Elyra ps 1

Manufactured by Zeiss

Sourced in Germany, United Kingdom, United States, Canada

The ELYRA PS.1 is a high-performance microscopy system designed and manufactured by Zeiss. It is a versatile platform that enables advanced imaging techniques, including super-resolution microscopy. The ELYRA PS.1 is capable of delivering high-resolution, detailed images of samples.

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Lab products found in correlation

Zen software, by Zeiss (11 mentions) Lsm 880, by Zeiss (10 mentions) Lsm 700, by Zeiss (6 mentions) Lsm 710, by Zeiss (6 mentions) Zen black software, by Zeiss (5 mentions) Zen 2011, by Zeiss (5 mentions) Zen 2, by Zeiss (4 mentions) Zen black, by Zeiss (3 mentions) Lsm 780, by Zeiss (3 mentions) Plan apochromat, by Zeiss (3 mentions) Zen 2012, by Zeiss (3 mentions) Axio observer z1, by Zeiss (3 mentions) Lsm 710 confocal microscope, by Zeiss (3 mentions) 710 confocal microscope, by Zeiss (3 mentions) Plan apochromat 63 1.4 oil objective, by Zeiss (2 mentions) Matlab, by MathWorks (2 mentions) Vectashield mounting medium, by Vector Laboratories (2 mentions) Lsm 780 confocal unit, by Zeiss (2 mentions) Centrin, by Merck Group (2 mentions) Gelvatol, by Thermo Fisher Scientific (2 mentions)

119 protocols using elyra ps 1

Confocal and Structured Illumination Microscopy

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Confocal imaging was performed with a Zeiss LSM 700 microscope equipped with a plan‐apochromat ×20, 0.75 NA and a ×63, 1.4 NA objective, and photomultiplier tube detectors, or on a Zeiss Elyra PS1 microscope (Carl Zeiss Microscopy, Jena, Germany), which is described below. Confocal images were acquired with optimized settings for laser power, detector gains and pin hole diameters. Large (2048 × 2048 pixels), high‐resolution images were acquired with a pixel size of 0.041 µm laterally and 0.110 µm radially to facilitate the comparison with structured‐illumination microscopy (SIM) images. Low‐resolution tile images were acquired with a pixel size of 0.274 µm.
Structured‐illumination imaging was done on a Zeiss Elyra PS1 system equipped with 488, 561 and 642 nm, 100 mW diode lasers; fluorescence was acquired with a Zeiss plan‐apochromat ×63, 1.4 NA objective and an Andor iXon DU 885 EMCCD camera (Andor Technology Ltd, Belfast, Northern Ireland, 1002 × 1004 pixels). Gratings were presented at five phases and five rotations for every depth. Sampling interval was 110 nm axially and the reconstructed super‐resolution image has a pixel size of 41 nm. The fluorophore signals were acquired sequentially. Reconstructions were made with built‐in algorithms using ZEN 2012 SP1 black (v8.1.3.484).

Sierksma M.C., Slotman J.A., Houtsmuller A.B, & Borst J.G. (2020). Structure–function relation of the developing calyx of Held synapse in vivo. The Journal of Physiology, 598(20), 4603-4619.

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Peptidoglycan Dynamics Visualized by Fluorescence Microscopy

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For TDL labeling, 100 µl of culture in early exponential phase was stained with 1 mM TDL (TAMRA Red D‐lysine) at 37°C for 5 minutes (PG insertion labeling experiments) or 20 min (PG degradation pulse‐chase experiments). Cells were rinsed twice in culture medium and 5 µl of washed cells deposited on 1% agarose pads poured in frames glued on microscope slides (Gene Frame from Thermo Scientific). The imaging was done on Zeiss Elyra PS1 using ZEN software. Cells were imaged in 3D‐SIM mode with a 63× objective, 0.12 µm z step (20 steps), 50 ms exposure time and 20% laser power (561 nm). Image reconstruction was performed in ZEN with automatic parameter setting.
Samples for phase contrast and epifluorescence microscopic observations were prepared as above and imaged by an inverted Nikon microscope (Ti‐E) using a 100× phase lens, or on Zeiss Elyra PS1 as above. For measurement of cell width and length, cells were incubated in the presence of FM4‐64 (1 μg ml⁻¹). Cell width and length measurements were done in a custom program in MATLAB.

