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18 protocols using zen 2 3 sp1

1

Imaging and Quantifying Plant Oil Bodies

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Five-day-old thalli were used for observation. For BODIPY staining, thalli were incubated in 200 nM BODIPY 493/503, dissolved in water for 30 min, washed twice in water, and used for microscopic observation. For β-estradiol treatment, gemmae were grown on a 1/2 × Gamborg’s B5 medium plate for 3 days, then soaked in a liquid medium containing 20 μM β-estradiol or 0.1% (v/v) DMSO for 48 h. The samples were mounted in a 1/2 × Gamborg’s B5 liquid medium and observed using an LSM780 confocal microscope (Carl Zeiss) equipped with an oil immersion lens (63 ×, numerical aperture = 1.4) and lambda and Airyscan detectors. For spectral imaging, the samples were excited at 488 nm (Argon 488) and 561 nm (DPSS 561–10), and emissions between 482 and 659 nm were collected. For high-resolution imaging using the Airyscan detector, samples were excited at 488 and 561 nm, and the emission was separated using a BP495-550 + BP570-630 filter. The images were acquired using line scanning. Spectral unmixing and Airy processing of the obtained images were performed using ZEN2.3 SP1 software (Carl Zeiss). We calculated the circularity of the oil bodies and analyzed colocalization using ImageJ and the Coloc_2 plugin in ImageJ Fiji (Schindelin et al., 2012 (link)), respectively.
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2

Immunofluorescence Staining of Cryosections

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Frozen sections were fixed in methanol at −20 °C for 15 min, washed, blocked in 3% bovine serum albumin in PBS salt solution, and incubated overnight at 4 °C with the antibodies diluted in blocking solution. The antibodies used for staining cryosections are listed in Table 1 (#3, 5, 7, 13).
After washing for 3 × 5 min in 1×PBS, sections stained for Hv1 were additionally incubated for 1 h at room temperature with an appropriate secondary antibody (#16). Sections were stained with DAPI solution (Invitrogen, 1 µg/mL) to visualize nuclei and mounted with Fluoromount G (eBioScience, San Diego, CA, USA) mounting media. The specificity of the secondary antibody was verified by omitting the primary antibody from the staining procedure. Sections were examined using a LSM800 microscope and Zen 2.3 SP1 software (Zeiss, Jena, Germany).
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3

Stomatal Aperture Visualization and Measurement

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Foliar disks (7 mm in diameter) from 3 to 4-week-old plants were prepared with a cork-borer and immersed in RL or control solutions. After 3 h, disks were placed on glass slides and observed under a scanning confocal microscope (Carl Zeiss, Oberkochen, Germany). Auto-fluorescence of chlorophyll was observed using laser emissions at 638 and 488 nm. The images were optimized by scanning in XY mode while adjusting laser transmissivity and voltage of photomultiplier tubes. Then, in XYZ mode, Z-scans were performed. Three-dimensional reconstructions of images were done using ZEN 2.3 SP1 software (Carl Zeiss). The width of the stomatal aperture was measured using ImageJ software1. Aperture corresponded to the minor axis of an ellipse fitted on each stoma. A total of at least 140 stomata from 10 disks of 10 different plants per condition were used for average and standard error determinations.
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4

Live-Dead Staining of Microtissues

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Calcein-AM (Sigma, # 17783, Buchs, Switzerland) and Ethidium Homodimer-1 (EthD-1, Sigma, # 46043, Buchs, Switzerland) staining was used for live dead staining. A staining solution was prepared by adding 2 μl of Calcein AM (stock: 1 mM in DMSO) and 1 μl of EthD-1 (stock: 1 mM in DMSO) per 1 ml culture medium. MT were stained for 2 h under standard culture conditions. Prior to fluorescence imaging, MT were washed twice with PBS. A ZEISS LSM 800 with Airyscan (Zeiss, Feldbach, Switzerland) confocal laser scanning microscope was used for image acquisition. Z-stack images of 20 μm in z-dimension were taken and 20 individual images assembled to a maximum intensity project using the Zeiss ZEN 2.3 SP1 software.
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5

Blinded Assessment of Skin Damage

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Based on the severity of erythema/hemorrhage, erosion, dryness and scabbing, the degree of skin damage was assessed by five independent investigators in a blinded randomized analysis to limit investigator bias and variability, and categorized as 0 (none), 1 (mild), 2 (moderate) and 3 (severe), according to the method previously described (Kim et al., 2013 (link)). The total SCORAD (mean ± SD, minimum 0, maximum 12) was used as the total score for each mouse.
For the histological assessment, the dorsal skin and ear samples of BALB/c mice were removed, fixed in 4% paraformaldehyde and embedded in paraffin. The sections were subjected to HE staining with hematoxylin and eosin solution and to toluidine blue staining with toluidine blue working solution (1% toluidine blue and 1% aluminum potassium sulfate). The slides were imaged using a Nikon optical microscope (Japan) equipped with an eyepiece micrometer by the magnification (×200) and analyzed using Zen 2.3 SP1 software (Carl Zeiss). Mast cells are labeled and counted using image pro plus 6.0 (Measure/count/size plug-in).
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6

