Zen black 2011

Manufactured by Zeiss

ZEN Black 2011 is a software platform designed for Zeiss microscopy systems. It provides a user interface and tools for controlling and configuring the hardware, as well as for image acquisition, processing, and analysis.

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Zen 2011 software (273 citations) Zen Black (127 citations) ZEN 2011 (black edition) software (11 citations) Zen 2011 Black software (7 citations) Zen 2011 (Black Edition) (7 citations) ZEN 2011 (black version) software (3 citations) ZEN Black Edition 2011 acquisition software (3 citations)

6 protocols using zen black 2011

Characterization of Muse-AT Cell Lineages

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Muse‐AT cells were harvested after the indicated time in culture, spun onto glass slides, and fixed by the addition of cold methanol. The cells were incubated with the following primary antibodies: anti‐stage‐specific embryonic antigen (SSEA‐3; BioLegend, San Diego, CA,
http://www.biolegend.com), anti‐human embryonic cell marker panel (Oct‐4, Nanong, Sox‐2, Tra1‐60, and SSEA‐4; Abcam), and anti‐TGF‐β (Santa Cruz Biotechnology, Santa Cruz, CA,
http://www.scbt.com). The secondary antibodies, used at 1 to 200 dilution, were either mouse or rabbit Alexa Fluor 647 conjugated dye (Thermo Fisher), rat Alexa Fluor 647 conjugated dye (Abcam), and mouse or rabbit Alexa Fluor 488 conjugated dye (Thermo Fisher). The slides were mounted with Mowiol (Sigma‐Aldrich). Images were acquired on an inverted Zeiss LSM 710 (Carl Zeiss Microscopy GmbH, Jena, Germany,
http://www.zeiss.com). Data acquisition was performed using ZEN Black 2011 software (Carl Zeiss Microscopy) and quantification using Fiji (software. For identification of cell lineages, mouse anti‐human SMA (Thermo Fisher), rabbit anti‐human MAP‐2 (AbD Serotech [now Bio‐Rad Laboratories], Hercules, CA,
http://www.bio-rad.com), and rabbit anti‐human α‐fetoprotein (Dako, Agilent Technologies, Santa Clara, CA,
http:www.dako.com) were used, followed by secondary conjugated antibodies.

Gimeno M.L., Fuertes F., Barcala Tabarrozzi A.E., Attorressi A.I., Cucchiani R., Corrales L., Oliveira T.C., Sogayar M.C., Labriola L., Dewey R.A, & Perone M.J. (2016). Pluripotent Nontumorigenic Adipose Tissue‐Derived Muse Cells have Immunomodulatory Capacity Mediated by Transforming Growth Factor‐β1. Stem Cells Translational Medicine, 6(1), 161-173.

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Immunolocalization of 14-3-3 proteins in T. gondii-infected DCs

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DCs were plated on poly-L-lysine coated coverslips and incubated with freshly egressed T. gondii tachyzoites (MOI 3, 6 h or ON). Cells were fixed in 4% paraformaldehyde for 20 min and permeabilized with 0.1 % Triton X-100 in PBS with 100 mM glycine for 20 min. Blocking was done in 5% FBS in PBS for 1 h and incubated with primary antibodies: pan 14-3-3 (H-8) sc-1657 (Santa Cruz Biotechnology), pan 14-3-3 (Rabbit) #8312 (Cell Signaling Technologies), pan 14-3-3 (K-19) sc-629 (Santa Cruz Biotechnology), mAb DG52 to the surface protein SAG1 and polyclonal rabbit Ab to the dense granule protein 7 – GRA7 (R6; Statens Bakteriologiska Laboratorium, Solna, Sweden) for 2 h at RT or ON at 4°C. After washing with PBS, cells were incubated with secondary antibodies for 1 h. Coverslips were mounted and imaged by confocal microscopy. Images were acquired on a Zeiss LSM780 confocal microscope equipped with a GaAsP detector using Zen black 2011 software (Zeiss). Digital images were processed an analyzed using Photoshop CS6 software (Adobe). Color balance, brightness, and contrast settings were manipulated to generate final images. All changes were applied equally to entire image.

Weidner J.M., Kanatani S., Uchtenhagen H., Varas-Godoy M., Schulte T., Engelberg K., Gubbels M.J., Sun H.S., Harrison R.E., Achour A, & Barragan A. (2016). Migratory activation of parasitized dendritic cells by the protozoan Toxoplasma gondii 14-3-3 protein. Cellular microbiology, 18(11), 1537-1550.

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Confocal Microscopy of Labeled Neurons

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Fluorescent antibody labeling of fixed neuronal preparations was visualized at room temperature using an inverted laser-scanning confocal microscope (LSM 780; Carl Zeiss) equipped with a digital microscope camera (AxioCam; Carl Zeiss) and a GaAsP detector (Nikon). Z stacks with optical sections of 0.5-µm intervals were collected using a 40×, 1.3 NA, and 60× oil, 1.4 NA, objective lenses and the Zen 2011 acquisition and imaging software (Zen Black 2011; Carl Zeiss). 3D rendering of confocal z stacks was performed using the Volocity software (PerkinElmer) with the 3D rendering option set to opacity.

