Zen blue lite software

Manufactured by Zeiss

Sourced in Germany

Zen Blue lite software is a digital imaging and analysis platform designed for microscope systems. It provides core image acquisition and analysis capabilities for users.

Automatically generated - may contain errors

Lab products found in correlation

Axio scan z1, by Zeiss (2 mentions) Lsm 880 confocal microscope, by Zeiss (2 mentions) Lsm 800 instrument, by Zeiss (1 mentions) Axio scanner z1, by Zeiss (1 mentions) Trypan blue dye, by Bio-Rad (1 mentions) Carl epifluorescence microscope, by Zeiss (1 mentions) Tc20 automated cell counter, by Bio-Rad (1 mentions) Axio imager 2 microscope, by Zeiss (1 mentions) Zen black software, by Zeiss (1 mentions) Thunder imager tissue microscope, by Leica camera (1 mentions) Sp 9002, by ZSGB-BIO (1 mentions) Axio scope a1 microscope, by Zeiss (1 mentions)

8 protocols using zen blue lite software

Immunofluorescence Staining and Imaging of LMPs and Rab13

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Cells were seeded on glass slide and fixed with 4% PFA solution for 10 minutes. Fixed cells were permeabilized with 0.5% Triton X-100/PBS solution and blocked with 20% newborn goat serum (NGS). Subsequently, cells were incubated with a cocktail of primary antibodies against LMPs and Rab13 for an hour and then a cocktail of secondary antibodies for an additional half hour. Finally, cells were incubated with a solution of Hoechst 33258 (10 μg/mL) for 10 minutes to stain nuclear DNA and dehydrated sequentially from 70% to 90% to 100% ethanol. ProLong anti-fade was applied to the slide and sealed with a No. 1.5 coverslip. Image acquisition was performed at the Brigham and Women’s Hospital core facility with the Zeiss LSM 800 instrument. Image analysis was performed with the Zeiss ZEN Lite (Blue) software. For measurements of cell diameter, differential interference contrast (DIC) microscopy was performed and cells were picked out by eye from the micrographs. Circular ROIs were drawn around the cells and diameters were automatically computed by the ZEN Lite (Blue) software.

Wang L.W., Wang Z., Ersing I., Nobre L., Guo R., Jiang S., Trudeau S., Zhao B., Weekes M.P, & Gewurz B.E. (2019). Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival. PLoS Pathogens, 15(9), e1008030.

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Quantifying Cardiomyocyte Hypertrophy and Collagen Cross-Linking

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Formaldehyde-fixed heart tissue was paraffin-embedded and sectioned. Midventricular sections (4 μm) were stained following manufactures protocols. Staining with Wheat Germ Agglutinin (WGA) was performed to measure CM cross sectional area (CSA). High-resolution images of histological sections were acquired using an automated slide scanner system (Axio Scan Z1, Carl Zeiss Microscopy, Munich, Germany). Images were inspected using the Zen Lite Blue software (Carl Zeiss Microscopy). CSA was analyzed and calculated blinded to genotype using ImageJ (NIH) software. Staining with Picrosirius Red was performed to measure collagen cross-linking under polarized light [27 (link)]. Images of histological sections were acquired using a confocal laser scanning microscope (LSM800, Carl Zeiss Microscopy, Munich, Germany). Analysis and calculations were performed blinded to genotype using ImageJ (NIH). Amount of collagen cross-linking was quantified by measuring area of cross-linking divided by the area of the whole midventricular section (%).

Andenæs K., Lunde I.G., Mohammadzadeh N., Dahl C.P., Aronsen J.M., Strand M.E., Palmero S., Sjaastad I., Christensen G., Engebretsen K.V, & Tønnessen T. (2018). The extracellular matrix proteoglycan fibromodulin is upregulated in clinical and experimental heart failure and affects cardiac remodeling. PLoS ONE, 13(7), e0201422.

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Histomorphometric Analysis of Ground Sections

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High‐resolution images of the ground sections were acquired using an automated slide scanner system (Axio Scan Z1, Carl Zeiss Microscopy) and assessed by histomorphometry in duplicate by two independent and calibrated examiners (DP and MR) using a dedicated image analysis software (Zen lite Blue software, Carl Zeiss Microscopy). Intraclass correlation coefficients were generated to estimate the intra‐ and inter‐examiner reproducibility. The mean from duplicate measurements was used for the analysis.

Palombo D., Rahmati M., Vignoletti F., Sanz‐Esporrin J., Haugen H.J, & Sanz M. (2021). Hard and soft tissue healing around implants with a modified implant neck configuration: An experimental in vivo preclinical investigation. Clinical Oral Implants Research, 32(9), 1127-1141.

