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242 results for “microfluidics”
3D super-resolution datasets associated with the paper "Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet"
<p>3D single-molecule super-resolution datasets corresponding to reconstructions shown in <em>Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet</em> by Saliba & Gagliano, Gustavsson et. al.</p>
Real-time monitoring of a 3D blood-brain barrier model maturation and integrity with a sensorized microfluidic device
<p><span>A significant challenge in the treatment of central nervous system (CNS) disorders is represented by the presence of the blood-brain barrier (BBB), a highly selective membrane that regulates molecular transport and restricts the passage of pathogens and therapeutic compounds. Traditional <em>in vivo</em> models are constrained by high costs, lengthy experimental timelines, ethical concerns, and interspecies variations. <em>In vitro</em> models, particularly microfluidic BBB-on-a-chip devices, have been developed to address these limitations. These advanced models aim to more accurately replicate human BBB conditions by incorporating human cells and physiological flow dynamics. In this framework, here we developed an innovative microfluidic system that integrates thin-film electrodes for non-invasive, real-time monitoring of BBB integrity using electrochemical impedance spectroscopy (EIS). EIS measurements showed frequency-dependent impedance changes, indicating BBB integrity and distinguishing well-formed from non-mature barriers. The data from EIS monitoring was confirmed by permeability assays performed with a fluorescence tracer. The model incorporates human endothelial cells in a vessel-like arrangement to mimic the vascular component and three-dimensional cell distribution of human astrocytes and microglia to simulate the parenchymal compartment. By modeling the BBB-on-a-chip with an equivalent circuit, a more accurate trans-endothelial electrical resistance (TEER) value was extracted. The device demonstrated successful BBB formation and maturation, confirmed through live/dead assays, immunofluorescence and permeability assays. Computational fluid dynamics (CFD) simulations confirmed that the device mimics <em>in vivo</em> shear stress conditions. Drug crossing assessment was performed with two chemotherapy drugs: doxorubicin, with a known poor BBB penetration, and temozolomide, conversely specific drug for CNS disorders and able to cross the BBB, to validate the model predictive capability for drug crossing behavior. The proposed sensorized microfluidic device represents a significant advancement in BBB modeling, offering a versatile platform for CNS drug development, disease modeling, and personalized medicine.</span></p>
VISION Invited lecture - Microfluidic technologies and their applications in cell biology
<p>Recording and presentation of the invited lecture that took place online on 27 April 2021 - <strong>Thorsten Knoll - Microfluidic technologies and their applications in cell biology.</strong></p> <p>In the past twenty years, microfluidic devices and systems have gained in importance in the field of bioanalytics and biomedicine, not only in research but also in the market. Lab-on-chip systems with microfluidic structures serve for medical tests with body fluids or extractions from fluids. Besides, microfluidic systems are also used for cell handling and culturing, for the mixing of liquids and for measuring quantitative amounts of components in liquid samples.</p> <p>Fraunhofer IBMT develops microfluidic systems for various applications in the field of life sciences. Different miniaturized approaches and solutions exist e.g. for transport studies or toxicological assays with single cells, 2D cell layers or 3D cell aggregates.</p> <p>The online lecture will cover some basic considerations regarding microfluidics and IBMT’s technological solutions for the fabrication of microfluidic devices and their use in different application scenarios. Furthermore, the presentation describes solutions for the integration of the microfluidic devices in a complete set-up comprising of peripheral fluidic components and optical or electrical measurement systems.</p>
A self-purifying microfluidic system for identifying drugs acting against adult schistosomes
<p><span>The discovery of novel antihelmintic molecules to combat the development and spread of schistosomiasis, a disease caused by several <em>Schistosoma</em> flatworm species, mobilizes significant research efforts worldwide. With a limited number of biochemical assays for measuring the viability of adult worms, the anti-schistosomicidal activity of molecules is usually evaluated by microscopic observation of worm mobility and/or integrity upon drug exposure. Even if these phenotypical assays enable multiple parameters analysis, they are often conducted during several days and need to be associated with image-based analysis to minimized subjectivity. We describe here a self-purifying microfluidic system enabling the selection of healthy adult worms and the identification of molecules acting instantly on the parasite. The worms are assayed in a dynamic environment that eliminates unhealthy worms that cannot attach firmly to the chip walls prior to being exposed to the drug. The detachment of the worms is also used as a second step readout for identifying active compounds. We have validated this new fluidic screening approach using the two major antihelmintic drugs, Praziquantel and Artemisinin. The reported dynamic system is simple to produce and to parallelize. Importantly, it enables quick and sensitive detection of antischistosomal compounds in no more than one hour. </span></p>