Lorenzo D.N., Badea A., Davis J., Hostettler J., He J., Zhong G., Zhuang X, & Bennett V. (2014). A PIK3C3–Ankyrin-B–Dynactin pathway promotes axonal growth and multiorganelle transport. The Journal of Cell Biology, 207(6), 735-752.

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Immunofluorescence Imaging of Type VII Collagen in RDEB Keratinocytes

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RDEB keratinocytes were cultivated in Lab-Tek Chamber slides (Sigma-Aldrich), fixed in 4% formaldehyde (Sigma-Aldrich) for 30 min and blocked in 1% bovine serum albumin (BSA), 0.5% Triton X-100 (Sigma Aldrich) in PBS (Invitrogen, Paisley, UK) for 45 min. As primary antibody, a polyclonal anti-type VII collagen antibody (Calbiochem, San Diego, CA, USA) was used and diluted 1:100 in PBS. After incubation for 1 h at room temperature, cells were incubated with the secondary antibody anti-rabbit AF594 (Invitrogen) for an additional hour in a dilution of 1:400 in PBS in the dark. DAPI (Sigma-Aldrich) staining of the nuclei was performed in a dilution of 1:2000 for 10 min. After mounting (Dako, Vienna, Austria), the sections were analyzed under an inverted confocal laser scanning microscope (LSM700, Carl Zeiss). Images were converted to tiff files with the ZEN Black 2011 (Carl Zeiss) software.

Peking P., Koller U., Duarte B., Murillas R., Wolf S., Maetzig T., Rothe M., Kocher T., García M., Brachtl G., Schambach A., Larcher F., Reichelt J., Bauer J.W, & Murauer E.M. (2017). An RNA-targeted therapy for dystrophic epidermolysis bullosa. Nucleic Acids Research, 45(17), 10259-10269.

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Quantitative Analysis of Mitochondrial DNA

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Cells were seeded on 12 mm glass coverslips, left to attach overnight and treated as indicated. Cells were fixed in 4% paraformaldehyde for 20 min, washed three times in PBS, permeabilized in 0.1% Triton X-100 in PBS for 5 min and blocked in blocking buffer (5% FBS & 2% BSA in PBS) for 1 h. Cells were then incubated in primary antibodies overnight, followed by three washes in PBS and incubation in secondary antibodies for 1.5 h. Samples were then mounted in ProLong^TM Diamond anti-fade mounting medium with DAPI (Life Technologies, P36962), and imaged on an Zeiss LSM 710 confocal microscope at ×60 magnification using ZEN Black 2011 (Zeiss) or Olympus FV3000 confocal microscope at ×100 magnification using FV31-ASW (Olympus). For mtDNA immunostaining, 10 z-stack slices encompassing the entire cell was taken per field. Analysis of mtDNA volume was performed using Imaris v7.4 (Oxford Instruments) as previously described^{12 (link)}. Specifically, cells were individually processed with image segmentation using surface smoothing of 90 nm, background subtraction of 300 nm, and an intensity threshold of 100. Identified structures were identified as mtDNA volumes if the DAPI channel intensity did not exceed the value of 1200.

Tan H.W., Lu G., Dong H., Cho Y.L., Natalia A., Wang L., Chan C., Kappei D., Taneja R., Ling S.C., Shao H., Tsai S.Y., Ding W.X, & Shen H.M. (2022). A degradative to secretory autophagy switch mediates mitochondria clearance in the absence of the mATG8-conjugation machinery. Nature Communications, 13, 3720.

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Immunofluorescence Staining of Tumour Sections

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Tumours arising from Cle-H3 cells with or without the expression of RNF43(3SA) mutant were fixed with 10% formalin and subsequently sectioned at 7 μm using a cryostat (HM550-VPD, Thermo Fisher Scientific). Sections were treated with 0.1% Triton-X in PBS for permeabilization and then with LAB solution (Polyscience, #24310) for antigen retrieval. Each sample was stained with anti-β-catenin mouse IgG1 (BD-TDL #199220) at 1:500 dilution, anti-Vimentin mouse IgM (Sigma, #V5255) at 1:2000 dilution and DAPI (1 μM) in combination with anti-mouse IgG1-Alexa555 (Invitrogen, #A-21127) at 1:1000 dilution and anti-mouse IgM-Alexa488 (Invitrogen, #A-21042) at 1:1000 dilution in 1.5% NGS and 0.1% BSA in TBST after blocking with 5% NGS in TBST. Tumour images were taken using a confocal laser scanning microscope (Carl Zeiss, Axio Imager Z1 & LSM700) equipped with a water-immersion ×40 objective lens (C-Apochromat 40 × /1.20 W Corr M27) and ZEN Black 2011 software (Zeiss). Z-stack images were processed and arranged using ImageJ software (1.52 v, NIH) and Photoshop CS5 (12.0 × 64, Adobe).

Tsukiyama T., Zou J., Kim J., Ogamino S., Shino Y., Masuda T., Merenda A., Matsumoto M., Fujioka Y., Hirose T., Terai S., Takahashi H., Ishitani T., Nakayama K.I., Ohba Y., Koo B.K, & Hatakeyama S. (2020). A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis. Nature Communications, 11, 4586.

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