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Ovarian Follicle Quantification Protocol

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Ovaries were dissected and placed in 4% formaldehyde (Chek1 cKO (Ddx4)) & Bouin’s fixative solution (70% saturated picric acid solution (Applichem, A2520, 1000), 25% formaldehyde, 5% glacial acetic acid (Merck, 1.00063.2500)) or 4% formaldehyde for Chek1 cKO (Ddx4-Cre) overnight at 4 °C. The ovaries were washed two times with cold PBS for 30 minutes followed by dehydration with an increasing concentration of ethanol. Subsequently, the samples were submerged in Histo-Clear II (Cat. # HS-202, National Diagnostics) for 30 min. at room temperature. This was repeated another two times (three times in total) with fresh Histo-Clear II. Ovaries were embedded in paraffin blocks and cut to a thickness of 7 μm (sCHEK1 and Chek2) and 6 μm (Chek1 cKO (Ddx4-Cre)) and mounted on poly-L-lysine coated slides. After de-paraffinization and rehydration, the slides were stained with PAS-hematoxylin. The tissue was imaged using a Zeiss Axio scanner Z.1 and follicles with a visible nucleus were counted using the Zen Blue lite software from Zeiss. Primordial follicles contain one layer of flat granulosa cells surrounding the oocytes, primary follicles have one layer of cuboid granulosa cells. Secondary follicles contain two or more layers of granulosa cells and antral follicles are those with one or several cavities (the antrum).

Ruth K.S., Day F.R., Hussain J., Martínez-Marchal A., Aiken C.E., Azad A., Thompson D.J., Knoblochova L., Abe H., Tarry-Adkins J.L., Gonzalez J.M., Fontanillas P., Claringbould A., Bakker O.B., Sulem P., Walters R.G., Terao C., Turon S., Horikoshi M., Lin K., Onland-Moret N.C., Sankar A., Hertz E.P., Timshel P.N., Shukla V., Borup R., Olsen K.W., Aguilera P., Ferrer-Roda M., Huang Y., Stankovic S., Timmers P.R., Ahearn T.U., Alizadeh B.Z., Naderi E., Andrulis I.L., Arnold A.M., Aronson K.J., Augustinsson A., Bandinelli S., Barbieri C.M., Beaumont R.N., Becher H., Beckmann M.W., Benonisdottir S., Bergmann S., Bochud M., Boerwinkle E., Bojesen S.E., Bolla M.K., Boomsma D.I., Bowker N., Brody J.A., Broer L., Buring J.E., Campbell A., Campbell H., Castelao J.E., Catamo E., Chanock S.J., Chenevix-Trench G., Ciullo M., Corre T., Couch F.J., Cox A., Crisponi L., Cross S.S., Cucca F., Czene K., Smith G.D., de Geus E.J., de Mutsert R., de Vivo I., Demerath E.W., Dennis J., Dunning A.M., Dwek M., Eriksson M., Esko T., Fasching P.A., Faul J.D., Ferrucci L., Franceschini N., Frayling T.M., Gago-Dominguez M., Mezzavilla M., García-Closas M., Gieger C., Giles G.G., Grallert H., Gudbjartsson D.F., Gudnason V., Guénel P., Haiman C.A., Håkansson N., Hall P., Hayward C., He C., He W., Heiss G., Høffding M.K., Hopper J.L., Hottenga J.J., Hu F., Hunter D., Ikram M.A., Jackson R.D., Joaquim M.D., John E.M., Joshi P.K., Karasik D., Kardia S.L., Kartsonaki C., Karlsson R., Kitahara C.M., Kolcic I., Kooperberg C., Kraft P., Kurian A.W., Kutalik Z., Bianca M.L., LaChance G., Langenberg C., Launer L.J., Laven J.S., Lawlor D.A., Marchand L.L., Li J., Lindblom A., Lindstrom S., Lindstrom T., Linet M., Liu Y., Liu S., Luan J., Mägi R., Magnusson P.K., Mangino M., Mannermaa A., Marco B., Marten J., Martin N.G., Mbarek H., McKnight B., Medland S.E., Meisinger C., Meitinger T., Menni C., Metspalu A., Milani L., Milne R.L., Montgomery G.W., Mook-Kanamori D.O., Mulas A., Mulligan A.M., Murray A., Nalls M.A., Newman A., Noordam R., Nutile T., Nyholt D.R., Olshan A.F., Olsson H., Painter J.N., Patel A.V., Pedersen N.L., Perjakova N., Peters A., Peters U., Pharoah P.D., Polasek O., Porcu E., Psaty B.M., Rahman I., Rennert G., Rennert H.S., Ridker P.M., Ring S.M., Robino A., Rose L.M., Rosendaal F.R., Rossouw J., Rudan I., Rueedi R., Ruggiero D., Sala C.F., Saloustros E., Sandler D.P., Sanna S., Sawyer E.J., Sarnowski C., Schlessinger D., Schmidt M.K., Schoemaker M.J., Schraut K.E., Scott C., Shekari S., Shrikhande A., Smith A.V., Smith B.H., Smith J.A., Sorice R., Southey M.C., Spector T.D., Spinelli J.J., Stampfer M., Stöckl D., van Meurs J.B., Strauch K., Styrkarsdottir U., Swerdlow A.J., Tanaka T., Teras L.R., Teumer A., Porsteinsdottir U., Timpson N.J., Toniolo D., Traglia M., Troester M.A., Truong T., Tyrrell J., Uitterlinden A.G., Ulivi S., Vachon C.M., Vitart V., Völker U., Vollenweider P., Völzke H., Wang Q., Wareham N.J., Weinberg C.R., Weir D.R., Wilcox A.N., van Dijk K.W., Willemsen G., Wilson J.F., Wolffenbuttel B.H., Wolk A., Wood A.R., Zhao W., Zygmunt M., Chen Z., Li L., Franke L., Burgess S., Deelen P., Pers T.H., Grøndahl M.L., Andersen C.Y., Pujol A., Lopez-Contreras A.J., Daniel J.A., Stefansson K., Chang-Claude J., van der Schouw Y.T., Lunetta K.L., Chasman D.I., Easton D.F., Visser J.A., Ozanne S.E., Namekawa S.H., Solc P., Murabito J.M., Ong K.K., Hoffmann E.R., Murray A., Roig I, & Perry J.R. (2021). Genetic insights into biological mechanisms governing human ovarian ageing. Nature, 596(7872), 393-397.