Cep152 Centrosome Dynamics Analyzed by FRAP

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U2OS cells were cultured on the Lab-Tek II chambered coverglass with a No. 1.5 borosilicate glass bottom (Thermo Fisher Scientific), then treated with 20 nM Cep152 siRNA for 24 h and infected with adenoviruses expressing the indicated mGFP-Cep152 constructs for 14 h. The cells were washed once with phosphate-buffered saline (PBS), replenished with fresh medium, and subjected to time-lapse imaging using a Zeiss LSM880 Airyscan microscope. Centrosome-localized mGFP-Cep152 signals were photobleached with the 75% acousto-optic tunable filter-modulated transmission power of the 488-nm laser at 30 iterations and 3.87 µs pixel dwell time. Fluorescence recovery was monitored by collecting images at three-minute intervals over 42 min. Images were processed using the ZEN 2.3 SP1 software (Carl Zeiss Microscopy LLC), and the processed images were analyzed using the FRAP module of the ZEN software to plot recovery curves.
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7

Live-Cell Imaging of Flower Bud Development

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Live cell imaging was performed as described previously (Prusicki et al, 2019 (link)). In short, up to six flower buds of 0.2–0.6 mm were carefully positioned in a petri plate filled with half-strength MS medium, pH 5.8 and solidified with 0.8% (w/v) agar. Time lapse was performed using an upright Zeiss LSM 880 confocal microscope with ZEN 2.3 SP1 software (Carl Zeiss AG, Oberkochen, Germany) and a W-plan Apochromat 40X/1.0 DIC objective (Carl Zeiss AG, Oberkochen, Germany). GFP and TagRPF were excited at λ = 488 nm and 561 nm, respectively, and detected between 498 and 560 nm and 520 and 650 nm, respectively. Auto-fluorescence was detected between 680 and 750 nm. With a time interval of 10 min, a series of six Z-stacks with 50 µm distance was acquired under a thermally controlled environment (21°C/30°C/34°C [± 0.15%]) in an incubation chamber. Due to sample movement, the Z-planes were manually selected using the review multi-dimensional data function of the software Metamorph version 7.8 and the XY movement was corrected using the Stack Reg plugin of Fiji.
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8

Tissue Autofluorescence Imaging for MALDI Analysis

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Tissue autofluorescence images used for overlaying with MALDI images were captured prior to MALDI matrix application. Autofluorescence images were acquired using a Zeiss 710 confocal microscope and a W plain-Apochromat 20× objective. Tissue sections were excited with 405 and 490 nm laser wavelengths and corresponding emission wavelengths were collected from 404 to 488 nm and 495–720 nm, respectively, for analysis.23 (link) Using the tile scan function in ZEN 2.3 SP1 software (Zeiss), several 303.6 μm × 303.6 μm images were stitched over different areas on the slides to acquire mosaic images of whole tissue sections. Since, such large area mosaic acquisition takes time, z stack imaging of the 10 μm thick tissue sections was avoided by adjusting the pinhole size to an equivalent of 4.63 airy units. The pinhole adjustments allowed acquisition of image information above and below the focal plane. All microscopy images were analyzed using the ZEN image analysis software (Zeiss).
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9

Live-Cell Imaging of Fluorescent Protein Markers

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Live-cell imaging was performed using the same protocol and sample preparation as described by Prusicki et al. (2019) (link). Up to 10 samples including WT control next to the mutants were followed in the same Petri dish. A W-plan-Apochromat 40×/1.0 differential interference contrast water-immersion objective on a Zeiss LSM880 confocal microscope with Zen 2.3 SP1 software (Carl Zeiss) permitted the time-lapse acquisition. mTurquoise2 was excited at λ 458 nm and detected at λ 460–510 nm; GFP was excited at 488 nm and detected at 495–560 nm; mVenus was excited at 514 nm and detected 520–620 nm; and TagRFP was excited at 561 nm and detected at 570–650 nm. Time lapses were acquired as series of eight Z-stacks with 4-µm intervals (step size) using fluorescence autofocusing. Acquisitions were performed at 18°C. Image drift on Z plane was corrected manually using the review multidimensional data option on Metamorph v7.8. Image drift on XY plane was corrected using the Stack Reg plugin (Rigid Body option) of Fiji.
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10

Imaging and Analyzing Plant Roots in EcoFABs

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The plant roots in the Imaging EcoFABs were imaged using a Zeiss LSM 710 confocal microscope system using Zen 2.3 SP1 software (Zeiss, Oberkochen, Germany). Before imaging, the EcoFAB device was removed from the magenta box and placed on a microscope stage in inverted configuration. Images were colorized through Zen 2.3 SP1 software for multichannel, overlaid images. Images were analyzed with scikit-image (version 0.18) [29 (link)]. From the Zeiss-specific propriety LSM file for the 40× multispectral image (Figure 3C), Kmeans was used to detect the number of distinct colors of proteins by clustering pixel-by-pixel to find bins of channels. The results were expressed in a binned dendrogram (Figure S3). The segmentation analysis was conducted also by using the 40× multispectral image (Figure 3C), with the dilation and erosion operations using the circular structural element applied to the image to separate out the individual bacterium. This analysis counted 478 cells in the image. The environment, code, and parent data file are available in the Supplementary Materials.
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