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Zen digital imaging software

Manufactured by Zeiss
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Sourced in Germany

Zen digital imaging software is a comprehensive platform for microscopy image acquisition, processing, and analysis. It provides a user-friendly interface for controlling Zeiss microscope hardware and managing experimental data.

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Lab products found in correlation

Lsm 710 confocal microscope, by Zeiss (2 mentions) Prolong gold antifade mountant, by Thermo Fisher Scientific (2 mentions) Rnascope multiplex fluorescent detection kit v2, by Advanced Cell Diagnostics (2 mentions) Plan apochromat, by Zeiss (1 mentions) Laser scanning microscope 700, by Zeiss (1 mentions) Lsm 510 meta, by Zeiss (1 mentions) Axio imager z1 microscope, by Zeiss (1 mentions) Lsm780 confocal laser scanning microscope system, by Zeiss (1 mentions) Prism 7, by GraphPad (1 mentions) Axio observer, by Zeiss (1 mentions) Lsm 800 microscope, by Zeiss (1 mentions) Axiocam 503, by Zeiss (1 mentions) Axio imager a2 microscope, by Zeiss (1 mentions)

Spelling variants of this product

ZEN software (2479 citations) ZEN imaging software (320 citations) ZEISS ZEN Digital Imaging (6 citations) Zen Lite digital imaging software (5 citations) Zeiss Zen Blue 3.4 Lite Digital Imaging Software (2 citations)

10 protocols using zen digital imaging software

1

Immunofluorescence Imaging of Fixed Cells

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Cells were fixed with 4% PFA and washed and blocked with blocking buffer (PBS, 1% bovine serum albumin, and 0.1% saponin). Primary and secondary antibodies were diluted in the blocking buffer and incubated for 1 h. Nuclei were stained with Hoechst 33342 during the incubation with the secondary antibody for automated image acquisition. Alternatively, nuclei were stained with DAPI for confocal microscopy. Confocal microscopy was performed at room temperature using a laser-scanning microscope 700 (ZEISS) with a 63× 1.4 DIC Plan-Apochromat oil-immersion objective. ZEN digital imaging software (ZEISS) was used for image acquisition and processing of the images. All images were exported as TIFF images, and figures were finalized in Adobe Illustrator (Adobe).
Mauthe M., Langereis M., Jung J., Zhou X., Jones A., Omta W., Tooze S.A., Stork B., Paludan S.R., Ahola T., Egan D., Behrends C., Mokry M., de Haan C., van Kuppeveld F, & Reggiori F. (2016). An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication. The Journal of Cell Biology, 214(5), 619-635.
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2

Confocal Microscopy of Stained Samples

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Stained explants were visualized using confocal microscopy and images were taken using an LSM 510 META confocal scanning laser system with a Zeiss AxioImagerZ1 microscope. Optical slice thickness was set to 8.49 μm. Zen digital imaging software (Carl Zeiss) was used to process and analyze the images.
Gunewardene N., Crombie D., Dottori M, & Nayagam B.A. (2016). Innervation of Cochlear Hair Cells by Human Induced Pluripotent Stem Cell-Derived Neurons In Vitro. Stem Cells International, 2016, 1781202.
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3

Multiplex FISH Identification of Virus and Cell Types

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The RNAscope Multiplex Fluorescent Detection Kit v2 (Advanced Cell Diagnostics, Newark, CA) was used to perform dual or triple hybridizations with the MNV-1 minus-strand probe and cell-specific probes (CD11c and CD4 for DC [CD11c+CD4−] and Mφ [CD11c+CD4+]; CD19 for B cells; CD3 for T cells; and EpCAM for epithelial cells) on FFPE tissue sections. Serial sections from individual layers were hybridized with the viral minus-strand probe and one or two of the five cell-specific probes. After horseradish peroxidase (HRP) addition to the probes, a tryamide signal amplification (TSA)-conjugated cyanine 5 (Cy5) fluorophore (Perkin Elmer) was used to visualize viral minus-strand RNA and a TSA-conjugated Cy3 (CD11c, CD19, CD3, and EpCAM) or fluorescein (FITC; CD4) fluorophore was used to visualize the cell-specific transcript. Tissues were counterstained with DAPI and mounted using ProLong Gold Antifade Mountant (ThermoFisher Scientific). Images for FISH were acquired using a Carl Zeiss LSM710 confocal microscope (Germany) using the ZEN Digital Imaging software (Zeiss). Z-stacks were taken at 63x magnification using 0.5 or 1 intervals. Single color controls, along with positive and negative control probes (PPIB and DapB, respectively) were stained in parallel.
Grau K.R., Roth A.N., Zhu S., Hernandez A., Colliou N., DiVita B.B., Philip D.T., Riffe C., Giasson B., Wallet S.M., Mohamadzadeh M, & Karst S.M. (2017). The targets of acute norovirus infection are immune cells in the gut-associated lymphoid tissue. Nature microbiology, 2(12), 1586-1591.
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4

