Zen v3

Manufactured by Zeiss

Sourced in Germany

Zen v3.1 is a comprehensive software suite designed for operating and controlling microscope systems. It provides a unified interface for seamless integration of various Zeiss microscope models, enabling users to capture, process, and analyze images with efficiency.

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Lab products found in correlation

Lsm800 confocal microscope, by Zeiss (2 mentions) Lsm 880, by Zeiss (2 mentions) Lsm 700, by Zeiss (2 mentions) Prolong gold antifade reagent with dapi, by Thermo Fisher Scientific (1 mentions) Lab tek chamber slide, by Thermo Fisher Scientific (1 mentions) Airyscan, by Zeiss (1 mentions) Biotek cytation 5, by Agilent Technologies (1 mentions) Celldiscoverer 7, by Zeiss (1 mentions) Ttc solution, by Merck Group (1 mentions) Smz168 stereo zoom microscope, by Motic (1 mentions) Axiophot bright field microscope, by Zeiss (1 mentions) Axiocam mrc5 camera, by Zeiss (1 mentions) Lsm 800 microscope, by Zeiss (1 mentions) Duolink pla kit, by Merck Group (1 mentions) Hematoxylin, by Merck Group (1 mentions) Pt link system, by Agilent Technologies (1 mentions) Envision plus system, by Agilent Technologies (1 mentions) Axio observer z1 microscope, by Zeiss (1 mentions) Syto9, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

Zen software V3.1 ZEN Blue software v3.1 ZEN core v3.0 software ZEN v3.1 blue edition Zen Software (Blue Edition) v3.1

10 protocols using zen v3

Rg5 Modulates Lipid Accumulation in NCI-H292 Cells

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NCI–H292 cells were cultured on Lab-Tek chamber slides (Thermofisher Scientific) and incubated overnight with bovine serum albumin (BSA) or BSA-containing oleic acid. Cells were treated with Rg5 (0, 10, 25, or 50 μg/mL for 2 h), washed with 500 μL PBS, and incubated with BODIPY staining solution in the dark for 15 min at 37°C. The cells were washed with 1 mL PBS to remove the medium/serum. Thereafter, the cells were fixed with 4% paraformaldehyde in a PBS solution and washed with PBS three times for 5 min each. A drop of Prolong Gold antifade reagent with DAPI (Molecular Probes, Eugene, OR, USA) was added onto the slide as a mounting solution. Imaging was performed using an LSM800 confocal microscope (Zeiss, Jena, Germany) with the ZEN V3.4 software (Zeiss), and images were captured at 400× magnification. The relative intensity of BODIPY staining was measured using ImageJ software.

Heo H., Kim Y., Cha B., Brito S., Kim H., Kim H., Fatombi B.M., Jung S.Y., Lee S.M., Lei L., Lee S.H., Park G.W., Kwak B.M., Bin B.H., Park J.H, & Lee M.G. (2022). A systematic exploration of ginsenoside Rg5 reveals anti-inflammatory functions in airway mucosa cells. Journal of Ginseng Research, 47(1), 97-105.

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Visualizing Immortalized B-cell Microenvironment

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The immortalized B-cell culturing microenvironment and mRNA expression were visualized using Zeiss LSM 880 with Airyscan. All images were processed using ZEN V3.4 software (Zeiss, Oberkochen, Germany‎). For visualization of immortalized B-cell culturing microenvironment, immortalized B cell expressing red fluorescence protein (RFP) was stained with anti-CD40L mAb. Isotypic antibody was used for negative control.

Wang Z., Zhang T., Anderson A., Lee V., Szymura S., Dong Z., Kuang B., Oh E., Liu J., Neelapu S.S., Kwak L, & Cha S.C. (2023). Immortalized B Cells Transfected with mRNA of Antigen Fused to MITD (IBMAM): An Effective Tool for Antigen-Specific T-Cell Expansion and TCR Validation. Biomedicines, 11(3), 796.

