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127 protocols using las af lite

1

Quantifying Fluorescent Intensity Ratios

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Five regions of interest (ROIs) of equal size were placed in fixed positions across each analyzed image. The mean gray values in the ROIs were calculated in image analysis software (Leica LAS AF Lite). Average fluorescence intensities (0–65535) for pixels in the ROIs of the images captured through the red and green filters were recorded, representing red and green values, respectively. Yellow values were calculated as red-to-green ratios.
In a separate analysis, 12 small ROIs were used to isolate regions of ECM AF alone and Hoechst 33342 nuclei labeling alone (six ROI each). Mean gray values were calculated for each ROI (Leica LAS AF Lite). Average fluorescence intensity (0–65535) per pixel was reported for the nuclear ROI and the AF ROI. These mean gray values were used as a control to check that changes in the mean gray values in the red channels were not attributable to fluctuations in AF and/or Hoechst 33342 fluorescence intensities or their bleed-through into the red channels. The Hoechst 33342-to-ECM AF ratios for average fluorescence intensity per pixel values were calculated from these results.
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2

Fluorescent Microscopy Imaging Pipeline

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Fluorescent-labelled samples were mounted in 80% glycerol or Vectashield (Vector Laboratories) and analysed by confocal microscopy (LEICA TCS SP5, Zeiss Confocal LSM 780 PicoQuant FLIM or Zeiss LSM 800 Airyscan laser scanning confocal). Images were processed using Leica LAS AF Lite and Fiji (Image J 1.50e). Images were assembled using Photoshop 21.2.3 (Adobe). Adult eyes were imaged on a dissecting microscope using a Scitec Infinity1 camera. Images were processed, analysed, and assembled using some combination of LAS AF Lite (Leica), Zen 2012 (Zeiss), Fiji and Photoshop 21.2.3 (Adobe).
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3

Biofilm Viability Assessment by Confocal Microscopy

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Using the LIVE/DEAD® BacLightTM Bacterial Viability Kit (Thermo Fisher Scientific, Braunschweig, Germany), the plaque deposits were fluorescently stained according to the manufacturer’s protocol and fixed with 2.5% glutaraldehyde (Carl Roth GmbH + Co. KG, Karlsruhe, Germany). A phosphate-buffered saline solution (Biochrom GmbH, Berlin, Germany) was used to store the stained samples at 4 °C. This enabled the initial intraoral biofilm formation to be assessed under close-to in vivo conditions. Three-dimensional images of the biofilm were taken by CLSM (SP2, Leica Microsystems GmbH, Wetzlar, Germany). For each test specimen, five defined positions were microscopically examined at a magnification of 10 × and 63 ×. The biofilm volume per test specimen and the live/dead distribution were quantified using the Imaris software package (Imaris x64 6.2.1, Bitplane AG, Zurich, Switzerland). In addition, a representative three-dimensional reconstruction of the biofilm was carried out. The biofilm surface coverage per test specimen was determined using the Leica LAS AF Lite and the ImageJ software (Leica LAS AF Lite, Leica Microsystems GmbH, Wetzlar, Germany; ImageJ, Wayne Rasband, National Institutes of Health, Bethesda, MD, USA, http://imagej.nih.gov/ij/).
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4

Quantifying Fluorescence in Photoreceptors

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Fluorescence intensity in PR was rigorously and reproducibly quantified in an unbiased manner as previously described (63 (link)). Individual colour channel images were taken using a Leica microscope (Leica Microsystems GmbH). TIFF images were gray-scaled with image analysis software (LAS AF lite; Leica Microsystems GmbH). Six images of each eye were analyzed at 20× magnification by a masked observer. The PR (outer nuclear layer + OS) were selectively outlined in every image, and the total fluorescence for the enclosed area was calculated in an unbiased manner using the image analysis software. The fluorescence in PR was then averaged from six images collected from separate retinal sections from each eye. We then calculated the average fluorescence of the three eyes of each experimental group.
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5

Immunofluorescent Staining of Tyrosine Hydroxylase

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Cells were fixed by adding methanol, previously chilled to −20 °C, and incubating the plate at −20 °C for 20 min. The wells were washed with PBS, and the coverslips were removed and incubated with a tyrosine hydroxylase (TH) primary antibody (1:5000 v/v; Merck/MilliporeSigma, USA) in PBS/3%, BSA/0.02%, sodium azide at 4 °C overnight and then incubated with a fluorescent secondary antibody Alexafluor™ (Thermo Fisher Scientific, USA) in PBS/BSA for 30 min at room temperature in the dark. The coverslips were mounted with Fluoromount™ (Merck/MilliporeSigma, USA), and images were acquired using a confocal microscope LEICA SP5 II (Wetzlar, Germany), with excitation at 488 nm and emission at 530–568 nm, and processed using the software LAS AF Lite (Leica Microsystems AG, Wetzlar, Germany).
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6

