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21 protocols using deltavision omx v4

1

High-Resolution Confocal, Spinning Disk, and Structured Illumination Microscopy

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The confocal microscope used was a laser scanning confocal microscope LSM880 (Zeiss) equipped with an Airyscan detector (Carl Zeiss). Objectives used were ×40 water (NA 1.2) and ×63 oil (NA 1.4). The microscope was controlled using Zen Black (2.3) and the Airyscan was used in standard super-resolution mode.
The spinning disk microscope used was a Marianas spinning disk imaging system with a Yokogawa CSU-W1 scanning unit on an inverted Zeiss Axio Observer Z1 microscope controlled by SlideBook 6 (Intelligent Imaging Innovations, Inc.). Objectives used were a ×20 (NA 0.8 air, Plan Apochromat, DIC) objective (Zeiss), a ×63 oil (NA 1.4 oil, Plan-Apochromat, M27 with DIC III Prism) objective (Zeiss), or a ×100 (NA 1.4 oil, Plan-Apochromat, M27) objective. Images were acquired using an Orca Flash 4 sCMOS camera (chip size 2048 × 2048; Hamamatsu Photonics).
The structured illumination microscope (SIM) used was DeltaVision OMX v4 (GE Healthcare Life Sciences) fitted with a ×60 Plan-Apochromat objective lens, 1.42 NA (immersion oil RI of 1.514), used in SIM illumination mode (five phases × three rotations). Emitted light was collected on a front illuminated pco.edge sCMOS (pixel size 6.5 μm, readout speed 95 MHz; PCO AG) controlled by SoftWorx.
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2

Super-resolution 3D-SIM Imaging Protocol

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Super-resolution 3D-SIM images were acquired on a DeltaVision OMX V4 (GE Healthcare) equipped with a 60x/1.42 NA PlanApo oil immersion objective (Olympus), 405, 488, 568 and 642 nm solid state lasers (100 mW) and sCMOS cameras (pco.edge). Image stacks of 1 µm with 0.125 µm thick z-sections and 15 images per optical slice (3 angles and 5 phases) with were acquired using immersion oil with a refractive index 1.524. Images were reconstructed using Wiener filter settings of 0.005 and optical transfer functions (OTFs) measured specifically for each channel with SoftWoRx 6.1.3 (GE Healthcare) to obtain super-resolution images with a twofold increase in resolution both axially and laterally. Images from different color channels were registered using parameters generated from a gold grid registration slide (GE Healthcare) and SoftWoRx 6.1.3 (GE Healthcare).
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Super-resolution Imaging of Neuromuscular Junctions

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Super-resolution images were obtained with a structured illumination microscope (Delta Vision OMX V4; GE Healthcare) as previously described (Hong et al., 2020 (link)). All images of NMJ4 from abdominal segments A2 or A3 were captured using appropriate settings for better visualization. Raw data were reconstructed to images by default reconstruction parameters of softWoRx 6.5.2 (GE Healthcare). Images were subsequently processed with Imaris 6.0 software (http://www.bitplane.com).
The inner and outer diameters of the GluR rings were measured by drawing a line through the longest diameter of the rings with ImageJ. For quantifying the numbers of GluR nanoclusters, freehand lines along the rings were drawn to trace the changes of intensities analysed with the plot profile. An intensity peak in the plot profile was counted as a GluR nanocluster.
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4

Visualizing SORLA-GFP Trafficking in Breast Cancer

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Lentiviral transduced SORLA-GFP-expressing MDA-MB-361 cells were kept on ice and washed twice with ice-cold PBS. Alexa-568-conjugated trastuzumab (0.15 μg/ml) in Hank’s Balanced Salt Solution was incubated with the cells on ice for 1 h protected from light. The cells were washed twice with ice-cold PBS before addition of pre-warmed culture media supplemented with 5% HEPES (without serum). Imaging was performed with Deltavision OMX V4 total internal reflection microscopy (TIRFM; GE Healthcare) every 250 ms with a ×60/1.49 objective (Olympus TIRF objective).
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5

