Zen lite

Manufactured by Zeiss

Sourced in Germany

ZEN lite is a software package designed for microscope image acquisition and basic image processing. It provides a user-friendly interface for controlling Zeiss microscopes and capturing high-quality images.

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ZEN lite software (176 citations) ZEN lite 2011 software (7 citations) ZEN lite blue edition (6 citations) Zen Lite digital imaging software (5 citations) ZEN 2.5 lite software (5 citations) ZEN Blue Edition software version 2.3 lite (4 citations) Zen blue lite 2.3 (4 citations) ZEN 2.6 lite software (4 citations) ZEN 2.6 lite (3 citations) ZEN lite 2010 software (3 citations)

78 protocols using zen lite

Confocal Imaging and Quantification of SARS-CoV-2 Infection

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Immunostaining images were obtained using a Zeiss LSM 780 confocal microscope equipped with a 40x, numerical aperture 1.1 water objective. The following laser lines were used DPSS 561nm (detection range 560–612nm) for Alexa Fluor 546; Diode 405nm (detection range 410–480nm) for DAPI; and Argon 488nm (detection range 490–550nm) for Alexa Fluor 488. Images for the same primary antibody across different samples were acquired and exported under the same settings. Before exporting, contrast adjustment was applied as necessary for individual channels using Zen lite (Zeiss) under the “Display” option. Images were cut by Photoshop and assembled by Illustrator.
For quantification, at least 5 images were collected from each specimen using 40x objectives under the tile scan and z stack mode at same depth. Positive cells were identified according to the subcellular staining pattern and were counted manually using “Events” function of Zen lite (Zeiss). Cells in olfactory or respiratory mucosa were quantified per mm of surface epithelium. By measuring the whole length of Tuj1⁺ epithelium, The SARS-CoV2 infected axons were quantified per μm diameter of axon bundle. Microglia in the olfactory bulb or shedding cells in nasal cavity were quantified per mm² tissue.

Chen M., Pekosz A., Villano J.S., Shen W., Zhou R., Kulaga H., Li Z., Beck S.E., Witwer K.W., Mankowski J.L., Ramanathan M J.r., Rowan N.R, & Lane A.P. (2022). Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants. bioRxiv.

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Intracellular NO and ROS Quantification

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According to a previous method, intracellular NO production was measured using the fluorescence probe 4-amino-5-methylamino-2′,7′-difluorofluorescein diacetate (DAF-FM-DA). Mycelia were stained with DAF-FM-DA for 30 min, and NO was detected with a laser scanning confocal microscope (Carl Zeiss LSM700, Oberkochen, Germany) (14 (link)). The ROS concentration was assessed according to a previously described method, and intracellular ROS production was measured by the fluorescence probe DCFH-DA (52 (link)). The fluorescence was analyzed using Zeiss software (ZEN lite, Zeiss, Göttingen, Germany) (53 (link)).

Hou L., Zhao M., Huang C., Wu X, & Zhang J. (2020). Nitric Oxide Improves the Tolerance of Pleurotus ostreatus to Heat Stress by Inhibiting Mitochondrial Aconitase. Applied and Environmental Microbiology, 86(5), e02303-19.

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Adipocyte Measurement in Para-Ovarian Tissue

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A biopsy of para-ovarian tissue was obtained and fixed in 10% formalin/paraldehyde. Fixed adipose tissue was embedded and stained with haematoxylin and eosin (H&E). Three section levels were obtained from each animal. The slides were scanned and the images analysed using Zen Lite software (Carl Zeiss AG, Germany). A single blinded observer assessed all slides to prevent bias in the analysis. 12 separate fields of view from each whole-image slide were used to assess adipocyte size, which was measured to the nearest µm². The fields for analysis were selected using a randomly placed grid. The results were analysed using a hierarchical logistic regression model, with fixed effects for offspring age and grand-maternal diet. Random effects in the model were included for each animal and each litter-of-origin.

Tarry-Adkins J.L., Aiken C.E., Ashmore T.J, & Ozanne S.E. (2018). Insulin-signalling dysregulation and inflammation is programmed trans-generationally in a female rat model of poor maternal nutrition. Scientific Reports, 8, 4014.

