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24 protocols using zen 2 pro software

1

Fluorescent Imaging Analysis of Cells

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Animals were mounted in sodium azide (NaN3) 25 µM. A Zeiss AXIO Imager M2 fitted with an Axiocam 506 mono camera and Zen 2 pro software (Zeiss) was used to take fluorescent and DIC images. Images were analyzed using Zen 2 pro software (Zeiss) and ImageJ v1.53c. Corrected Total Cell Fluorescence is calculated as integrated density–(area × mean gray of background).
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2

Imaging Adult Caenorhabditis elegans

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Age-synchronized animals at day 1 of adulthood (4-day old animals) were mounted on 3% agarose pads and immobilized using 0,5 mM levamisole in M9. Animals were imaged with a Zeiss Axio Imager.Z2 upright epifluorescence microscope connected to an Orca Flash 4.0 LT, 4 megapixel monochrome sCMOS camera (Hamamatsu) and Zen 2 pro software (Zeiss). Images were acquired with 40x 0.75 NA EC Plan Neofluar objective. Micrographs were processed with Photoshop CS6 software (Adobe Systems).
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3

Fluorescence Imaging of Worms

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Worms tagged with fluorescence were imaged under DIC and fluorescence using an Axio Imager M2 microscope (ZEISS). Images were processed and viewed using ZEN 2 pro software (ZEISS). An Immersol 518F oil (Zeiss) was used. All the images were captured at 20°C (Gan et al., 2019 (link)).
Time-lapse imaging of HIS-24::mCherry in N2 and trim-21 mutants was performed at 20°C under a ×100 oil objective using an Axio Imager M2 microscope (ZEISS). Images were focused on specific corpses and were taken every few minutes until the corpses disappeared.
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4

Immunohistochemical Analysis of Tau Protein

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At 0, 1, 4, 7, and 14 days post sciatic nerve crush, four rats from each group were intracardially perfused with 4% freshly depolymerized, neutral-buffered paraformaldehyde. Sciatic nerves were excised, immersed, and post-fixed in paraformaldehyde overnight at 4°C, and then dehydrated by 30% hypertonic sucrose solution for 48 hours. Following dehydration, tissues were embedded in Optimal Cutting Temperature compound and sectioned into 15-μm-thick slices on a cryostat microtome (CM3050, Leica Biosystems, Solms, Germany). Tissue slices with comparatively complete morphological structure were selected for subsequent observation. The slices were mounted on microscope slides, washed with phosphate-buffered saline, blocked with 5% goat serum for 30 minutes at room temperature, incubated with rabbit anti-total tau polyclonal antibody (1:200; Abcam) or rabbit anti-p-tau (Ser 404) polyclonal antibody (1:50; Thermo Fisher Scientific) overnight at 4°C, and then incubated with anti-rabbit Cy3 IgG (1:1,000; Sigma-Aldrich, St. Louis, MO, USA) for 2 hours at room temperature. Labeled sections were viewed with an optical and epifluorescence microscope (Axio Imager M2, Carl Zeiss Microscopy GmbH, Jena, Germany), and images were captured and analyzed using Zen 2 Pro software (Zeiss).
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5

Microscopic Imaging of Fluorescent Microbes

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Still pictures were taken using an EOS Rebel T3i camera (Canon) and processed using Photoshop CC 2017 version: 14.2.1 and Illustrator CC 2017 version: 17.1.0 (Adobe). Using Photoshop, the levels of some images were adjusted to improve contrast.
For microscopy, motile colonies were examined using an Axio Zoom.V16 microscope (Zeiss). To visualize fluorescent strains, filter set 43 HE DsRed was used with a 1.5-s exposure, shown with pseudocolor orange, as well as filter set 47 HE cyan fluorescent protein, with a 600-ms exposure, shown with pseudocolor turquoise. Images were captured using an AxioCam 503 monocamera, with a native resolution of 1,936 by 1,460 pixels. For image acquisition and processing, we used Zen 2 Pro software (Zeiss).
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6

Quantifying C. elegans Embryonic Cell Corpses

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Embryos mounted on 2% agar pads were anesthetized in 3 µl M9 buffer (1 liter contains 3 g KH2PO4, 6 g Na2HPO4, 5 g NaCl, and 1 mM MgSO4) containing 33 mM sodium azide. The numbers of button-like cell corpses and pit-like vacuoles in the head region of living embryos at various developmental stages (comma, 1.5-fold, 2-fold, 2.5-fold, 3-fold, and 4-fold) were scored using DIC optics. 15 embryos at each developmental stage were scored for each strain. To examine embryonic cell corpse duration, embryos at the two-cell stage were mounted on 2% agar pads in egg salt buffer (118 mM NaCl and 48 mM KCl) at 20°C. Images in 30 Z-sections (1.0 µm/section) were captured every minute for 400 min using an Axioimager M2 microscope (ZEISS) equipped with an AxioCam monochrome digital camera (ZEISS). Images were processed and viewed using ZEN 2 pro software (ZEISS).
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7

