Male and female mastlkt441b/wt; TgBac(foxa2:Kaede)+/− fish were crossed and resulting embryos were labeled with Histone H2A-mCherry by injecting RNA into a blastomere at the 1-cell stage or into a blastomere at the 8-cell stage. Embryos that had Histone H2A-mCherry labeling in the tailbud region were selected for imaging. Embryos at the 6-somite stage were embedded in 0.5% low-melting-point agarose in 1/3 Ringer’s solution and imaged using a Leica SP8 confocal microscope with a 40x water immersion lens. Z-stacks were collected at 3–4 min intervals for 3–4 h. Cell movements were tracked manually, checking the orthogonal view with Las (Leica) or ImageJ. Images were compiled to movies with ImageJ.
Imagej
Manufactured by Leica
Sourced in United States, Germany
ImageJ is an open-source image processing and analysis software. It provides a wide range of tools for image manipulation, analysis, and processing. ImageJ's core function is to enable users to view, edit, analyze, process, save, and print 8-bit, 16-bit, and 32-bit images.
Automatically generated - may contain errors
Lab products found in correlation
Las x, by Leica (16 mentions)
Las af, by Leica (5 mentions)
Las af lite, by Leica (3 mentions)
Tcs sp5, by Leica (3 mentions)
Las af software, by Leica (3 mentions)
Dmi8 fluorescence microscope, by Leica (3 mentions)
Ax70 epifluorescence microscope, by Olympus (3 mentions)
Tcs sp2 spectral confocal laser microscope, by Leica (3 mentions)
Laf suite, by Leica (3 mentions)
Dp70 digital camera, by Olympus (3 mentions)
Uorescence microscope, by Leica (3 mentions)
Las x software, by Leica (2 mentions)
Sp8 confocal microscope, by Leica (2 mentions)
Tcs sp8, by Leica (2 mentions)
Bovine serum albumin (bsa), by Merck Group (2 mentions)
Dmi3000b, by Leica (2 mentions)
Imagescope, by Leica (2 mentions)
Opaque 96 well plate, by Corning (2 mentions)
Aperio digital pathology slide scanner, by Leica (2 mentions)
Calcein am, by Thermo Fisher Scientific (2 mentions)
106 protocols using imagej
1
Embryo Cell Tracking in Live Imaging
2
Confocal Imaging of Neurobiotin Staining
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Once mounted, immunostained sections were imaged using a SP5 confocal microscope (Leica, Germany) using a 20X oil-immersion objective with a numerical aperture of 1.25, as well as with a 63X oil-immersion objective with a numerical aperture of 1.32 and a 1X digital zoom magnification. Serial optical sections were acquired with a Z-step of 3 µm (20X) and 0.78 µm (63X). Images (1024 X 1024; 8 to16 bit grayscale) were acquired using Leica software LAS-AF and analyzed using ImageJ (National Institutes of Health, USA).
Colocalization with neurobiotin staining was assessed in three axes using a single confocal slice and x and y orthogonal views of the stack (ImageJ 1.5).
Colocalization with neurobiotin staining was assessed in three axes using a single confocal slice and x and y orthogonal views of the stack (ImageJ 1.5).
3
Quantifying Calcium Imaging in Neurons
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Raw TIFFs were exported and analyzed with ImageJ as previously described28 (link). An experimenter manually traced the activated cells and determined cell size and relative fluorescent intensity off-line after completing the study. Briefly, Small, medium, and large diameter neurons were defined as having somal areas of <450 μm2, 450–700 μm2, and >700 μm2, respectively. The average fluorescence intensity in the baseline period was taken as F0 and measured as the average pixel intensity during the first two frames of each imaging experiment. The maximum fluorescence intensity, Ft, was measured by calculating the average (peak − background) pixel values in a given region of interest for each image frame recorded during a time interval before and during the stimulation period. The Ft was then used to calculate ΔF/F using the formula ΔF/F = (Ft − F0)/F0. We used ImageJ or Fiji (National Institutes of Health) and LIF (Leica Microsystems GmbH) to analyze calcium imaging data using standard functions and a custom macro. An activated neuron to the stimulation was defined by Ft/F0 > 1.2, as that shown in previous studies26 (link)–28 (link).
4
Quantifying Synaptic and Neuronal Markers
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Image processing was performed using ImageJ and LASX software applications (Leica Microsystems). The quantification of synapsin and peripherin was obtained by LASX software, and the calculation of the relative fluorescence intensity (RFI) was performed by dividing the fluorescence intensity (F(t)) of each image by the fluorescence of the nuclear marker (F(0)), subtracting their respective background fluorescence (Fb). (RFI = [F(t)-Fb(t)]/[F(0)-Fb(0)]). Graphical and statistical analyses were based on the RFI of 20 images and were performed using Prism software (GraphPad), applying an unpaired t-test with Welch’s correction.
