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134 results for “Matlab”
Raw data mzXML and MATLAB code for Variation in chemical composition of dissolved organic matter during the winter to spring transition in the northern Barents Sea
<p>MATLAB code and raw data mzXML for Variation in chemical composition of dissolved organic matter during the winter to spring transition in the northern Barents Sea.</p> <p>Seawater samples were collected during three distinct periods: early winter (December 2019), late winter (March 2021), and spring (May 2021). The sampling transect extended from the northern Barents Sea into the Nansen Basin (76°N – 83°N) as part of <em>The Nansen Legacy</em> project (Research Council of Norway, RCN #276730). The molecular composition of dissolved organic matter (DOM) was analyzed using an Orbitrap mass spectrometer.</p>
Datafile DF1 + Matlab Scripts
<table> <tbody> <tr> <td>Supporting datafile </td> <td>DF1.csv</td> </tr> </tbody> </table> <table> <tbody> <tr> <td> <p>This file provides all experimental data associated with paper: Matrix gas flow through ‘impermeable’ rocks - shales and tight sandstone , by Ernest Rutter, Julian Mecklenburgh and Yusuf Bashir</p> <p>Matlab Scripts is a compressed archive containing scripts for (a) the finite element simulaton of the stress state in a hydrostatically loaded sample with end piston constraints and (b) scripts for processing permeability data. A readme file is provided to explain the diferent fiels that make up the archive.</p> </td> </tr> </tbody> </table>
MATLAB codes for : "Diagnosis and Prognosis of Faults in High-Speed Aeronautical Bearings with a Collaborative Selection Incremental Deep Transfer Learning Approach".
<p>The package contains all the materials needed to reproduce the findings of our paper. The paper is published by MDPI Applied Sciences journal and its details are as follow.</p> <p>Berghout, T.; Benbouzid, M. Diagnosis and Prognosis of Faults in High-Speed Aeronautical Bearings with a Collaborative Selection Incremental Deep Transfer Learning Approach. <em>Appl. Sci.</em> <strong>2023</strong>, <em>13</em>, 10916. https://doi.org/10.3390/app131910916</p> <p>1) Please you need to download the dataset from original link provided by introductory paper (Please read the above paper to find out about the datset used).<br> 2) Put the data in folders "RawData" for both experments.<br> 3) Please run the files for each experiment as provided, in alphabetical order.</p>
Matlab code for a multipolar decomposition of optical forces
<p>This dataset supplements Figure 5 from the publication "Multipolar Origin of the Unexpected Transverse<br> Force Resulting from Two-Wave Interference*" by Karim Achouri, Andrei Kiselev, and Olivier J. F. Martin. Here, we provide the code for the multipolar analysis of the optical force based on the vector spherical harmonic decomposition. Based on the Mie solution, electric fields can be obtained numerically in the far-field by using the software developed by Dr. Karim Achouri https://github.com/kachourim/MieScatteringPEC. This code analyzes the far-field scattered by a perfect electric conductor sphere placed in vacuum for different sphere radii. In the framework of the Maxwell stress tensor, we find the optical force acting on a sphere along the z-direction in the illumination configuration presented in Figure 1*. The use of the vector spherical decomposition allows to observe contributions from different multipolar interactions. In this code,we analyze the force appearing as a result of the interaction between electric dipole aligned along x, px, and electric quadrupole with components xz, Qexz and compare it with the total force along the z-axis appearing as a result of interaction between all multipoles supported by the sphere with given radius.</p>
Automated sarcomere detection Matlab tool
<p>The Matlab code presented was developed by Dr. Ian Estabrook in 2019-2023 to automatically detect sarcomeres in multi-channel z-stack images of developing myofibrils, as used in the preprint: "A tension-driven sarcomere division mechanism facilitates muscle growth" by Clement Rodier, Ian Estabrook, Vincent Loreau, Dirk Görlich, Benjamin M. Friedrich, Frank Schnorrer. We thank Yasmin Magdy Emadeldin Mohamed Abdelghaffar for help with preparing this repository and the documentation of the code. An example data set with corresponding sarcomere tracking is included.</p>
Bubble/Foam Simulations for Malej et al. 2023, source codes, input files, matlab files, data files