Dajkovic A., Tesson B., Chauhan S., Courtin P., Keary R., Flores P., Marlière C., Filipe S.R., Chapot‐Chartier M, & Carballido‐Lopez R. (2017). Hydrolysis of peptidoglycan is modulated by amidation of meso‐diaminopimelic acid and Mg2+ in B acillus subtilis. Molecular Microbiology, 104(6), 972-988.

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Superresolved Fluorescence Microscopy Protocols

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3D-SIM data was collected using ELYRA PS.1 (Carl Zeiss Microscopy) with a Plan-Apochromat 63x or 100x/1.4 Oil immersion objective lens with an additional 1.6x optovar. An Andor iXon 885 EMCCD camera was used to acquire images with 101 nm/pixel z-stack intervals over a 5–10 μm thickness. For each image field, grid excitation patterns were collected for five phases and three rotation angles (−75°; −15°, +45°). The raw data was reconstructed and channel aligned using SIM module of ZEN Black Software (version 8.1). STORM data was collected using PALM mode in ELYRA PS.1 (Carl Zeiss Microscopy) with a Plan-Apochromat 63x or 100x/1.4 Oil immersion objective lens with an additional 1.6x optovar. An Andor iXon 885 EMCCD camera was used to acquire images using TIRF mode. Lasers of wavelength 647 nm and 405 nm were used to activate the fluorophore. Raw data was reconstructed using PALM module of Zen Black Software (version 8.1), with the account for overlapping molecules. Reconstructed data was further processed for drift correction and binning using home-written MATLAB script (can be accessed via the following link: https://drive.google.com/open?id=11fuWn7kmZ-loCn79CKChJI5FeMme0fDU).

Liu Z., Nguyen Q.P., Nanjundappa R., Delgehyr N., Megherbi A., Doherty R., Thompson J., Jackson C., Albulescu A., Heng Y., Lucas J.S., Dell S.D., Meunier A., Czymmek K., Mahjoub M.R, & Mennella V. (2020). Super-resolution Microscopy and FIB-SEM Imaging Reveal Parental Centriole-Derived, Hybrid Cilium in Mammalian Multiciliated Cells. Developmental cell, 55(2), 224-236.e6.

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Structured Illumination Microscopy of Cilia

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Motile cilia in fixed cortical sections were imaged by structured illumination microscopy (SIM) with a Zeiss ELYRA PS.1 super-resolution microscope (Carl Zeiss MicroImaging, Thornwood, NY) using a ×63 oil objective lens with 1.4 NA at room temperature. Three orientation angles of the excitation grid were acquired for each Z plane, with Z spacing of 110 nm between planes. SIM processing was performed with the SIM analysis module of the Zen 2012 BLACK software (Carl Zeiss MicroImaging) and exported as tiff images.

Eom T.Y., Han S.B., Kim J., Blundon J.A., Wang Y.D., Yu J., Anderson K., Kaminski D.B., Sakurada S.M., Pruett-Miller S.M., Horner L., Wagner B., Robinson C.G., Eicholtz M., Rose D.C, & Zakharenko S.S. (2020). Schizophrenia-related microdeletion causes defective ciliary motility and brain ventricle enlargement via microRNA-dependent mechanisms in mice. Nature Communications, 11, 912.