5
Image Processing for Microscopy Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
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.
6
Measuring Calcium Responses in Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cytosolic calcium responses were indicated as the increase in green fluorescence intensity. The raw images (Tagged Image File Format) were exported and analyzed using image analysis software (ImageJ, National Institutes of Health, Bethesda, MD, USA ImageJ.nih.gov/ij/">https://ImageJ.nih.gov/ij/ accessed on 2 May 2022) [27 (link),28 (link)] and LIF (Leica Microsystems GmbH). An experimenter traced the activated cells manually to determine cell size and fluorescence intensity. Fluorescence intensity at the baseline level was taken as F0. Evoked calcium response was expressed as the ratio of the post-treatment fluorescence intensity (F) to the basal level, as shown in our previous studies [10 (link),25 (link)]. Activation in neurons was defined as an increase in F/F0 ≥ 1.5 fold.
7
Confocal Microscopy of Stained Samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Confocal microscopy was undertaken using a Leica TCS SP5 (Leica Microsystems) confocal Microscope equipped with the following lasers: 405 nm (violet), 514 nm (blue), 561 nm (green), and 633 nm (red) [25 (link)]. Data were collected using a 63× oil immersion lens (numerical aperture 0.7) and refraction index of 1.52. Samples were sliced with a razor blade 2 × 5 mm (approximately) then stained with solution containing 0.066% (w/v) rhodamine B (protein stain) and 0.002% (w/v) FITC (starch stain) in water. Approximately 50 μL of dye was added to each sample, which was then left for five minutes in the dark prior to imaging in a FluoroDish (35 mm diameter, Thermo Fisher Scientific (Rockford, IL, USA)). Images were collected in sequential scan mode using the 488 nm laser then the 561 nm laser. The scan speed was 400 Hz, scan mode xyz, pinhole 95.5 μm, pixel size 1024 × 1024, step size 1.09 μm, with six ‘line averages’. Three biological and three technical replicates were examined for each condition. The resulting images were visualised in ImageJ and LAS X software (Leica Microsystems).
8
Proximity Ligation Assay in HK-2 Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
HK-2 cells were fixed in 4% paraformaldehyde and permeabilized in 0.5% Triton X-100. The proximity ligation assay was carried out according to the manufacturer’s instructions of the Duolink In Situ PLA kit (Sigma, Cat# DUO92101). The signal was visualized using a Leica SP8 confocal microscope (Leica Microsystems, RRID: SCR_008960 ) and analyzed by ImageJ (RRID: SCR_003070 ) software.
9
Visualizing NLRP3 Inflammasome Activation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
HCASMC were seeded at a density of 1 × 104 cells per cm2 on 25-mm coverslips 24 h before the start of the experiment. HCASMC were treated with extracellular NLRP3-YFP inflammasome particles for 4 h (3:1 particles/ cell). Coverslips were then washed with HBS and incubated with Cell Mask Deep Red plasma membrane stain (Invitrogen, Carlsbad, California, United States) for 10 min at 37 °C according to the manufacturer's protocol. Coverslips were mounted and imaged using a Leica DMI8/SP8 confocal laser scanning microscope (Leica Microsystems, Wetzlar, Germany). Pinhole adjustment was set to 1 Airy unit. For YFP excitation a 488 nm and for CellMask Deep Red plasma membrane stain a 638 nm Laser was used. Emission filters were adjusted accordingly. Images were analyzed using LasX (Leica Microsystems, Wetzlar, Germany) and ImageJ.
10
Quantifying Extracellular Matrix Remodeling
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For staining, myotubes were fixed with 4% paraformaldehyde after co-culturing with WJ-MSCs or treatment with MMP-1 protein. Picro-Sirius red staining (Abcam, Cambridge, UK) was performed to detect collagen deposition in each group, and the image was analyzed using light microscopy, with quantification using Image J (NIH, New Bethesda, MD, USA).
The gastrocnemius muscles of mice were fixed in 4% paraformaldehyde and then embedded in paraffin, sectioned at 4 μm, and stained with Sirius red staining solution or Alizarin red staining solution. Sirius red staining was used to detect fibrosis, and Alizarin red to detect large accumulations of calcium/necrotic fibers, according to standard procedures. Analysis was conducted using a ScanScope AT (Leica Microsystems, Buffalo Grove, IL, USA), and the images were quantified using Image J.
The gastrocnemius muscles of mice were fixed in 4% paraformaldehyde and then embedded in paraffin, sectioned at 4 μm, and stained with Sirius red staining solution or Alizarin red staining solution. Sirius red staining was used to detect fibrosis, and Alizarin red to detect large accumulations of calcium/necrotic fibers, according to standard procedures. Analysis was conducted using a ScanScope AT (Leica Microsystems, Buffalo Grove, IL, USA), and the images were quantified using Image J.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!