Image J was used to randomly select 440 data points in photos of hiPSC‐CMs on butterfly wings to measure the angle distribution of fiber, and statistical analysis was carried out to draw the angle distribution map and the ratio of cell length to width. The expression of Cx43 was also analyzed by image J. The calcium imaging traces were analyzed by Leica Application Suite X 3.5.6. FlowJo was used to analyze the results of flow cytometry.
Application suite x 3
Manufactured by Leica
Sourced in United States
Leica Application Suite X 3.5.5.19976 is a software platform that provides a comprehensive suite of tools for image acquisition, processing, and analysis. The software is designed to work seamlessly with Leica's range of microscopes and imaging systems, enabling users to capture, manage, and analyze high-quality images efficiently.
Automatically generated - may contain errors
Lab products found in correlation
Dmi8 confocal microscope, by Leica (3 mentions)
Sp8 lightning confocal system, by Leica (2 mentions)
Alexa fluor 594 conjugated anti rabbit igg, by Jackson ImmunoResearch (2 mentions)
Ab13970, by Thermo Fisher Scientific (2 mentions)
Ab81086, by Abcam (2 mentions)
Vt1000, by Leica (2 mentions)
Af5647, by Abcam (2 mentions)
Rat anti mcherry, by Thermo Fisher Scientific (2 mentions)
Tcs sp8, by Leica (2 mentions)
Fluorescent microscope, by Leica (1 mentions)
Rhod 2, by Thermo Fisher Scientific (1 mentions)
Pymol molecular graphics system, by Schrödinger (1 mentions)
Prism 9, by GraphPad (1 mentions)
Prolong diamond, by Thermo Fisher Scientific (1 mentions)
Tcs sp8 sted 3x microscope, by Leica (1 mentions)
Star 635p, by Abberior (1 mentions)
Rbpms, by GeneTex (1 mentions)
Dfc9000 gt camera, by Leica (1 mentions)
Dm6b z epifluorescence microscope, by Leica (1 mentions)
Hc pl apo 100 8 na, by Leica (1 mentions)
14 protocols using application suite x 3
1
Angle Distribution and Cell Morphology Analysis of hiPSC-CMs
2
Measuring Intracellular Calcium Dynamics in hiPSCs-CMs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
hiPSCs-CMs were incubated with 5 mM rhod2 (R14220, LIFE TECHNOLOGIES, United States) for 60 min at 37°C. Prior to fluorescence measurements, cells were washed in indicator-free 1,640, and then incubated for a further 30 min. Afterwards, spontaneous increases in intracellular Ca2+ concentration was imaged using a fluorescent microscope (Leica, Germany) at 561 nm wavelength. Substrates were connected to a pacemaker (YC-3 Bipolar Programmable Electrical Stimulator, CHINA) and paced 2 ms, 5 V/cm, 1 Hz. The experiment was repeated 3 times, where each experiment was recorded for at least 1 minute. Data were analyzed using Leica Application Suite X 3.5.6.
3
Confocal Imaging and Structural Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Confocal images were taken using a Leica SP8 LIGHTNING confocal system with the built-in software Leica Application Suite X 3.5.5.19976. Images were processed and assembled in Adobe Photoshop 20.0.4. Schematic illustrations were made with Microsoft Office Power Point Professional Plus 2016 and Biorender. AlphaFold structure of ATG2A was visualized in the PyMOL Molecular Graphics System, Version 2.4.0 Schrödinger, LLC. Cartwheel drawing of amino acid sequence was performed with HeliQuest54 . Unpaired, two-tailed t-tests Statistical analysis was performed in Microsoft Office Excel Professional Plus 2016. Graphs were generated in Excel and GraphPd Prism 9.0.0. For colocalization quantification, Pearson's correlation coefficient was quantified by Coloc 2 version 3.0.5 in ImageJ (Fiji 1.53f51).
4
Multimodal Imaging and Data Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A Leica SP8 LIGHTNING confocal system and its built-in software Leica Application Suite X 3.5.5.19976 were used to collect confocal images as well as for living cell imaging. Images were processed in Adobe Photoshop 20.0.4. Schematic illustration figures were made with Biorender and Microsoft Office PowerPoint Professional Plus 2016. Protein structures were visualized in the PyMOL, Version 2.4.0. Graphs were generated in GraphPad Prism 9.0.0. Images were quantified using custom-coded algorithms tailored according to specific experiments to incorporate quality control measures, minimize errors, and ensure accuracy and reliability.
5
Analyzing Microneedle Skin Penetration Depth
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The depth of the microchannels created by MNs was analyzed using confocal laser scanning microscopy (CLSM). Fluorescein isothiocyanate (0.35%, 200 µL) was applied to the skin after treatment with MNs for 1 min. Excess dye was removed with Kimwipes. The MN treated skin samples were placed on a glass slide without distortion or fixation artifacts. The slides were observed using a computerized Leica TCS SPE II confocal microscope (Leica microsystems, Heerbrugg, CH9435 Switzerland) with 10X objective at an excitation wavelength of 488 nm. Leica Application Suite X 3.5.5.19976 fluorescence software was used to process the images. The depth of the microchannels created and pattern of distribution of fluorescein in the microchannels was studied using X-Z sectioning [13] .
