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8 results for “iterative methods”
Iterative Bleaching Extends multi-pleXity (IBEX) imaging method, mouse spleen
<p>This dataset was acquired using the Iterative Bleaching Extends multi-pleXity (IBEX) imaging method described in: “IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues“, A. Radtke et al., 2020, <a href="https://doi.org/10.1073/pnas.2018488117">doi:10.1073/pnas.2018488117</a>.</p> <p>It is comprised of a three cycle IBEX experiment performed on mouse spleen sections labeled with the nuclear marker JOJO-1 and membrane label CD4 AF594. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 mm), y (0.284 mm), and z (1 mm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p> </p> <p>Markers per channel in each of the three cycles:</p> <ol> <li>spleen_panel1.nrrd (6 channels): B220 PE, CD8 BV421, IgD AF700, CD4 AF594, JOJO, Foxp3 eF660</li> <li> <p>spleen_panel2.nrrd (7 channels): CD169 PE, F480 BV421, MHCII AF700, CollIV AF488, JOJO, CD11c AF647, CD4 AF594</p> </li> <li> <p>spleen_panel3.nrrd (7 channels): CD31 PE, CD68 BV421, Ki67 AF700, CD45 AF488, CD4 AF594, JOJO, CD3 AF647</p> </li> </ol> <p>The panels can be registered using the code available on github: <a href="https://github.com/niaid/sitk-ibex">https://github.com/niaid/sitk-ibex</a></p> <p>To view these multi-channel images, in <a href="http://teem.sourceforge.net/nrrd/format.html">nrrd format</a>, use the <a href="https://imagej.net/Fiji">Fiji viewer</a>. The data is stored in XYZC order.</p>
Data for paper "An adaptive nonlinear iterative method for predicting seafloor topography from altimetry-derived gravity data"
<p>LM is the linear inversion seafloor topography model</p> <p>NLM is the nonlinear inversion seafloor topography model</p> <p>PM is the prior seafloor topography model</p>
Landmine Detection Using Electromagnetic Time Reversal-Based Methods. Part 1: Classical TR, Iterative TR, DORT and TR-MUSIC
<p>In this repository, you can find the simulation files used to reproduce the results presented in the paper titled "Landmine Detection Using Electromagnetic Time Reversal-Based Methods." If you find these files useful, please cite the paper as it helps acknowledge the work and support future research.</p> <p>This repository is organized into three main folders, each serving a distinct purpose and containing specific types of files:</p> <p><strong>CST-MWS Files</strong>: This folder contains the necessary files to simulate the examples discussed in the paper using CST Microwave Studio (CST-MWS). These files are essential for setting up and running the simulations that replicate the experimental results. </p> <p><strong>TR-MUSIC</strong>: In this folder, you will find the MATLAB m-file required to implement the TR-MUSIC (Time Reversal-MUltiple SIgnal Classification) method proposed in the paper. This MATLAB script is designed to help users apply the TR-MUSIC algorithm to their data, enabling them to detect landmines effectively. </p> <p><strong>2D-GFB</strong>: The 2D-GFB folder contains the MATLAB m-file necessary to run the 2D TR-MUSIC and DORT (Decomposition of the Time Reversal Operator) methods. These advanced techniques are crucial for analyzing two-dimensional data and enhancing the accuracy of landmine detection. </p> <p><br>By organizing the repository in this manner, we aim to make it easier for researchers and practitioners to access and utilize the simulation files effectively. Whether you are replicating the study's results or applying these methods to new datasets, the files and instructions provided should serve as a valuable resource.</p> <p>If you encounter any issues or have questions regarding the use of these files, please do not hesitate to reach out for support. We hope this repository aids your research and contributes to advancements in landmine detection technologies.</p> <p> </p>
Accompanying dataset for: "IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues"
<p>These datasets were acquired using either the manual or automated IBEX multiplex imaging protocols and accompany the manuscript “IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, A. Radtke <em>et al.</em>, 2021, Nature Protocols.</p> <p>All image data are stored using the <a href="https://imaris.oxinst.com/support/imaris-file-format">Imaris file format</a>. To view these multi-channel images, you can either use one of these <strong>free</strong> viewers, <a href="https://imaris.oxinst.com/imaris-viewer">Imaris viewer</a>, <a href="https://imagej.net/Fiji">Fiji</a>.</p> <p>Each experiment has an associated imaging meta-data file in xlsx format and the resulting image in Imaris format.</p> <p><strong>Human Jejunum (Automated)</strong></p> <p>Dataset is a 24 parameter IBEX experiment performed on a human jejunum section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Kidney (Automated)</strong></p> <p>Dataset is a 16 parameter IBEX experiment performed on a human kidney Formalin-Fixed Paraffin-Embedded (FFPE) section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Lymph Node (Automated)</strong></p> <p>Dataset is a 25 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Skin (Automated)</strong></p> <p>Dataset is an 18 parameter IBEX experiment performed on a human skin section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Liver (Manual)</strong></p> <p>Dataset is a 22 parameter IBEX experiment performed on a human liver section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Human Lymph Node (Manual)</strong></p> <p>Dataset is a 38 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Human Spleen (Manual)</strong></p> <p>Dataset is a 25 parameter IBEX experiment performed on a human spleen section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p>
Data from: A superlinear iteration method for calculation of finite length journal bearing's static equilibrium position
Solving the static equilibrium position is one of the most important parts of dynamic coefficients calculation and further coupled calculation of rotor system. The main contribution of this study is testing the superlinear iteration convergence method - twofold secant method, for determination of the static equilibrium position of journal bearing with finite length. Essentially, the Reynolds equation for stable motion is solved by finite difference method and the inner pressure is obtained by successive over-relaxation iterative method reinforced by the compound Simpson quadrature formula. The accuracy and efficiency of the twofold secant method are higher in comparison with the secant method and dichotomy. The total number of iterative steps required for the twofold secant method are about one-third of secant method and less than one-eighth of dichotomy for the same equilibrium position. The calculations for equilibrium position and pressure distribution for different bearing length, clearance and rotating speed were done. In the results, the eccentricity presents linear inverse proportional relationship to the attitude angle. The influence of the bearing length, clearance and bearing radius on the load-carrying capacity were also investigated. The results illustrate that larger bearing length, larger radius and smaller clearance are good for the load-carrying capacity of journal bearing. The application of twofold secant method can greatly reduce the computational time for calculation of the dynamic coefficients and dynamic characteristics of rotor-bearing system with a journal bearing of finite length.
Data from: A superlinear iteration method for calculation of finite length journal bearing's static equilibrium position
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A Schwarz iterative method to evaluate ocean- atmosphere coupling schemes. Implementation and diagnostics in IPSL-CM6-SW-VLR. GMD-2020-307
<p>These files are associated with an article submitted to Geoscientific Model Development (https://www.geoscientific-model-development.net) with reference GMD-2020-307 : A Schwarz iterative method to evaluate ocean- atmosphere coupling schemes. Implementation and diagnostics in IPSL-CM6-SW-VLR.<br> By Olivier Marti, Sébastien Nguyen, Pascale Braconnot, Sophie Valcke, Florian Lemarié, and Eric Blayo</p> <p>It contains :<br> - The model code used for the study<br> - The model outputs used for the study<br> - The script used to produce the figures.</p> <p>Contact : Olivier Marti - olivier.marti@lsce.ipsl.fr</p>
Use of Iterative Reconstruction Method in Ultralow-dose CT for Follow-up of Patients With Intraabdominal Abscess: Comparison With Standard Dose CT
ClinicalTrials.gov study NCT03681665. IPD Sharing: NO. Countries: 1. Publications: 0.
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