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Podocyte Effacement Measurement via Super-Resolution

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For evaluation of the slit diaphragm density as a direct marker for podocyte effacement, we used the recently established super resolution microscopy-based podocyte effacement measurement procedure (PEMP) (Siegerist et al., 2017 (link)). Briefly, 2 μm paraffin sections were performed and cooked in 10 mM citrate buffer (pH 6) in a pressure cooker. After blocking in 1% normal goat serum, 1% bovine serum albumin, 1% fetal calf serum and 0.05 % fish gelatin for 1 h at room temperature, guinea pig anti-nephrin serum (gpN2, Progene, Heidelberg, Germany, diluted 1:300 in blocking solution) was incubated at 4°C overnight. After washing steps (PBS) followed by a second blocking step, primary antibodies were detected by Cy3-conjugated donkey antiguinea pig antibodies (Jackson Immuno, diluted 1:600). Sections were mounted in Mowiol (Carl Roth, Karlsruhe, Germany) for microscopy and imaged by a Zeiss Elyra PS.1 (Carl Zeiss, Jena, Germany) super resolution structured illumination microscopy system. For measurement of the D_SD custom-built Fiji plugin was used. D_SD values of 28-30 glomeruli of at least two mice per group were quantified.

Schell C., Sabass B., Helmstaedter M., Geist F., Abed A., Yasuda-Yamahara M., Sigle A., Maier J.I., Grahammer F., Siegerist F., Artelt N., Endlich N., Kerjaschki D., Arnold H.H., Dengjel J., Rogg M, & Huber T.B. (2018). ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier. Developmental Cell, 47(6), 741-757.e8.

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DENV-2 Infection Assay in Aag2 Cells

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Aag2 cells were seeded in a glass bottle cell culture dish (Nest Biotechnology, Cat. No# 801001) for 12 hrs. The 2 μg purified AaHig protein was premixed with 10 M.O.I. DENV-2 in 500 μL medium, and the mixture was then added to the cells. After the cells were cultured at 28°C for a time course, the cells were washed with PBS and fixed in 4% paraformaldehyde for 1 hr. Permeabilization was performed using 0.05% Triton X-100 for 30 min. After three washes in PBS, the cells were blocked using the Perm/Wash buffer (BD, Cat. No# 51-2091KZ). After the primary and secondary antibodies staining, the cells were imaged using a Zeiss ELYRA PS.1 structured illumination microscope (Carl Zeiss, Germany).

Xiao X., Zhang R., Pang X., Liang G., Wang P, & Cheng G. (2015). A Neuron-Specific Antiviral Mechanism Prevents Lethal Flaviviral Infection of Mosquitoes. PLoS Pathogens, 11(4), e1004848.

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Protein Aggregation Detection in MEFs

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MEFs were cultivated on glass coverslips (Laboratory Glassware Marienfeld). 24 h after seeding, cells were heat stressed at 42 °C for 1 h or treated with 0.5 µM MG-132 for 48 h or 100 nM BafA1 for 48 h. Cells were fixed for 15 min with 4 % paraformaldehyde in PBS pH 7.4 and permeabilized with 0.5% (v/v) Triton X-100, 3 mM EDTA pH 8.0, and 5% goat serum in PBS for 30 min at room temperature and then stained with Proteostat® (Enzo Life Sciences, Inc.) at a dilution of 1:2000 in 1× assay buffer (ENZO) for 20 min. Cells were then mounted in Fluorshield with DAPI (Sigma). Fluorescence microscopy was performed using a Zeiss ELYRA PS.1 equipped with an LSM880 (Carl Zeiss, Oberkochen) with a 63 × oil immersion objective. Super-resolution images were generated by the Structured Illumination (SIM) technology. SIM confocal images were processed using the ZEN2.1 software (Carl Zeiss, Jena).

Furthmann N., Bader V., Angersbach L., Blusch A., Goel S., Sánchez-Vicente A., Krause L.J., Chaban S.A., Grover P., Trinkaus V.A., van Well E.M., Jaugstetter M., Tschulik K., Damgaard R.B., Saft C., Ellrichmann G., Gold R., Koch A., Englert B., Westenberger A., Klein C., Jungbluth L., Sachse C., Behrends C., Glatzel M., Hartl F.U., Nakamura K., Christine C.W., Huang E.J., Tatzelt J, & Winklhofer K.F. (2023). NEMO reshapes the α-Synuclein aggregate interface and acts as an autophagy adapter by co-condensation with p62. Nature Communications, 14, 8368.