Droplet-Based Microfluidics Platform for the Synthesis of Single-Atom Heterogeneous Catalysts
<p>Data set supporting the publication of : "Droplet-Based Microfluidics Platform for the Synthesis of Single-Atom Heterogeneous Catalysts" (<a href="https://doi.org/10.1002/sstr.202200284">https://doi.org/10.1002/sstr.202200284</a>) by T. Moragues, S. Mitchell, D. Faust Akl, J. Pérez-Ramírez, and A. deMello.</p>
MarrowDLD: a microfluidic method for label-free retrieval of fragile bone marrow cells
<p>We introduce here a label-free cytometry microsystem, MarrowDLD, based on deterministic lateral displacement. MarrowDLD enables the isolation of fragile cells based on intrinsic size properties while preserving their viability and functionality. Bone marrow adipocytes, obtained from mouse and human stromal line differentiation, as well as megakaryocytes, from primary human CD34+ hematopoietic stem and progenitor cells, were used for validation.</p>
Data from: Evaporation induced acoustic emissions in microfluidic vessels
<p>Fluid flow processes such as drainage and evaporation in porous media are crucial in geological and biological systems. The motion of the displacement front of a moving fluid through multi-phase interfaces is often associated with abrupt mechanical energy release, detectable as acoustic emissions. The exact origin of these pulses and their damping mechanisms are still subjects of debate. Here, we study the characteristics of such acoustic emissions during evaporation of water from artificial microfluidic vessels, inspired by the physiology of vascular water-transport in plants. From the extracted settling times of the recorded acoustic emissions, we identify three pulse types and attribute their origins to bubble formation, snap-off events and rapid pore invasion. We also show that the resonance frequencies between 10 and 70 kHz present in specific pulse types decrease with increasing vessel radius (ranging from 0.25 to 1.0 mm) and length (ranging from 2.5 to 10.0 mm). Our findings provide insight into evaporation-induced acoustic emissions from microfluidic systems, both natural and artificial, and their potential use in non-invasive inspection or vascular health monitoring.</p>
Analysis of division and replication cycles in E. coli using time-lapse microscopy, microfluidics and the MoMA software
<p>Dataset used in the publication "Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism" by Guillaume Witz, Erik van Nimwegen and Thomas Julou (<a href="https://doi.org/10.1101/593590">https://doi.org/10.1101/593590</a>).</p> <p>The zip folder contains four subfolders each containing data corresponding to a given growth condition. Each subfolder contains one folder with images of time-lapses of E. coli cells growing in single microfluidics growth lanes and one folder with data obtained by analysing those images with the software MoMA (<a href="https://github.com/fjug/MoMA">https://github.com/fjug/MoMA</a>).</p>
Data from: Evaporation induced acoustic emissions in microfluidic vessels
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Data from: Artificial intelligence enabled multi-purpose smart detection in active-matrix electrowetting-on-dielectric digital microfluidics
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A self-purifying microfluidic system for identifying drugs acting against adult schistosomes
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Microfluidic monitoring of the growth of individual hyphae in confined environments
Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass, and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared to measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behavior of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to adress its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters
<p>Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and evaluates the utility of microfluidic droplets, also termed ultraminiaturized bioreactors, for rapid detection of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash water acquired from a major Mid-Atlantic produce processing facility (denoted as Producer) in the U.S. Using a fluorescentlylabeled anti- S. Typhimurium antibody and relative fluorescence intensities, paired with in-droplet incubation, S. Typhimurium was detected and identified with 100% specificity in less than 5 h. In initial optimization experiments using S. Typhimuriumspiked sterile water, the relative fluorescence intensity of S. Typhimurium was approximately two times that of the observed relative intensities of five non- S. Typhimurium negative controls at 4-h incubation in droplets containing Rappaport-Vasiliadis (RV) broth at 37 ° C: relative fluorescence intensity for S. Typhimurium = 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16), Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium - and E. aerogens -spiked shredded lettuce wash waters acquired from the Producer were then incubated 4 h in-droplet at 37 ° C with RV broth. The observed relative fluorescence of S. Typhimurium was significantly higher than that of E. aerogens , 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12), respectively. While further optimization focusing on compatible concentration methodologies for highly-dilute produce water samples is needed, this application of droplet microfluidics shows great promise in dramatically shortening the time necessary – from days to hours – to confirm viable bacterial contamination in ready-to-eat produce wash waters used throughout the domestic and international food industry.</p>