Super-Resolution Microscopy Setup and Image Analysis

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Images from two commercially available SIM microscopes were analysed, obtained on a Delta-Vision|OMX v4 by GE Healthcare (Issaquah, WA, USA) and on an Elyra S1 by Zeiss (Jena, Germany). Also, raw images were acquired on a home-built, SLM-based two-beam interference illumination SR-SIM microscope. This system consists of a 60 × , 1.2 numerical aperture water immersion objective (Olympus, Hamburg, Germany), a 642 nm, 85 mW fiber-coupled diode laser for excitation, a charge-coupled device camera (Coolsnap HQ, Photometrics, Tuscon, AZ, USA) and a liquid crystal display-based SLM for light modulation (LC-R 1920, Holoeye Photonics, Berlin, Germany). A sketch of the set-up can be found in Fig. 2e. The TIRF SR-SIM set-up is documented by Kner et al.5 (link).
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6

Visualizing Cell Membrane Lipid Rafts

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Cells were plated onto confocal dishes (coverglass-bottom dishes) and stained with Hoechst (Sigma) for 20 min to visualize the cell nuclei. Then, the cells were washed twice with PBS and labeled with Alexa Fluor 555-labeled cholera toxin B subunit (Molecular Probes, Invitrogen Corporation, Carlsbad, CA) for 2 min. The samples were labeled with Alexa 488-tagged LIP after washing with PBS and analyzed by 3D-SIM superresolution microscopy. The 3D-SIM images of the cells were acquired on a DeltaVision OMX V4 imaging system (GE Healthcare).
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7

High-Resolution Telomere Imaging by 3D-SIM

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Three dimensional-structured illumination microscopy (3D-SIM) was performed using DeltaVision OMX™ V4 equipped with Blaze Module (GE Healthcare) and a PLAN APO N 60×/1.42 OIL objective. A 568 nm OPSL laser was used for excitation and a pco.edge 5.5 sCMOS camera for signal detection. Raw images were acquired in a z-stack with 125 nm step, 8 z slices, 15 images per slice, pixel size 80 nm. The image reconstruction was performed using SoftWorX software (GE Healthcare). Blinded analysis of telomeres in maximal projection images was done as previously described (33 (link)). Only telomere without gaps in telomere staining >500 nm were scored. Branched and overlapping telomeres (30–60% of molecules) were excluded from analysis.
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8

Super-resolution Imaging Acquisition and Analysis

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Super-resolution 3D-SIM images were acquired on a DeltaVision OMX V4 (GE Healthcare) equipped with a 60×/1.42 NA PlanApo oil immersion lens (Olympus), 405-, 488-, 568-, and 642-nm solid-state lasers and sCMOS cameras (pco.edge). Image stacks of 5–6 µm with 0.125-µm thick z-sections and 15 images per optical slice (3 angles and 5 phases) which were acquired using immersion oil with a refractive index 1.518. Images were reconstructed using Wiener filter settings of 0.003 and optical transfer functions measured specifically for each channel with SoftWoRx 6.1.3 (GE Healthcare) to obtain super-resolution images with a twofold increase in resolution both axially and laterally. Images from different color channels were registered using parameters generated from a gold grid registration slide (GE Healthcare) and SoftWoRx 6.1.3 (GE Healthcare).
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9

Super-Resolution Microscopy Protocol

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The fixed samples were imaged with a commercial SR-SIM microscope (DeltaVision|OMX v4, GE Healthcare, USA). 3D-SIM stacks were recorded with the z-range indicated in Figure 6.
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10

Super-resolution Imaging of Cellular Structures

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Super-resolution 3D-SIM images were acquired on a DeltaVision OMX V4 (GE Healthcare) equipped with a 60×/1.42 NA PlanApo oil immersion lens (Olympus), 405, 488, 568 and 642 nm solid state lasers and sCMOS cameras (pco.edge). Image stacks of 10 μm with 0.125 μm thick z-sections and 15 images per optical slice (three angles and five phases) were acquired using immersion oil with a refractive index of 1.514. Images were reconstructed using Wiener filter settings of 0.008 for the 405 channel, 0.006 for the 528 channel, and 0.003 for the 508 and 683 channels. Optical transfer functions (OTFs) were measured specifically for each channel with SoftWoRx 6.1.3 (GE Healthcare) to obtain super-resolution images with a 2-fold increase in resolution both axially and laterally. Images from different color channels were registered using parameters generated from a gold grid registration slide (GE Healthcare) and SoftWoRx 6.5.2 (GE Healthcare). Volume renderings were generated in ImageJ v1.50g.
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