<p><i>.F are source codes, *.m are matlab scripts for analysis and postprocessing, .txt are data files including bathymetry and data from sensitivity tests</i></p>
Matlab tools to solve the viscous Taylor Goldstein equation for both instabilities and waves
<p><strong>Matlab tools to solve the viscous Taylor Goldstein equation for both instabilities and waves</strong><br> Fourier-Galerkin method is faster and more accurate than the previous finite-difference version.<br> <strong>File list:</strong><br> wave_analysis_FG.m : code to solve demonstration problem (internal gravity waves on the Columbia River plume; data courtesy J. Nash)<br> nash_data.txt : observational data for demonstration problem<br> vTG_FG.m : the main subroutine<br> BaryL.m : auxiliary subroutine<br> vTG_FGprep.m : auxiliary subroutine (call before vTG_FG)<br> Lian_Smyth_Liu20.pdf : Paper to reference for description and testing of code.<br> The underlying theory is described in<em> Instability in Geophysical Flows,</em> by W.D. Smyth and J.C. Carpenter, Cambridge University Press: Available from <a href="https://www.amazon.com/Instability-Geophysical-Flows-William-Smyth-dp-1108703011/dp/1108703011/ref=mt_other?_encoding=UTF8&me=&qid=1573683499">Amazon</a> and others.</p>
Simulator dataset and associated matlab routine
<p>This archive integrates 4 data files in csv format generated in ONERA's simulator.</p> <p>These files have been used for an ERF paper, also available on zenodo (10.5281/zenodo.6673941) :</p> <p>VERSATILE OFFLINE SIMULATION TOOL FOR SYSTEMS DESIGN</p>
Data and MATLAB Code for the paper entitled "A modified Chezy formula for one-dimensional unsteady frictional resistance in open channel flow"
<p>This link includes the data and MATLAB code files for the research paper entitled "A modified Chezy formula for one-dimensional unsteady frictional resistance in open channel flow" by Zhou, J.W.; Bro, W.M.; Tick*, G.R.; Mofatakari, H.; Li, Y.; and Cheng, L., which has been submitted to the Journal of Fluids Engineering. These files are edited under the GB18030 character set standard.</p>
Surveying the communities of users of MATLAB and similar languages (Responses)
<p>This upload includes responses gathered from a survey applied to the users of MATLAB and its clone languages. It covers the participants' programming experience, how they interact with these languages, the importance they give to the reusability of their programs, object-oriented programming and how satisfied they are with these languages.</p>
MATLAB script for data sorting
<p>Supporting information associated with the publication "New insights into single-molecule junctions using a robust, unsupervised approach to data collection and analysis", <em>J. Am. Chem. Soc.</em>, 2015, DOI: 10.1021/jacs.5b05693. This MATLAB script is a representative example of that used to objectively sort <em>I</em>(<em>s</em>) traces obtained from <strong>1,8-ODT</strong>-coated and blank (uncoated) Au substrates. A short 'Guide to...' document is also included to introduce the user.</p>
System Matrices and Matlab Code for Loewner for Index-2 Systems
<p>This code accompanies the paper</p><blockquote><p><i>Implicit and explicit matching of non-proper transfer functions in the Loewner framework</i> by Ioan Victor Gosea and Jan Heiland</p></blockquote><p>that we submitted for presentation at the CDC 2024.</p>
Matlab code to calibrate a structured-PDE model to data from in vitro experiments
<p>Matlab code for the calibration of a PDE model of evolutionary dynamics of a well-mixed population of aggressive breast cancer cells from in vitro data on MCF7-sh-WISP2 cell line and bootstrapping for uncertainty quantification. For more details, see the associated publication: "Evolutionary dynamics of glucose-deprived cancer cells: insights from experimentally-informed mathematical modelling", by L. Almeida, J. Denis, N. Ferrand, T. Lorenzi, A. Prunet, M. Sabbah, C. Villa (corresponding author, author of code), 2023. In press in the journal of the Royal Society Interface.</p>
MATLAB code for 'Bounds on quantum evolution complexity via lattice cryptography'
<p>We provide the MATLAB code and data to reproduce the numerical results presented in the paper https://arxiv.org/abs/2202.13924.</p>
Matlab example for Local Enrichment Analysis (LEA) analysis with real data