Visualizing YFP-tagged Vc2c-Cyclop1 in V. carteri

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V. carteri transformants expressing YFP-tagged Vc2c-Cyclop1 were examined using an inverted LSM780 confocal laser scanning microscope system (Carl Zeiss GmbH, Germany) and the ZEN digital imaging software (ZEN 2011, Carl Zeiss GmbH, Germany). Excitation was performed using the 514-nm emission line of an argon ion (Ar+) laser. YFP was detected between 520 and 550 nm [60 (link)], and chlorophyll was detected between 650 and 700 nm. Transmission images were obtained by using a transmission-photomultiplier tube (PMT) detector.
Tian Y., Gao S., von der Heyde E.L., Hallmann A, & Nagel G. (2018). Two-component cyclase opsins of green algae are ATP-dependent and light-inhibited guanylyl cyclases. BMC Biology, 16, 144.
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5

Retinal Morphometry Analysis of Kcnj13 Mutants

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H&E stained retinae were imaged using a Zeiss Axio Observer inverted microscope to capture 20x objective magnification images. Individual images were processed into a single stitched image using Zen Digital Imaging Software (Blue edition, Zeiss). Retinomorphometric data was collected from H&E stained wild-type and Kcnj13 mutant retinae. The thickness of the outer nuclear layer (ONL) was measured at 4 equally spaced (300 μm) intervals, starting at the optic nerve (ON) and moving toward the distal ciliary body. At each interval, 3 measurements were taken, and mean value was calculated. A minimum of 3 mice were used per genotype. For comparing age and ONL thickness, mean ONL thickness was calculated, excluding ON values. Percent of ONL thickness relative to wild-type was calculated by dividing the mean Kcnj13 mutant ONL thickness by wild-type ONL thickness. ONL thickness was plotted using GraphPad Prism 7 software (GraphPad Software, La Jolla, CA, USA).
Roman D., Zhong H., Yaklichkin S., Chen R, & Mardon G. (2018). Conditional Loss of Kcnj13 in the Retinal Pigment Epithelium Causes Photoreceptor Degeneration. Experimental eye research, 176, 219-226.
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6

Tissue Rehydration and Immunostaining Protocol

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Slides were rehydrated by incubating in Histoclear solution twice for 5 min each, followed by incubation in 100% ethanol twice for 5 min each, in 95% ethanol twice for 5min each, 70% ethanol twice for 5 min each, once in 35% ethanol for 5 min, and in water for 5 min. Pressure cooker– mediated heat-induced epitope retrieval was carried out in 250 ml of unmasking buffer containing sodium citrate at pH 6. After retrieval, slides were blocked for 30 min in PBS containing 3% normal horse serum after which they were incubated with primary antibody in blocking solution overnight at 4°C. Slides were washed twice with PBS and incubated with secondary antibody at room temperature for 1 hour in the dark. After two PBS washes, 20 ml of mounting medium was added, then slide contents were topped with coverslips, and stored in the dark for 24 hours before imaging on a Zeiss LSM800 microscope and analyzed using the Zen Digital Imaging software.
Ognjenovic N.B., Bagheri M., Mohamed G.A., Xu K., Chen Y., Saleem M.A., Brown M.S., Nagaraj S.H., Muller K.E., Gerber S.A., Christensen B.C, & Pattabiraman D.R. (2020). Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors. Developmental cell, 55(5), 544-557.e6.
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7

Fiber Type-Specific Satellite Cell Analysis

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Images for analysis were captured at 20× magnification, using the Zeiss AxioImager M1 microcope (Zeiss, Oberkochen, Germany). Analysis was performed, using Zen digital imaging software (Zeiss). Fiber type‐specific satellite cell density was assessed using a Pax7 antibody in conjunction with antibodies against MyHC I (fiber type), laminin (fiber borders), and DAPI (nuclei). Cells within the laminin border and positive for both Pax7 and DAPI were counted as satellite cells within each given fiber type. A minimum of 150 fibers per subject was used for fiber type and fiber type‐specific size analysis. For satellite cell analysis, an average of 333 (range 183–631) muscle fibers and 12 satellite cells (range 8–45) per biopsy at each time point were identified. A total of 8002 muscle fibers and 567 satellite cells were included in the analysis.
Murach K.A., Walton R.G., Fry C.S., Michaelis S.L., Groshong J.S., Finlin B.S., Kern P.A, & Peterson C.A. (2016). Cycle training modulates satellite cell and transcriptional responses to a bout of resistance exercise. Physiological Reports, 4(18), e12973.
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8