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Fluorescence and 2-Photon Microscopy Imaging

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Example 6

Fluorescence and brightfield microscopy were performed using a Zeiss AxioScope A1. All images were acquired at 1388×1040 pixels using a 40× water objective, N.A. 1.0 (epifluorescence). Fluorescence emission was detected using a charge-coupled device (CCD) camera (MRm). All image acquisition parameters were fixed for each imaging channel for exposure time, excitation intensity and gain. Cells that were dimmer or brighter than the fixed initial acquisition dynamic range were not included for analysis. Time-series images were collected using an open-shutter video configuration in ZenLite (Zeiss). Images were acquired every 167 milliseconds with exposure times of 260 milliseconds. For in vivo 2 photon imaging, juvenile mice (P10-P20) were anaesthetized using ketamine/xylazine/acepromazine and a 4×4 mm square window was made through the skull using a dental drill fitted with a 0.45 mm drill burr. The meninges were carefully removed and the exposed brain was covered with 1% optically clear agar and sealed with a No. 1 round coverslip. The coverslip was secured to the skull using dental cement and a mounting fixture was also placed (FIG. 4A, right panel) to facilitate securing the mouse under the objective to minimize animal movement, breathing artifacts and vibration. Images were acquired at 512×512 pixels using a 40× water objective, N.A. 1.0.

US11300509B2. Cleavable linkers for protein translation reporting (2022-04-12). 9412-1126 Québec inc. [CA]. Inventors: Brian Chen [CA], El Cheikh Ibrahim Kays [US].

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Visualizing Yeast Cells with GFP

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Yeast cells were visualized using an Axio Scope A1 Zeiss microscope (Zeiss, Germany). A GFP filterset (Zeiss), operated at excitation of 470/40 nm, and emission of 525/50 nm, was used to detect green fluorescence. Microscopy data were stored using ZEN lite (Zeiss).

Mirończuk A.M., Biegalska A, & Dobrowolski A. (2017). Functional overexpression of genes involved in erythritol synthesis in the yeast Yarrowia lipolytica. Biotechnology for Biofuels, 10, 77.

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Live/Dead Cell Quantification on Scaffolds

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The cells-containing scaffolds retrieved from the bioreactor were stained for 30 min with 4 μM of calcein AM (Life Technologies Inc., CA, USA) for live cells, and with 4 μM of propidium iodide (PI, Life Technologies, Inc., USA) for dead cells. Live cells stained by calcein AM showed green fluorescence (ex/em ~495 nm/~515 nm), whereas dead cells stained by PI showed red fluorescence (ex/em ~540 nm/~615 nm). Cell survival rate was estimated by a confocal microscope (LSM 780, Zeiss, Germany), and the 3-dimentional images were reconstructed using the supplied software (ZEN lite, Zeiss, Germany).

Chen C.Y., Tseng K.Y., Lai Y.L., Chen Y.S., Lin F.H, & Lin S. (2017). Overexpression of Insulin-Like Growth Factor 1 Enhanced the Osteogenic Capability of Aging Bone Marrow Mesenchymal Stem Cells. Theranostics, 7(6), 1598-1611.

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RNAscope® Analysis of Central Amygdala

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For RNAscope® (ACD, Newark, CA, USA) investigations, central amygdala containing brain sections (12 μm thick) were cut and fixed in 10% formalin (Thermo Fisher Scientific) for 30 minutes. Following two quick washes in phosphate‐buffered saline, brain slices were dehydrated in 50% (5 minutes), 70% (5 minutes) and twice in 100% (5 minutes each) ethanol and then pretreated with protease solution at room temperature for 30 minutes. The protease was washed away with phosphate‐buffered saline. Target probe for GLP‐1R (Rn‐GLP‐1R 315221‐C1), IL‐6 (Rn‐IL‐6‐C3 427141‐C3) and negative control probes were applied directly on the sections to cover them completely and incubated at 40°C for 2 hours in a HybEZ oven (ACD). Then, preamplifier and amplifier probes were added (AMP1, 40°C for 30 minutes; AMP2, 40°C for 15 minutes; AMP3, 40°C for 30 minutes; AMP4‐Alt C for 15 minutes). Finally, brain sections were incubated for 30 seconds with DAPI and mounting medium for fluorescence (Vectashield; Vector Laboratories, Inc., Burlingame, CA, USA). Fluorescence images of the central amygdala were captured at 40× using a LSM700 Zeiss confocal microscope and images were processed using zen lite (Carl Zeiss). The cartoon in Figure 2A is adapted from Paxinos and Watson.49

Anesten F., Dalmau Gasull A., Richard J.E., Farkas I., Mishra D., Taing L., Zhang F., Poutanen M., Palsdottir V., Liposits Z., Skibicka K.P, & Jansson J. (2019). Interleukin‐6 in the central amygdala is bioactive and co‐localised with glucagon‐like peptide‐1 receptor. Journal of Neuroendocrinology, 31(6), e12722.