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Trypan Blue Dye Exclusion Assay

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Trypan blue dye (Cat. # 1450021; BioRad, Hercules, CA, USA) exclusion tests were carried out using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA). Phase contrast images of the cells were visualized using a 20× objective lens on Carl Zeiss epifluorescence microscope (Zeiss, Thornwood, NY, USA) and captured via a charge-coupled device (CCD) camera fitted to the microscope. The Zen Blue Lite software (Carl Zeiss Microscopy GmbH, Jena, Germany) was used to process the images.

Varghese E., Samuel S.M., Varghese S., Cheema S., Mamtani R, & Büsselberg D. (2018). Triptolide Decreases Cell Proliferation and Induces Cell Death in Triple Negative MDA-MB-231 Breast Cancer Cells. Biomolecules, 8(4), 163.

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Photostability and Mechanical Stability of Physically Unclonable Functions

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The photostability test was carried
out with an exposure time of 600 ms. 100 fluorescence microscope images
were taken consecutively with 1 min intervals from the same area of
the sample. The ZEN Blue Lite software of the ZEISS Axio Imager 2
microscope was used for the fluorescence intensity measurements of
randomly generated PUF features. For UV stability, the surface was
exposed to UV light with a power of 3 W at a wavelength of 365 nm
for 6 h. The mechanical stability of PUFs was studied with a linear
abrasion test. Specifically, the sample was glued under a weight of
200 g and moved 30 cm against aluminum foil.

Esidir A., Kayaci N., Kiremitler N.B., Kalay M., Sahin F., Sezer G., Kaya M, & Onses M.S. (2023). Food-Grade Physically Unclonable Functions. ACS Applied Materials & Interfaces, 15(35), 41373-41384.

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Confocal Imaging of Cornea and Lacrimal Gland

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LG images were acquired using Zen Black software (version 2.3 SP1, Zeiss, France) on an LSM 880 confocal microscope (Zeiss, France). Whole LG section images were obtained using a 20×/0.8 objective while co-immunostaining of GFP with E-cadh or Krt19 proteins were observed via 0.36-μm step size z stacks using a 63×/1.4 oil immersion objective. Images were then processed with Zen Black software (version 2.3 SP1, Zeiss) and Zen Blue lite software (version 3.2, Zeiss). Whole-cornea images were acquired using the navigator module on a Leica Thunder Imager Tissue microscope with the large volume computational clearing (LVCC) process. Images were obtained using a 20×/0.55 objective with LAS X software (3.7.4) and processed with Imaris Bitplane software (version 9.8.0). All of the images from a single panel were acquired and processed with the same parameters.

Gautier B., Meneux L., Feret N., Audrain C., Hudecek L., Kuony A., Bourdon A., Le Guiner C., Blouin V., Delettre C, & Michon F. (2022). AAV2/9-mediated gene transfer into murine lacrimal gland leads to a long-term targeted tear film modification. Molecular Therapy. Methods & Clinical Development, 27, 1-16.

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Immunohistochemical Analysis of FLJ20294 Expression

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Paraffin-embedded tissue sections (4.0 µm) were deparaffinized, dehydrated, and rehydrated in a graded ethanol series. Three percent H₂O₂ was added to block endogenous peroxidase activity. After a rinse in distilled water and phosphate-buffered saline (PBS) successively, sections were placed in citrate buffer (10 mM/pH 6.0) and heated in a microwave oven at 95 °C for 30 min. Then, the sections were incubated with primary antibody (Anti-FLJ20294, 1:200, Abclonal) at room temperature for 1.5 h and 4 °C over-night. The color reaction was developed with the HRP-linked polymer detection system (SP9002, ZSGB-BIO, Beijing, China) and counterstaining with hematoxylin. Images were captured with an Axio Scope A1 microscope (Carl Zeiss, Germany) and analyzed using the ZEN Blue Lite software (Carl Zeiss, Germany).

Chen L., Sun Y., Tang M., Wu D., Xiang Z., Huang C.P., You B., Xie D., Ye Q., Yu D, & Chang C. (2022). High-dose-androgen-induced autophagic cell death to suppress the Enzalutamide-resistant prostate cancer growth via altering the circRNA-BCL2/miRNA-198/AMBRA1 signaling. Cell Death Discovery, 8, 128.

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