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Quantitative Analysis of Burn Wound Depth and Area

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The prepared tissue slices were imaged in full using either the Biotek Cytation 5 (BioTek Instruments GmbH, Germany) or the slide scanner Axio Scan.Z1 (Carl Zeiss Microscopy GmbH, Germany) and used for quantitative measurements of the maximum depth and total area of the burn damage with ImageJ v1.512 software^{23 (link)} or Zen v3.1 (blue edition; Carl Zeiss Microscopy GmbH, Germany) software. The transmission images were recorded with a 10× objective. Markers of tissue injury, e.g. presence of inflammatory cells and disrupted collagen structure, were identified from fully imaged tissue slices in H&E stained sections by light microscopy. Multiple slices per skin sample were measured for wound area and wound depth by multiple operators (in total 129 values). Skin tissue sections that could not be accurately measured due to separation of the dermis and epidermis or ruptures in tissue structure occurring during processing and sectioning were excluded from the analysis.

von Müller C., Bulman F., Wagner L., Rosenberger D., Marolda A., Kurzai O., Eißmann P., Jacobsen I.D., Perner B., Hemmerich P, & Vylkova S. (2020). Active neutrophil responses counteract Candida albicans burn wound infection of ex vivo human skin explants. Scientific Reports, 10, 21818.

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Quantifying Micronuclei and Blebs

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Following treatments, cells were fixed with 4% PFA in PBS and stained with an anti-phospho-HistoneH3 (Ser10) antibody (1:500, Millipore, Cat# 06-570) as described above. After imaging with a fluorescence microscope (Celldiscoverer 7, Zeiss), the number of cells with MN or blebs was determined. Phospho-HistoneH3 (Ser10)-positive cells were omitted because of nuclear membrane disappearance. At least 200 cells were analyzed per sample (Zen v3.1, Zeiss).

Igarashi T., Mazevet M., Yasuhara T., Yano K., Mochizuki A., Nishino M., Yoshida T., Yoshida Y., Takamatsu N., Yoshimi A., Shiraishi K., Horinouchi H., Kohno T., Hamamoto R., Adachi J., Zou L, & Shiotani B. (2023). An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress. Nature Communications, 14, 4991.

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Measuring Myocardial Infarct Area and Risk

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To assess the ischemic area at risk after 22-26 hours of reperfusion, hearts were excised, infused with PBS and freshly prepared 10% phthalo-blue (PBS with 0.75% tween 20) through the aorta and coronary arteries in a retrograde fashion, frozen at −20°C for 10 minutes, and sliced into five to six 1 mm cross-sections with the aid of a pre-freeze acrylic matrix (ZIVIC Labs). The heart sections were incubated with freshly prepared 1% TTC solution (Sigma-Aldrich) at 37°C for 10 minutes and fixed with formalin. Viable myocardium stained red, and infarcted tissue appeared white. Images (Fig. 5A) were acquired by an MU130 color-complementary metal-oxide-semiconductor (CMOS) camera (AmScope) equipped on an SMZ168 Stereo Zoom microscope (Motic). The infarct area (white), the area at risk (red and white), and the total left ventricle area from each section were measured using ZEN v3.1 (Zeiss). Ratios of infarct area/area at risk (Fig. 5B) and of area at risk/left ventricle (Fig. 5C) were calculated and expressed as percentages.

Liu W., Cronin C.G., Cao Z., Wang C., Ruan J., Pulikkot S., Hall A., Sun H., Groisman A., Chen Y., Vella A.T., Hu L., Liang B.T, & Fan Z. (2022). Nexinhib20 inhibits neutrophil adhesion and β2 integrin activation by antagonizing Rac-1-GTP interaction. Journal of immunology (Baltimore, Md. : 1950), 209(8), 1574-1585.

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Chromosome Preparation and Imaging Workflow

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The chromosome preparation followed Jong and Möller (2000 (link)). Images were captured with a Zeiss Zen v.3.1 and an AxioCam MRc5 camera mounted on an Axiophot brightfield microscope (Zeiss, Welwyn Garden City, UK). Images were manipulated in Gimp v.2.10.24 (The GIMP Development Team, 2019 ), chromosomes measured with Zen, and the karyotype created manually in Powerpoint (Microsoft Office).

Nishii K., Hart M., Kelso N., Barber S., Chen Y., Thomson M., Trivedi U., Twyford A.D, & Möller M. (2022). The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem‐driven shoot diversity. Plant Direct, 6(4), e388.