Quantitative Analysis of Autophagy in Hypoxic Cells

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After 24 h under normoxia or hypoxia, HT-29 cells were stained with LysoTracker Yellow-HCK-123 and MitoTracker Deep Red FM (Thermo Fisher Scientific) according to manufacturer’s instructions. For LC3 staining, HT-29 cells subjected to normoxia or hypoxia for 24 h were fixed with 4% paraformaldehyde for 20 min and then permeabilized in 100% methanol. After blocking with 3% bovine serum albumin, cells were incubated with LC3 antibody (Cat. No. PM036; MBLI, Woburn, MA) at 1:200 dilution overnight at 4 °C. Cells were then incubated with Alexa 488 conjugated secondary rabbit antibody (Invitrogen) for 1 h and DAPI for 5 min before mounting with antifade medium (Dako). Cells were analysed by a Leica SP5 laser scanning confocal microscope (Leica Microsystems, Wetzlar, Germany). Fluorescence images of the same sample were acquired and processed using Leica confocal software (LAS-AF Lite; Leica Microsystems). Quantification of LC3/DAPI was performed by two independent, blinded investigators using ImageJ software in at least tenareas of interest pooled from four independent experiments.
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7

Autophagy Quantification in Colon Cancer Cells

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After 24 hours under hypoxia, HT-29 and Caco-2 cells were fixed with 4% paraformaldehyde for 20 minutes and then permeabilized in 100% methanol. After blocking with 3% bovine serum albumin, cells were incubated with LC3 antibody (cat. no. 2775; Cell Signaling Technology) at 1:500 dilution overnight at 4°C. Cells then were incubated with Alexa 488–conjugated secondary rabbit antibody (Invitrogen, Carlsbad, CA) for 1 hour and 4′,6-diamidino-2-phenylindole for 5 minutes before mounting with antifade medium (Dako). Cells were analyzed by a Leica SP5 laser scanning confocal microscope (Leica Microsystems, Wetzlar, Germany). Fluorescence images of the same sample were acquired and processed using Leica confocal software (LAS-AF Lite; Leica Microsystems). Quantification of puncta was performed by 2 independent blinded investigators in at least 8 areas of interest from 2 independent experiments.
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8

UTMD-Mediated SDF-1 Biodistribution

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Three normal rats were used to visualize the target release of SDF-1 in the left kidneys. FITC-MBSDF-1 was infused instead when UTMD was applied. The untreated right kidneys, hearts, lungs, livers, and spleens served as a control. Immediately after the treatment, the rats were sacrificed, the tested organs were harvested to be frozen, and then sectioned into 8 μm tissue slices. After nuclear counterstaining with 4′,6-diamidino-2-phenylindole (DAPI), the biodistribution of FITC-labeled SDF-1 in the tested organs was detected using a CLSM. The quantitative fluorescence of FITC, represented by a gray-scale value (ranging from 0 to 255), was assessed using the LAS AF Lite software from Leica Microsystems. Ten random fields within each slice were photographed, while avoiding possible perturbation from the fluorescence of major blood vessels, and the mean gray-scale values of the entire image were measured.
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9

Image Processing for Microscopy Analysis

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Images were analysed and processed using LAS AF Lite (Leica Microsystems, Germany) and MacBiophotonics ImageJ (http://rsbweb.nih.gov/ij/) software. The displayed images were not manipulated beyond adjusting the γ-function, as noted in the figure legends.
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10

HDL and TNF-Induced Autophagy Visualization

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After treatment of cells with HDL for 18 hours and TNF for 3 hours, the cells were washed with PBS and fixed with 4% paraformaldehyde (PFA) for 15 minutes. For LC3 staining, fixed cells were washed with PBS, permeabilized in 100% methanol at –20°C for 10 minutes, washed with PBS, and blocked with 3% bovine serum albumin for 1 hour at room temperature. Cells were subsequently incubated with LC3/p-IKK antibody (1:200 dilution; Cell Signaling Technology) overnight at 4°C. After 3 PBS-Tween washes, cells were incubated with Alexa 488 conjugated secondary rabbit antibody (Invitrogen) for 1 hour at room temperature and then washed three times in Tris-buffered saline with Tween before mounting with antifade medium (Dako, Glostrup, Denmark). Cells were analyzed by confocal microscopy in a Leica SP5 laser scanning confocal microscope (Leica Microsystems, Wetzlar, Germany) using a Zeiss AxioCam HRm CCD camera, and Zeiss EC Plan-Neofluar 10×/0.3 and Zeiss LD Plan-Neofluar 20×/0.4 objectives (Carl Zeiss Microscopy GmbH, Jena, Germany). After sequential excitation, green and blue fluorescent images of the same sample were acquired and processed using Leica confocal software (LAS-AF Lite; Leica Microsystems).
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