoshop Version6 in each adipose tissue section (termed vacuolarity). All data reported as mean ± SEM.
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8

Multimodal Microscopic Imaging Protocol

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Digital images were acquired using an Axio Imager M2 (Carl Zeiss) with a digital camera (AxioCam, Zeiss) using Zen Pro 2 software (Zeiss). Digital images of fluorescent ISH were acquired using a Nikon A1si inverted confocal microscope and Nikon Elements software at the University of Michigan BRCF Microscopy Core. Photomicrographs of films were acquired using a SteREO Discovery.V8 stereomicroscope with a digital camera (AxioCam, Carl Zeiss), using the same magnification, illumination, and exposure time for each image. Dark field photomicrographs for silver grains (hybridization signal) were acquired using the same illumination and exposure time for each section, at 10× magnification.
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9

Senescence-Associated β-Galactosidase Staining

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A total of 5 × 105 cells per well were seeded in six‐well plates and stained for senescence‐associated ß‐galactosidase (SA‐ß‐Gal) activity using the cellular senescence assay kit (Cell Biolabs, Inc., San Diego, CA, USA) according to manufacturer’s instructions. Cells were incubated with staining solution overnight (MDA‐MB‐468, BT‐549, MDA‐MB‐231) or for 4 h (HCC‐1500) and visualized using an inverted light microscope (Zeiss Primo Vert, 40× objective, Oberkochen, Germany) and the zen pro 2 (Oberkochen, Germany) acquisition and analysis software.
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10

Microscopic Imaging of Fluorescent ISH

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Digital images were acquired using an Axio Imager M2 (Carl Zeiss) with a digital camera (AxioCam, Zeiss) using Zen Pro 2 (Zeiss). Digital images of fluorescent ISH were acquired using a Nikon A1si inverted confocal microscope and Nikon Elements at the University of Michigan BRCF Microscopy Core. Photomicrographs of films were acquired using a SteREO Discovery.V8 stereomicroscope with a digital camera (AxioCam, Carl Zeiss), using the same magnification, illumination and exposure time for each image. Dark field photomicrographs for silver grains (hybridization signal) were acquired using the same illumination and exposure time for each section, at 10× magnification.
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