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Quantifying Trichomonas vaginalis Attachment

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Attachment of T. vaginalis to Ects was performed as described previously (10 (link)). Briefly, 5 × 10⁴ CellTracker blue CMAC (7-amino-4-chloromethylcoumarin; Thermo Fisher Scientific)-labeled T. vaginalis organisms were incubated with confluent Ects for 30 min, and the coverslips were fixed in 4% formaldehyde in PBS and mounted on slides using Mowiol (Calbiochem). Fifteen images of each coverslip were acquired using an Axioscope 2 epifluorescence microscope (Zeiss), and cell counts were quantified using Zen lite (Zeiss) and ImageJ software (74 (link)).
Attachment assays that included rCLP ECD to compete for Ect binding were performed using WT, nontransfected RU393 parasites, and the difference in the procedure was addition of 0.25 μg, 1 μg, or 4 μg of rCLP ECD or 4 μg of BSA as a negative control to Ects for 30 min prior to parasite addition. Medium was then removed and replenished with new medium containing CellTracker blue-labeled parasites.

Chen Y.P., Riestra A.M., Rai A.K, & Johnson P.J. (2019). A Novel Cadherin-like Protein Mediates Adherence to and Killing of Host Cells by the Parasite Trichomonas vaginalis. mBio, 10(3), e00720-19.

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Visualizing Yeast Cell Morphology

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Differential interference contrast (DIC) images of yeast cells were captured using a Zeiss Scope A1 Microscope using a Plan-Neofluar 40x objective. Images were taken of the indicated strains following 24 h growth in YPD medium. Microscopy data were stored using ZEN lite (Zeiss). The GFP signal was used for screening of Y. lipolytica transformants. Agar plates were observed using the 5x objective. The GFP filter set (Zeiss), operated at excitation of 470/40 nm, and emission of 525/50 nm, was used to detect green fluorescence.

Rzechonek D.A., Szczepańczyk M, & Mirończuk A.M. (2023). Mutation in yl-HOG1 represses the filament-to-yeast transition in the dimorphic yeast Yarrowia lipolytica. Microbial Cell Factories, 22, 155.

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Quantitative Microscopy of Blood-Brain Barrier

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All stained samples were imaged using a Zeiss Observer.Z1 fluorescence microscope with an Orca-Flash4.OLT camera. To acquire the images of the entire CSF, 10-μL drops of the brain tissue sections were examined with a 5× objective combined with the function “Tiles” of the imaging program Zen 2 (Zeiss). For imaging with higher magnification of BBB vascular endothelium (tomato lectin) and astrocytes (anti-GFAP antibody followed by Alexa Fluor 488-conjugated goat anti-mouse), a 63× objective combined with the function “Stacks” of the imaging program Zen 2 was used; each image taken was a merge of 15 to 20 stacks imaged. Confocal microscopy analysis was performed using a Zeiss LSM980-Airy2 confocal system. To acquire images, the program ZEN lite (Zeiss) was used, while 3D modeling after image acquisition was performed using Imaris (Oxford Instruments). During the confocal microscopy imaging, each z-stack image included 15 stacks with a total thickness of 15 μm. For the microscopy analysis with high-magnification objectives (both ordinary fluorescence and confocal microscopy), we decided to focus on the septum, in the tissue between the area underneath the subarachnoid space and the more external part of the cerebral cortex.

Generoso J.S., Thorsdottir S., Collodel A., Dominguini D., Santo R.R., Petronilho F., Barichello T, & Iovino F. (2022). Dysfunctional Glymphatic System with Disrupted Aquaporin 4 Expression Pattern on Astrocytes Causes Bacterial Product Accumulation in the CSF during Pneumococcal Meningitis. mBio, 13(5), e01886-22.

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