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Zen 3.3 blue edition

Manufactured by Zeiss
Sourced in Germany

The Zen 3.3 Blue Edition is a powerful microscope software suite developed by Zeiss. It provides a comprehensive set of tools for image acquisition, processing, and analysis across a wide range of microscopy techniques. The software offers advanced features for streamlining workflows and enhancing the quality of microscopic images.

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7 protocols using zen 3.3 blue edition

1

Placenta Imaging Using Light Sheet Microscopy

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Imaging was performed using a Zeiss Lightsheet 7 (Carl Zeiss Microscopy Deutschland GmbH, Oberkochen, Germany) at various magnifications. The placenta samples were mounted in an upright position onto the sample holder and placed in the corresponding holder in the sample chamber filled with ethyl cinnamate. The subsequent digital three-dimensional reconstruction of the light sheet image stacks was performed using Imaris Viewer (Oxford Instruments plc., Tubney Woods, Abingdon, UK). The qualitative analysis was performed visually using Zen 3.3. blue edition (Carl Zeiss Microscopy Deutschland GmbH, Oberkochen, Germany) and FIJI ImageJ (National Institute of Health, Bethesda, MD, USA). Generally, all samples showed the highest staining intensity at the surface of the sample; however, this can be overcome by computationally adjusting the intensity for every area of interest.
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2

RNAscope Imaging of Neurotransmitter Receptors

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Images of the RNAscope treated sections were acquired with wide field 20 × magnification using an Axio Imager.Z2 (Zeiss, Germany). Whole section images were acquired as tiles in the DAPI (150 ms), Cy3 (Glra3 detection, 4000 ms) and Cy5 (Slc17a6 or Slc32a1 detection, 900 ms) channels. The images were handled for figure representation using the ZEISS ZEN 3.3 (blue edition) software, where the area outliners of the targeted brain structures were determined using the Allen mouse brain atlas (https://mouse.brain-map.org/experiment/thumbnails/100048576?image_type=atlas).
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3

Quantification of Dermal Structures

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All quantifications were performed on orthogonally projected images of the original Z-stack confocal images. Dermal SC (DSC) area fraction and dermal nerve fibre (DNF) area fraction were determined from orthogonal average-projection images of the original Z-stack confocal images using FIJI (University of Wisconsin, WI, USA). Other quantifications were analysed on the orthogonal max-projection images of the original Z-stack confocal images using ZEN 3.3 (blue edition, Zeiss, Germany).
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4

Collagen Assessment in Tissue Samples

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For morphological diagnosis, sections (4 μm thick) were stained with hematoxylin and eosin (H&E). Masson's Tricromica Stain was used for the differential staining of collagen. All stained samples were examined under light and digital microscopes. The content of collagen fibers relative to the total adjacent normal tissue by image analysis using the software Zen 3.3 (blue edition, Zeiss) was also evaluated.
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5

Neutrophil NET Trapping and Parasite Death

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NET production over time and its effect on parasite entrapment/death were investigated by live cell imaging as previously described (32 (link)). Briefly, neutrophils (5 x 105) were seeded onto 35 mm CELLview plates (Greiner Bio-One, Brazil) and allowed to adhere for 30 min at 37°C. Parasites were added (5:1 parasite/neutrophil ratio) in the presence of propidium iodide. NET release and parasite entrapment/death were monitored for 4.5 h on a Zeiss Axio Observer Z1 microscope equipped with Definitive Focus and a HMR Axiocam monochrome camera, with temperature stabilized at 37°C. Spontaneous death of parasites in NET-enriched supernatant or culture medium alone were also evaluated as control conditions. Image acquisition and analysis were performed using Zen 3.3 Blue Edition (Zeiss, Germany) and ImageJ 1.52 (National Institutes of Health, USA), respectively.
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6

Quantifying Vascular αSMA Density

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Immunofluorescence staining of the tissue sections was performed using ASMA (1:100; ab8211, Abcam, Cambridge, MA, USA, and images were captured using an Axioscan Z1 whole slide scanner (Zeiss, Jena, Germany). Pictures were evaluated using Zen 3.3 Blue Edition (Zeiss Microscopy, Jena, Germany). The fluorescence channel for the α-smooth muscle actin (αSMA) was dimmed to enhance the blood vessel signal, and the density of the αSMA per mm² was measured using the ImageJ software, version 1.53e (developed by Wayne Rasband, National Institutes of Health, Bethesda, MD, USA), and Java 1.6.0_24 (64 bits). Counts matching 0.3 to 1.0 circularity were considered during our analysis.
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7

Quantifying Residual Water Content in Wound Dressings

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The epicitehydro samples taken from the wounds at the end of the in vivo experiments were stored in dry ice cooling until testing of the residual water content. Wet sample weight (mw) (n = 3) was determined directly after defrosting using an analytical balance (Kern ABJ 220-4NM). Afterwards, samples were air dried at room temperature until the mass achieved constancy. Dry mass (md) (n = 3) of samples was determined by weighing (Kern PCB 1000-2). The remaining water content (WC) of epicitehydro samples was calculated using the following formula: WC = ((mw − md)/mw) * 100%. To confirm these results, primary dressing average thickness (in µm) was measured through H&E-stained slides in triplicate (each slide was measured 15 times, for a total of 45 measurements per treatment). BNC dressings were not removed before fixation and posterior staining, and manual measurements of the primary dressing thickness were obtained using the Zen 3.3 Blue Edition (Zeiss Microscopy, Jena, Germany) image processing software.
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