Zen 2012

Manufactured by ZenBio

The Zen 2012 software is a core function software used for image acquisition, processing, and analysis. It provides a platform for managing and manipulating digital images obtained from microscopy and other imaging equipment.

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Lab products found in correlation

Axio observer z1, by Zeiss (3 mentions) Spss statistic, by IBM (1 mentions) Facscalibur software, by BD (1 mentions) Axio imager 2, by ZenBio (1 mentions) Elyra ps 1, by Zeiss (1 mentions) Apotome 2 module, by Zeiss (1 mentions) Axio observer 7, by Zeiss (1 mentions) Lsm 880 airyscan microscope, by Zeiss (1 mentions) Axio cam hr r3, by Zeiss (1 mentions)

8 protocols using zen 2012

Structured Illumination Microscopy for Dynamic Imaging

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Structured Illumination Microscopy was performed using a Zeiss Elyra PS.1 equipped with 488, 555 and 642 nm lasers. Images were acquired with 63×1.4 NA oil immersion objective using pco.edge sCMOS camera and Zen 2012 image analysis software. Typically, images were acquired with 51µm grating and 3 rotations by exciting fluorophores with 1-3% laser intensity and 120-150 ms exposure time. Post-acquisition, images were processed with Zen 2012 using the SIM reconstruction module with default settings and drift corrections between the channels were performed with respect to 100nm Tetraspec fluorescent microspheres (Molecular probes).
To create kymographs image sequences were opened within ImageJ. Curved processes were straightened using the "straighten" macro and kymographs created by the "multiple kymograph" macro. Resultant kymographs show the process along the x-axis and time across the y-axis.

Gupta S., Bazargani N., Drew J., Modi S., Marie H., Attwell D., & Kittler J.T. (2020). The non-adrenergic imidazoline-1 receptor protein Nischarin is a key regulator of astrocyte glutamate uptake.

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Measuring Border Cell Cluster Volume

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For measuring the volume, completely detached border cell clusters at stage 9 that have not reached the oocyte boundary have been considered for analysis.
The border cell clusters are generally spheroid in structure. To measure the size of the cluster, the whole cluster was imaged at 40X magnification taking z stacks at optimal Z intervals suggested by the Zen 2012 software. The image processing and analysis were done using Zen 2012 software. All the stacks were merged to obtain a 2-dimensional maximum intensity projection (MIP) image. The cluster was outlined in the MIP image, the maximum and minimum diameter of the cluster was drawn, and the length obtained from the software was noted. The minor and major axes of the spheroid cluster were obtained by dividing the maximum and minimum diameters by 2 respectively. The Border cell cluster volume was obtained using the formula for spheroid (4/3π a²b, where a is the major axis, and b is the minor axis. Images were acquired in Zeiss Axio observer 7 with Apotome.2 module.

Saha B., Acharjee S., Ghosh G., Dasgupta P, & Prasad M. (2023). Germline protein, Cup, non-cell autonomously limits migratory cell fate in Drosophila oogenesis. PLOS Genetics, 19(2), e1010631.

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Comprehensive Analytical Workflow for Cell Research

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The results are expressed as the mean ± standard deviation (SD). The sample size for analysis was as annotated in figure legends. The differences between two groups were assessed by two-tailed and unpaired t tests. Two-sided log-rank tests were used to analyze Kaplan-Meier curves. P* <0.05, P** <0.01 and P*** <0.001 were considered significant. NovoExpress (version number, 1.4.1.1901) and BD FACSCalibur Software (version number, 1.0.264.21) were used to collect data of flow cytometry. Living Image software (version number, 4.3.1.16427) was used for the bioluminescence and fluorescence imaging. ZEN 2012 (version number, 1.1.13346.204) was used for the immunofluorescence detection. ImageJ (version number, 1.8.0) was used for the semi-quantification of immunofluorescence images. FlowJo (version number, 10.0.0.0), NovoExpress (version number, 1.4.1.1901) and BD FACSCalibur Software (version number, 1.0.264.21) were used to analyze the data of flow cytometry. GraphPad Prism (version number, 8.3.0.538) and IBM SPSS Statistics (version number, 19.0) were used for the statistical analysis.

Ma X., Liang X., Yao M., Gao Y., Luo Q., Li X., Yu Y., Sun Y., Cheng M.H., Chen J., Zheng G., Shi J, & Wang F. (2023). Myoglobin-loaded gadolinium nanotexaphyrins for oxygen synergy and imaging-guided radiosensitization therapy. Nature Communications, 14, 6187.