<p>Phenotypic plasticity is essential to the immune system, yet the factors that shape it are not fully understood. Here, we comprehensively analyze immune cell phenotypes including morphology across human cohorts by single-round multiplexed immunofluorescence, automated microscopy, and deep learning. Using the uncertainty of convolutional neural networks to cluster the phenotypes of 8 distinct immune cell subsets, we find that the resulting maps are influenced by donor age, gender, and blood pressure, revealing distinct polarization and activation-associated phenotypes across immune cell classes. We further associate T-cell morphology to transcriptional state based on their joint donor variability, and validate an inflammation-associated polarized T-cell morphology, and an age-associated loss of mitochondria in CD4+ T-cells. Taken together, we show that immune cell phenotypes reflect both molecular and personal health information, opening new perspectives into the deep immune phenotyping of individual people in health and disease.</p>
Excitation energy transfer and vibronic coherence in intact phycobilisomes — multidimensional electronic spectroscopy data set and MATLAB and Julia analysis code
<p>Data sets used in the article "Excitation energy transfer and vibronic coherence in intact phycobilisomes" by Sil et al. The phycobilisomes were isolated from the short-filament mutant (SF33) of <em>Fremyella diplosiphon</em> UTEX 481 (also known as <em>Tolypothrix</em> sp. PCC 7601). Multidimensional electronic spectroscopy was performed with 6.7 fs mid-visible pulses (520–700 nm) using a pump–probe optical configuration using adaptive pulse shaping techniques. In addition to the full set of two-dimensional spectra and analysis files generated using global and target modeling and analysis of coherences (3DES oscillation maps), we provide here a linear absorption spectrum with phycobiliprotein component analysis as well as a set of 2D excitation–emission fluorescence spectra of intact and broken phycobilisome preparations. </p> <p>Sil, S.; Tilluck, R. W.; Mohan TM, N.; Leslie, C. H.; Rose, J. B.; Domínguez-Martín, M. A.; Lou, W.; Kerfeld, C. A.; Beck, W. F. Excitation energy transfer and vibronic coherence in intact phycobilisomes. Nat. Chem. (2022), DOI: 10.1038/s41557-022-01026-8.</p> <p><a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41557-022-01026-8__;!!HXCxUKc!yaVwTZFk8T-j3ROhygpOGW5Xy_E2wQvf-QgNGr9FZZbp4oNpfp_ZmhkdWYLdg2mKSDP8yYrNAZs$">https://www.nature.com/articles/s41557-022-01026-8</a></p> <p> </p> <p> </p>
Matlab scripts
Open the record for dataset details and reuse information.
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera
<p>The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analyzing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI – an open-source MATLAB package designed for the study of morphology using three-dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling, and rotation and, for an image of size 128x128x128 can be computed in less than 0.1 seconds. We applied our package as a case study on a collection of 300 X-ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyze morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution.</p>
Data for Matlab package locFISH to simulate realistic 3d smFISH images
<p>Different data-sets needed by the Matlab package locFISH. locFISH allows the simulation and analysis of realistic single molecule FISH (smFISH) images.</p> <p><strong>data_simulation.zip</strong><br> Contains all necessary data to simulated smFISH images. Specifically, the zip archive contains a library of 3D cell shapes, realistic imaging background, and a simulated PSF (Point Spread Function). </p> <p><strong>GAPDH.zip</strong><br> Contains the smFISH data of GAPDH and the corresponding analysis results, which were used to create the library of cell shapes provided in data_simulation.zip </p> <p>For more details on these data and how do to use them, please consult the detailed user-manual provided with <strong>locFISH</strong>, available at</p> <p>https://bitbucket.org/muellerflorian/fish_quant</p>
Matlab data for paper ""Non-Asymptotic Rates for Communication Efficient Distributed Zeroth Order Strongly Convex Optimization" by Sahu et al.
<p>This is a Matlab data file for paper A.K. Sahu, D.Jakovetic, D. Bajovic and S. Kar, “Non-Asymptotic Rates for Communication Efficient Distributed Zeroth Order Strongly Convex Optimization”, IEEE Global Conference on Signal and Information Processing(GlobalSIP), 2018, see also: <a href="https://zenodo.org/record/3333576#.XSibRegzZPY">https://zenodo.org/record/3333576#.XSibRegzZPY</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.