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Proximity Ligation Assay for LXRα and RXRα

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A PLA was performed using the Duolink PLA kit (Sigma) according to the manufacturer’s guidelines. Briefly, following isolation and differentiation for 5 d, primary murine BMMs were seeded onto coverslips and left overnight to adhere. BMMs were then fixed with 4% paraformaldehyde and permeabilized with 0.025% Triton-X/PBS, followed by incubation with LXRα and RXRα antibodies (Supplementary Table 4) overnight at 4 °C. BMMs were then incubated with PLA probes, followed by ligation and amplification steps. Image data were acquired on an LSM800 microscope (Zeiss) and analyzed using Zen v.3.8 software (Zeiss).

Astuti Y., Raymant M., Quaranta V., Clarke K., Abudula M., Smith O., Bellomo G., Chandran-Gorner V., Nourse C., Halloran C., Ghaneh P., Palmer D., Jones R.P., Campbell F., Pollard J.W., Morton J.P., Mielgo A, & Schmid M.C. (2024). Efferocytosis reprograms the tumor microenvironment to promote pancreatic cancer liver metastasis. Nature Cancer, 5(5), 774-790.

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Immunohistochemistry Protocol for Tissue Sections

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Deparaffinization and antigen retrieval were carried out using the PT-Link System (Dako), followed by immunostaining using the EnVision Plus System (Dako). Tissue sections were incubated with a primary antibody (Supplementary Table 4) at 4 °C overnight, followed by incubation with an HRP-conjugated polymer. Staining was developed using diaminobenzidine and counterstained with hematoxylin (Sigma). Image data were acquired on an Axio Observer Z1 microscope (Zeiss) and analyzed using Zen v.3.8 software (Zeiss).

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Vascular Image Analysis Workflow

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Images were analyzed as described elsewhere, with slight modifications [33 (link)]. All images were adjusted by deblurring and deconvolution. Then, the software was trained to detect vessels using the Instellesis Trainable Segmentation program. Briefly, six random images per condition were chosen, and three classes were distinguished in those images: background, vascular region, and avascular region. A deep segmentation of 120 features was selected, and a suitable classification and identification of vascular regions were performed. Then, the images were uploaded, image analysis was performed, identifying each class. Vascular regions are expressed in pixels² and µm². Statistical analysis was performed with the software ZEN v.3.5 (Carl Zeiss) [33 (link)].

Hernández-Aceves J.A., Cervantes-Torres J., Torres-García D., Zuñiga-Flores F.J., Patiño-Chávez O.J., Peña Agudelo J.A., Aguayo-Flores J.E., Garfias Y., Montero-León L., Romero-Romero L., Pérez-Torres A., Fragoso G, & Sciutto E. (2023). GK-1 effectively reduces angiogenesis and prevents T cell exhaustion in a breast cancer murine experimental model. Cancer Immunology, Immunotherapy, 72(11), 3825-3838.

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Confocal Microscopy of Biofilm Structure

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The biofilm structure was visualized by confocal laser scanning microscopy (CLSM) as described previously (Zhao et al., 2022 (link)) with minor modifications. Overnight cultures were diluted 1,000 (v:v) times in 50 mL fresh TSB broth and biofilms were grown in a beaker (100 mL volume), which were then observed using a confocal laser scanning microscope (ZEISS LSM700, Oberkochen, Germany). Biofilms without planktonic cells were stained using SYTO^® 9 (Thermo Fisher Scientific Inc., Waltham, MA, United States) at 25°C in the dark for 2 min. Biofilms were then visualized using a CLSM by a 20× objective lens with excitation at 488 nm and emission at 500–550 nm. The images were processed by using the Zeiss ZEN (v3.5).

Li Y., Chen N., Wu Q., Liang X., Yuan X., Zhu Z., Zheng Y., Yu S., Chen M., Zhang J., Wang J, & Ding Y. (2022). A Flagella Hook Coding Gene flgE Positively Affects Biofilm Formation and Cereulide Production in Emetic Bacillus cereus. Frontiers in Microbiology, 13, 897836.

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