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Visualizing Microbial Communities on Plastic

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Microbial communities on plastic particles were visualized by confocal laser scanning microscopy (CLSM) using a Zeiss LSM 780 and by superresolution-structured illumination microscopy (SR-SIM) with Zeiss Elyra PS.1 (Zeiss, Jena, Germany). For both methods, a 63X/1.4 plan apochromatic oil objective was used as standard except for Figure 2B were a 10X/0.3 objective lens was used. For CLSM we excited DAPI, Alexa488, Alexa594, and Alexa647 using lasers with wavelengths of 405, 488, 561, and 633 nm. For SR-SIM, SYBR green I was excited with a 488-nm laser and detected using a 502- to 538-nm bandpass filter. The used SIM grating had a period of 42 μm. We imaged with three rotations and five phase shifts. The camera exposure time was set to 50 ms, with an EMCCD gain of 40, and four frames averaging. On all images, z-stacks for three-dimensional reconstruction were recorded. Image processing and visualization was done using the ZEN software package (Zeiss, Jena, Germany). The 3D video animation was done using the software Imaris 64X 8.0.2 (Bitplane, Zurich, Switzerland) after 3D blind deconvolution with AutoQuant X3 (Media Cybernetics, Inc., Rockville, MD, United States).

Vaksmaa A., Knittel K., Abdala Asbun A., Goudriaan M., Ellrott A., Witte H.J., Vollmer I., Meirer F., Lott C., Weber M., Engelmann J.C, & Niemann H. (2021). Microbial Communities on Plastic Polymers in the Mediterranean Sea. Frontiers in Microbiology, 12, 673553.

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SIM Imaging of Biological Samples

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SIM images were collected on samples obtained as described above with a Zeiss ELYRA PS.1 illumination system (Carl Zeiss Microimaging) using a 63 X objective lens with a numerical aperture of 1.4 at room temperature as we have previously done [25 ,26 ]. Three orientation angles of the excitation grid were acquired for each z plane, with z spacing of 110 nm between planes. SIM processing was performed with SIM module of the ZEN BLACK software (Carl Zeiss Microimaging).

Bahl K., Naslavsky N, & Caplan S. (2015). Role of the EHD2 Unstructured Loop in Dimerization, Protein Binding and Subcellular Localization. PLoS ONE, 10(4), e0123710.

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Quantifying Granzyme B in CD8+ T Cells

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Stimulated CD8⁺ T cells (0.4 × 10⁶ cells) from adult and elderly mice were stained with anti‐granzyme B antibody (Biolegend) or anti‐CD8a antibody (BD). Briefly, CD8⁺ T cells were washed with PBS and for cell surface staining, FITC anti‐mouse CD8a antibody (1:100) was used and stained on ice to prevent endocytosis. The cells were washed once and settled onto 0.01% poly‐ornithine coated coverslips. The cells were then fixed with ice‐cold 4% PFA solution, washed 3 times with PBS and permeabilized with 0.1% TritonX‐100 (Sigma), then blocked with blocking buffer (0.1% TritonX and 5% BSA in PBS). The cells were then stained with anti‐human/mouse granzyme B coupled to Alexa647 (1:200) for 45 mins and mounted for SIM analysis (Zeiss ELYRA PS.1; Carl Zeiss Microscopy GmbH). Images were acquired by using Zen2012 software and a 63× Plan‐Apochromat (NA 1.4) objective was used with laser excitation of 488 and 561 nm. The images were then processed using the same software to obtain higher resolution. Z‐stacks of 200‐nm step size were used to scan the cells. The images were then analyzed using Fiji v1.46, and the granule count was done using 3D objects counter plugin.

Zöphel D., Angenendt A., Kaschek L., Ravichandran K., Hof C., Janku S., Hoth M, & Lis A. (2022). Faster cytotoxicity with age: Increased perforin and granzyme levels in cytotoxic CD8 + T cells boost cancer cell elimination. Aging Cell, 21(8), e13668.

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