Quantitative Cell Counting in Mice

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Images for counting were acquired using either a 20× or 40× objective and the Zeiss Zen digital imaging software. Both male and female mice, in equal number, were used for each assessment and two observers masked to genotype and experimental group performed the cell counting.
Ray M.C., Germon P., Vianney A., Portalier R, & Lazzaroni J.C. (2000). Identification by Genetic Suppression of Escherichia coli TolB Residues Important for TolB-Pal Interaction. Journal of Bacteriology, 182(3), 821-824.
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9

Multiplex FISH Identification of Virus and Cell Types

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The RNAscope Multiplex Fluorescent Detection Kit v2 (Advanced Cell Diagnostics, Newark, CA) was used to perform dual or triple hybridizations with the MNV-1 minus-strand probe and cell-specific probes (CD11c and CD4 for DC [CD11c+CD4−] and Mφ [CD11c+CD4+]; CD19 for B cells; CD3 for T cells; and EpCAM for epithelial cells) on FFPE tissue sections. Serial sections from individual layers were hybridized with the viral minus-strand probe and one or two of the five cell-specific probes. After horseradish peroxidase (HRP) addition to the probes, a tryamide signal amplification (TSA)-conjugated cyanine 5 (Cy5) fluorophore (Perkin Elmer) was used to visualize viral minus-strand RNA and a TSA-conjugated Cy3 (CD11c, CD19, CD3, and EpCAM) or fluorescein (FITC; CD4) fluorophore was used to visualize the cell-specific transcript. Tissues were counterstained with DAPI and mounted using ProLong Gold Antifade Mountant (ThermoFisher Scientific). Images for FISH were acquired using a Carl Zeiss LSM710 confocal microscope (Germany) using the ZEN Digital Imaging software (Zeiss). Z-stacks were taken at 63x magnification using 0.5 or 1 intervals. Single color controls, along with positive and negative control probes (PPIB and DapB, respectively) were stained in parallel.
Grau K.R., Roth A.N., Zhu S., Hernandez A., Colliou N., DiVita B.B., Philip D.T., Riffe C., Giasson B., Wallet S.M., Mohamadzadeh M, & Karst S.M. (2017). The targets of acute norovirus infection are immune cells in the gut-associated lymphoid tissue. Nature microbiology, 2(12), 1586-1591.
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10

Quantifying β-Catenin Localization in MMQ Cells

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We determined ␤-Catenin expression in membranes, cytoplasms and nuclei of control and TMZ treated MMQ cells. The technique is already described by us in [39] (link). Cells were collected after 48 h of treatment, washed with PBS, fixated with PFA 4% and let dry on a positive charged slide (60,000 cells/slide approximately). Then, they were permeabilized with 0.3% Triton -PBS and blocked with 5% non-fat milk in 0.3% Triton-PBS for 1 h. Anti total ␤-Catenin [1/100, #A2064, ABclonal, RRID:AB 2764087] and Anti-rabbit Alexa Fluor ® 488 Conjugate [1/200, #4412 Cell Signaling, RRID:AB 1904025] were employed. Replacement of the primary antibody with 0.3% Triton-PBS was used as negative control. DAPI was used for nuclei counterstaining, and slides were mounted with Mowiol mounting media. Slides were examined with an Axio Imager A2 microscope (ZEISS). Photos were taken with ZEISS Axiocam 503 mono at 40 X magnification and images were processed with Zen digital imaging software (ZEISS). Fifteen photos per each condition of three different experiments were analyzed. ␤-Catenin positive membranes, cytoplasms and nuclei were counted, relativized to total nuclei and expressed as percentages.
Demarchi G., Valla S., Perrone S., Chimento A., Bonadeo N., Vitale D.L., Spinelli F.M., Cervio A., Sevlever G., Alaniz L., Berner S, & Cristina C. (2022). β-Catenin is reduced in membranes of human prolactinoma cells and it is inhibited by temozolomide in prolactin secreting tumor models. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine, 44(1).
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