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CFTR Localization in BEAS-2B Cells

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BEAS-2B cells were grown on coverslips, transfected with the WT or mutants pTracer-CFTR, and treated 24 h later as previously described [19] (link) . Acquisitions were performed with an Axio Imager 2 and the Zen 2012 software. Fluorescence was collected with a X40/0.75 planneofluar lens. The DAPI and A488/FITC fluorescence filter set were fitted to optimize data acquisition and limit bleedthrough. At least, ten representative immunostaining images were taken by transfection.

Bergougnoux A., Billet A., Ka C., Heller M., Degrugillier F., Vuillaume M.L., Thoreau V., Sasorith S., Bareil C., Thèze C., Ferec C., Gac G.L., Bienvenu T., Bieth E., Gaston V., Lalau G., Pagin A., Malinge M.C., Dufernez F., Lemonnier L., Koenig M., Fergelot P., Claustres M., Taulan-Cadars M., Kitzis A., Reboul M.P., Becq F., Fanen P., Mekki C., Audrezet M.P., Girodon E, & Raynal C. (2023). The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy. Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, 22(3).

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Lipofuscin accumulation in nematode intestine

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Nematodes were treated with 94 μg/mL (C_L group) and 119 μg/mL (C_H group) WS-PM_2.5. At 5 d and 10 d, the intestinal autofluorescence of each nematode was observed under an upright fluorescence phase contrast microscope. The images were captured by ZEN2012 software in channel DAPI and the average pixel density was calculated to determine the accumulation of lipofuscin in the nematode intestine.

Zhang W., Li Z., Li G., Kong L., Jing H., Zhang N., Ning J., Gao S., Zhang Y., Wang X, & Tao J. (2023). PM2.5 induce lifespan reduction, insulin/IGF-1 signaling pathway disruption and lipid metabolism disorder in Caenorhabditis elegans. Frontiers in Public Health, 11, 1055175.

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Quantifying α-Synuclein Inclusions in Cells

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In total, 12 images per experiment and time point were captured at days 0, 3, and 6 after α-SYN oligomer exposure. Zen 2012 software was used to analyze the intensity and number of α-SYN inclusions from four independent experiments. The data were analyzed in GraphPad Prism 6.0 software using Kruskal–Wallis statistical analysis.

Rostami J., Holmqvist S., Lindström V., Sigvardson J., Westermark G.T., Ingelsson M., Bergström J., Roybon L, & Erlandsson A. (2017). Human Astrocytes Transfer Aggregated Alpha-Synuclein via Tunneling Nanotubes. The Journal of Neuroscience, 37(49), 11835-11853.

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Zeiss LSM 880 Airyscan Imaging

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For fixed cells imaging Zeiss LSM 880 Airyscan microscope was used to acquire images using 63x 1.4NA Oil DIC Plan-Apochromat objective. Argon (488 nm) and HeNe (633 nm) lasers were used to image the beads and the cells, respectively. Zen 2012 software was used as the interface for data acquisition.

Aramesh M., Mergenthal S., Issler M., Plochberger B., Weber F., Qin X.H., Liska R., Duda G.N., Huppa J.B., Ries J., Schütz G.J, & Klotzsch E. (2021). Functionalized Bead Assay to Measure Three-dimensional Traction Forces during T-cell Activation. Nano letters, 21(1).

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Epifluorescence Microscopy of Fungal Samples

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Samples for standard epifluorescence microscopy were prepared as previously described. 67 In brief, sterile 35-mm l-dishes with a glass bottom (Ibidi, Germany) containing liquid MM supplemented with NaNO3 and 0.1% glucose were inoculated from a spore solution and incubated for 18 h at 25 °C. The images were obtained using an inverted Zeiss Axio Observer Z1 equipped with an Axio Cam HR R3 camera. Image processing and contrast adjustment were made using the ZEN 2012 software while further processing of the TIFF files was made using Adobe Photoshop CS3 software for brightness adjustment, rotation, alignment and annotation.

Zantza I., Papadaki G., Raniolo S., Pyrris Y., Lambrinidis G., Limongelli V., Diallinas G., & Mikros E. (2022). Uracil/H⁺ symport by the FurE transporter challenges the rocking-bundle mechanism of transport in APC transporters.

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