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9 protocols using dfc9000 scmos camera

1

Organoid Diameter Quantification Protocol

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Organoids grown from all mice listed in “Organoid culture” were used for diameter quantification. Tilescans of organoid-containing wells were imaged using the bright-field setting on a Leica DMi8 Microscope using a Leica DFC9000 sCMOS camera and Leica Application Suite X (LASX) software. Organoids were always grown in at least technical duplicates and all technical replicate wells were imaged and quantified. Diameter measurement was performed by using the built-in “Draw scalebar” function on LASX. Ten to 50 organoids were measured and averaged in each technical replicate, and technical replicates were averaged for a final biological replicate, consisting of >30 organoids measured across all technical replicates. The resultant diameter from each biological replicate was then normalized to the average diameter of C1 organoids, which were grown as a control in at least one technical replicate for all experiments. Reported average diameter for each condition comes from at least n = 3 biological replicates.
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Fluorescence and Confocal Microscopy Imaging

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Fluorescence microscopy was performed with a Thunder imaging system (Leica) equipped with a DFC9000 sCMOS camera, a HC PL Fluotar 20x air (N.A. 0.4) or a HC PL Apo 63x (N.A. 1.4) oil immersion objective and using the LasX software (Leica).
Confocal microscopy was performed with a laser-scanning microscope (Leica DMi8) equipped with ACS APO 40x and 63x oil DIC immersion objectives. Images were acquired using the LasX software (Leica), with a resolution of 1024x1024 pixels and a number of Z-stacks (step size of 0.3 or 0.5 μm) encompassing the entire cell soma.
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3

Time-lapse Imaging of Bacterial Growth

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Agarose pads (Young et al., 2011 (link)) spotted with 5 μl of a 1:10 dilution of GBS cell cultures collected at mid-log phase of growth (OD600 0.5 in THY medium) were flipped and transferred to an imaging dish sealed with parafilm. Time-lapse imaging was performed using a Leica DMi8 widefield microscope, equipped with a 100× oil immersion objective (Leica HC PL Fluotar 100×/1.32 OIL PH3), a Leica DFC9000 sCMOS camera and driven by Leica LASX software. Experiments were performed using an environmental microscope incubator set at 37°C and bacteria were imaged in phase contrast, every 5-min and up to 6 h. Manual segmentation of individual cells and analysis of image stacks were performed using the ImageJ 1.52a software, as previously described (Manina et al., 2015 (link)). Data were analyzed using Prism 9.
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4

Microscopic Imaging Protocol for Publication

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All images were taken on Leica DMi8 Microscope using a Leica DFC9000 sCMOS camera and Leica Application Suite X (LASX) software. Immunofluorescent and brightfield images were taken at either 10x, 20x, or 63x using the z stack and extended depth-of-field functions. Images were minimally processed prior to quantification or publication by adjusting the lookup table to lower the signal-to-noise ratio.
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5

Fluorescence and Confocal Microscopy Protocol

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Fluorescence microscopy was performed with a Thunder imaging system (Leica) equipped with a DFC9000 sCMOS camera, an HC PL Fluotar 20X air (N.A. 0.4) objective and using the LasX software (Leica).
Confocal microscopy was performed with a laser-scanning microscope (Leica DMi8) equipped with an ACS APO 63X oil DIC immersion objective. Images were acquired using the LasX software (Leica), with a resolution of 1024 × 1024 pixels and a number of Z-stacks (step size of 0.3 μm) encompassing the entire cell soma.
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6

Fluorescence Microscopy Imaging Protocol

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Images were acquired on a DMI6000 inverted fluorescent microscope (Leica) using an ORCA-ER B/W CCD camera (Hamamatsu; native resolution 1344 × 1024 pixels) through Metamorph software (Molecular Devices, version 7.6) or on a DMI8 inverted fluorescent microscope (Leica; native resolution 2048 × 2048 pixels) using a Leica DFC9000 sCMOS camera through LASX software (Leica). Axons and soma were imaged using ×10 and ×20 air lenses. Images of axons showing CM-H2DCFDA, cyt c, and TMRE were imaged using ×63 oil lenses.
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7

Histological Analysis of Mouse Tissues

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Skin, small intestine, and liver samples were collected from mice belonging to each experimental group, 3-weeks after transplant. Mouse skin biopsies were collected from the interscapular region of the mice. The small intestine samples were collected from the 2 cm region above the cecum, while the liver tissue was harvested from the left lobes. The samples were fixed for at least 48 h in 4% paraformaldehyde and embedded in paraffin. The sections were stained with hematoxylin and eosin (H & E fast staining kit, Carl Roth, Karlsruhe, Germany) according to manufacturer’s recommendation. The images were captured using a Leica DMi8 inverted microscope with a Leica DFC9000 sCMOS camera and processed using Leica LAS X software, version 3.3 (Leica Microsystems, Wetzlar, Germany).
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8

Fluorescent Dye-Based Cellular Assays

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After the heat shock treatment (50 °C), cells were stained with 5 µM H2DCFDA (Sigma, D6883) for the detection of ROS accumulation, 5 µM C11-BODIPY™ 581/591 (Cayman, 27086) for the detection of lipid peroxidation, 3 µM JC-1 (Cayman, 10009172) for staining the mitochondrial membrane potential, 15 µm Calcium Green-1, AM (Cayman, 20400) for staining cytosolic calcium, and 1 µM FerroOrange (Merck, SCT210) for iron staining at room temperature for 20–30 min, followed by two washes with 1X PBS. Fluorescence images were captured using a Leica fluorescence microscope (Leica Microsystems, Germany) equipped with a Leica DFC9000 sCMOS camera. The excitation/emission of fluorescent dyes used the following filters: H2DCFDA (Ex/Em: 492/515 nm), C11-BODIPY™ 581/591 (Ex/Em: 460–495/510–550 nm), JC-1 (Ex/Em: 488/538 nm for monomers and 596 nm for oligomers), Calcium Green-1 (Ex/Em: 506/531 nm), and FerroOrange (Ex/Em: 543/580 nm). For fluorescence intensity, 100 µL of stained cells were transferred into a black 96-well plate and fluorescence was measured using a Synergy HTX Multi-mode Plate Reader (BioTek, VT, USA) with the indicated excitation and emission wavelengths.
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9

Intracellular ICG Imaging and Spectroscopy

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Intracellular ICG was imaged using a Leica Dmi8 microscope (Leica Microsystems, Wetzler, Germany) equipped with a Cy7 filter (Chroma Technology Corp, Bellows Falls, VT) and Leica DFC9000 sCMOS camera. ICG absorption spectra of recovered ICG supernatant from cell lysate and prepared ICG solutions were obtained with a DU 800 UV-Visible spectrophotometer (Beckman Coulter, Brea, CA). Spectra associated with DO studies were obtained using a 1 mL sample removed from the solution before and irradiation. ICG fluorescence was measured using an LS55 luminescence spectrophotometer (Perkin Elmer, Waltham, MA) with excitation of 400 nm and 780 nm.
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