Multicolor Immunofluorescence Staining Protocol

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Staining was performed as described (24 (link)). mAbs used were anti-CD11c-FITC (clone M17/4), anti-CD11c (clone N418), anti-IFNγ-APC (clone XMG1.2), B220-AF647 (clone RA3-6B2), anti-CD4-PE (clone GK1.5), anti-CD8-PE (clone 53-6.7), anti-GL7-biotin (clone GL.7), anti-CD38-PE (clone 90), goat anti-rat-AF555 all from eBioscience (ThermoFisher Scientific, MA, USA), anti-IgD-AF647 (clone 11-26c, BioLegend, CA, USA), anti-ER-TR7 (clone ER-TR7), anti-CD45-AF647 (clone MP33), and anti-MHCII-AF647 obtained from laboratory hybridomas. Biotin was detected using streptavadin-PerCP-Cy5.5 (eBioscience). Tissue was analyzed using a Zeiss fluorescent microscope (AXIO Imager.D2, Carl Zeiss) or Leica DM6000, captured with ZEN 2 pro software (version 2.0.0.0, Carl Zeiss) or Leica software and processed with Adobe Photoshop and Illustrator CS6.
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8

Quantifying Worm Morphology Variations

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For microscopy, all specimens were mounted on object slides with 5% Noble Agar pads which contained the sedative sodium azide (0.5% NaN3) and subsequently examined using a Zeiss Axio Imager.Z1 microscope with a Zeiss Plan-Apochromate 100 × 1.4 DIC objective. Image stacks were taken using a monochromatic Zeiss Axiocam 506 CCD camera. The Zen 2 Pro Software (Carl Zeiss Microscopy GmbH, 2011; version 2.0.14283.302; 64-bit) for digital microscopic analysis and image acquisition.
Relative ratios of eurystomatous (Eu) and stenostomatous (St) morphologies in each strain were scored using the aforementioned microscopy settings. Worms that had a large right ventrosublateral tooth, a hook-shaped dorsal tooth, and a promesostegostom whose anterior tips were clearly posterior to those of the gymnostom were classified as Eu morphs; animals that did not meet these combined characteristics were scored as St morphs. Statistical differences in morph ratios were assessed via a PERMANOVA (see “Dauer assays” section of the methods for details).
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9

Chromosome Localization of Watermelon BACs

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Bacterial Artificial Chromosome (BAC) DNA libraries were constructed using the genomic DNA of the watermelon variety 97 103. Four BAC clones located in the regions associated with chromosomal translocations were selected based on the previous report by Guo et al [26 (link)]. BAC DNA was extracted and purified using the Phase Prep BAC DNA Kit. The qualified BAC DNA was labeled with digoxigenin or Biotin Nick Translation Mix according to the instructions. Chromosome slides were prepared from flower buds, and subsequent hybridization was conducted following the method reported by Ren et al. [27 (link)] with slight modifications. At least 20 somatic metaphase samples were observed under a ZEISS Imager Z2 microscope equipped with fluorescent illumination and appropriate filters for DAPI, fluorescein, and Texas-Red fluorescence. Images were captured using a cooled black and white Charge-Coupled Device (CCD) camera (Axiocam 503 color, ZEISS) and processed with ZEN 2 pro software (ZEISS). Final image adjustments were made using Adobe Photoshop 6.0.
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10

Visualization of Nanostar Accumulation

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MDA-MB-231 breast cancer cell monolayers were seeded at a density of 50,000 cells/mL in 8-well chamber plates and grown overnight. The medium was replaced with fresh medium including nanostars for 2 h of incubation with THPC alone as a control. The nuclei were stained by 4′,6-diamidino-2-phenylindole (DAPI). The cells were washed using PBS. The intracellular accumulation of nanostars was visualized using a fluorescence microscope (Zeiss, Oberkochen, Germany) equipped with a transmitted light illuminator (Zeiss, Oberkochen, Germany), fluorescence filter set of 390/450 ex/em, 63× water immersion objective, an Axiocam camera (Zeiss, Oberkochen, Germany), and ZEN2 Pro software (Zeiss, Oberkochen, Germany).
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