6
STED Microscopy Imaging Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
For STED microscopy, cells were grown on polylysine coated coverslips and samples were prepared with prelysis as described above, and mounted using ProLong™ Diamond (Life Technologies).
STED and confocal images were recorded at the Core Facility Bioimaging at the Biomedical Center, LMU Munich. Gated STED images were acquired with a Leica TCS SP8 STED 3X microscope with pulsed white light laser excitation and pulsed depletion with a 775 nm laser using an HC PL APO CS2 100×/1.40 oil immersion objective. The fluorescence was recorded line sequentially at a scan speed of 200 Hz, a pinhole setting of 0.93 AU (at 580 nm) and the pixel size was set to 25 nm × 25 nm; z-step size of z-stacks was 160 nm. The signals were detected with hybrid detectors operated in photon counting mode with the time gate set to 0.5–8 ns and using the following settings:
Alexa Fluor 594: excitation 590 nm; emission: 600–625 nm; depletion power: 50%.
Abberior STAR 635P: excitation 635 nm; emission: 643–720 nm; depletion power: 25%.
Images were deconvolved with Huygens Professional (SVI) and processed in Leica Application Suite X 3.3.0.16799.
STED and confocal images were recorded at the Core Facility Bioimaging at the Biomedical Center, LMU Munich. Gated STED images were acquired with a Leica TCS SP8 STED 3X microscope with pulsed white light laser excitation and pulsed depletion with a 775 nm laser using an HC PL APO CS2 100×/1.40 oil immersion objective. The fluorescence was recorded line sequentially at a scan speed of 200 Hz, a pinhole setting of 0.93 AU (at 580 nm) and the pixel size was set to 25 nm × 25 nm; z-step size of z-stacks was 160 nm. The signals were detected with hybrid detectors operated in photon counting mode with the time gate set to 0.5–8 ns and using the following settings:
Alexa Fluor 594: excitation 590 nm; emission: 600–625 nm; depletion power: 50%.
Abberior STAR 635P: excitation 635 nm; emission: 643–720 nm; depletion power: 25%.
Images were deconvolved with Huygens Professional (SVI) and processed in Leica Application Suite X 3.3.0.16799.
7
Quantifying Axonal Projections in the Brain
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Collated images were stitched for each brain section using Leica Application Suite X 3.3.0.16799. Image processing was done in FIJI using customized macro scripts. First, hessian ridge detection and thresholding was performed as described elsewhere (Grider, Chen, & David Shine, 2006) (link). Briefly, this results in binary images of the eYFP + axons while eliminating background fluorescence. These images were then quantified with a second script where, similar to the rabies virus quantification, the custom-made ROI atlas was manually adjusted for every coronal section. Percent of total output was calculated from the thresholded image, with the eYFP + pixel count of each ROI normalized to the total of all eYFP + pixels identified from the individual brain. Additionally, percent innervation density was calculated as the proportion of eYFP + pixels covering the maximal pixel count for its ROI. Clearly distinguishable passing fiber bundles (such as in the striatum, cerebral peduncles, anterior commissure, internal-and external capsules, and pyramidal tract) were excluded from the analysis. As with the RV tracings, the starter volume was also excluded from all analysis.
8
Retinal Ganglion Cell Immunolabeling
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Freshly isolated eyes were immersion fixed in 4% paraformaldehyde for 30 min then cryoprotected in 30% sucrose with 0.02% sodium azide. Retinas were dissected out and vitreous removed. Immunolabeling included washes in 0.1 M PBS, then incubation in blocking solution (5% donkey serum, 1% Triton X-100 in 0.1 M PBS) for 1 h, primary antibody (diluted in 0.5% bovine serum albumin, 0.9% NaCl, 1% Triton X-100 in 0.1 M PBS) for 48–72 h, washes in 0.1 M PBS, blocking solution for 30 min, secondary antibody incubation for 18 h, washes, DAPI labeling, then coverslipping with Fluoromount-G. RBPMS (RNA binding protein, multiple splicing) primary antibody (Genetex, Irvine, CA) to label RGCs (1:250) and secondary antibody from Jackson ImmunoResearch (West Grove, PA) Alexa Fluor 594-conjugated anti-rabbit IgG (1:250) were used. Images were collected on a Leica DMi8 confocal microscope integrated with Leica application Suite X 3.1.1.15751 (Leica Microsystems, Buffalo Grove, IL, USA). Figures were created using Adobe Illustrator, Adobe Creative Cloud version 2017.
9
Quantitative Confocal Imaging of Retinal Microglia
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A Leica DMi8 confocal microscope integrated with Leica application Suite X 3.1.1.15751 (Leica Microsystems, Buffalo Grove, IL, USA) was used for microscopy. The same exposure time settings were used for capturing all the photomicrographs among all groups. Photomicrographs were obtained from the central part of retina and from proximal region of optic nerves. Immunoreactivity was quantified by using an optical density measurement within regions of interest (ROIs) using Fiji-ImageJ [37 (link)]. Minimum eight ROIs were used per antigen for quantification. For microglial quantification, five sections per retina and ON and five retinas and ONs for each group (a total of 25 sections per tissue) were used. Microglia were only counted if the DAPI-stained nucleus could be identified.
10
Immunolabeling Retinal Ganglion Cells
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!