Analysis of lac operon induction with single cell resolution using the DIMM microfluidics chip and the MoMA software
<p>In this work, we demonstrate the power of the DIMM (Dual Input Mother Machine), a new microfluidics setup allowing long term environmental control and single cell resolution, and MoMA (Mother Machine Analyzer), its companion image analysis sofware.</p> <p>We study the induction of the <em>lac</em> operon in <em>Escherichia coli</em> MG1655 when nutrients alternate between glucose and lactose, using a translational fusion of LacZ with GFP integrated at the endogeneous locus.</p> <p>The dataset is made of two archives:</p> <ul> <li>DIMM_MoMA_images.tar.gz contains the image data produced in this study in a form ready to be used in MoMA</li> <li>DIMM_MoMA_data.tar.gz contains textual data files produced by MoMA and its postprocessing, with the cell identifier, length and fluorescence intensity of each cell in each frame.</li> </ul> <p>Detailed instructions are provided in the ReadMe.md file (NB: this is a text file using markdown syntax, you can open it in your favorite text editor).</p>
Phase-contrast time-lapse recordings of four bacterial species growing in microfluidic microtraps
<p>This dataset and software accompany the article <a href="https://doi.org/10.1371/journal.pcbi.1011181">"Label-free deep learning based species classification of bacteria imaged by phase-contrast microscopy"</a> for reproducing the results. The study applies deep-learning based image and video models for species classification of the bacteria <em>Enterococcus faecalis</em>, <em>Escherichia coli</em>, <em>Klebsiella pneumoniae</em>, and <em>Pseudomonas aeruginosa</em> growing in microfluidic chip traps.</p>
Design and assembly of core/shell nanostructures as investigated by microfluidics and molecular dynamics simulation_dataset_DLS_TEM_MD
<p><span>He we like to publish data related to modified and non-modified MSN cores analysed using microfluidics platform against acetalated dextran (AcDEX)/spermine modified acetalated dextran (SpAcDEX) polymers. </span></p> <p><span>The data contains Dynamic light scattering (DLS) and TEM images which help us to to the demarcation of combinations which formed successful core/shell particles along with, <em>in-silico</em> modelling and molecular dynamics (MD) simulations data showing molecular interactions between the core particles and <a>the encapsulant </a></span><span><span></span></span><span>polymer. </span></p>
Data and software for "Metal Pad Sensing: exploiting the electrical double layer to improve resistance-based microfluidic cell tracking, with applications to label-free mechanophenotyping"
<p>Data and software for "Metal Pad Sensing: exploiting the electrical double layer to improve resistance-based microfluidic cell tracking, with applications to label-free mechanophenotyping"</p>
Supplementary Table S1 (raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA "
<p>Supplementary Table S1 (all raw data) of "Filtration extraction method using microfluidic channel for measuring environmental DNA ". Each data of the validation experiment; Experiment 1-4 was located in different sheets..</p>
In-operando visualization of redox flow battery in membrane-free microfluidic platform
<p>Images are raw data of main figure 1.(B-D) from "In-operando visualization of redox flow battery in membrane-free microfluidic platform"</p>
Annotated pixels from brightfield images from yeast cell in microfluidic traps - Training and Test sets - DetecDiv (id02)
<p>This dataset has been generated by manual segmentation from timelapse images of yeast cells dividing using the DetecDiv software (see below).</p> <p>It contains ~1950 raw images (folder "images") associated with their mask (folder "labels") with 3 classes of pixels according to their value on the mask image, "1. background", "2. mother", "3. other".</p> <p>A splitSets.mat indicates which images have been used for training or for testing.</p> <p>It is related to the trained network <a href="https://doi.org/10.5281/zenodo.5553851">doi.org/10.5281/zenodo.5553851</a> from the software DetecDiv: github.com/gcharvin/DetecDiv</p> <p><a href="https://biorxiv.org/content/10.1101/2021.10.05.463175v1">biorxiv.org/content/10.1101/2021.10.05.463175v1</a></p> <p>-------------------------------------------------------</p> <p><strong>Data type</strong>: 2D microscopy images (brightfield) (.tif) + mask image (.tif)</p> <p><strong>Microscopy data type</strong>: Brightfield images</p> <p><strong>Imaging</strong>: 20x 0.45 NA brightfield, 6.5µm*6.5µm sCMOS</p> <p><strong>Cell type</strong>: Budding yeast wild type cell (BY4742)</p> <p><strong>File format</strong>: .tif (16-bit RGB, 1 color per z-stack) + .mat</p> <p><strong>Image size</strong>: Brightfield: 60x60x1 (Pixel size: x,y: 325 nm) // Mask: 60x60x1 (Pixel size: x,y: 325 nm), 3 pixel values (one per class).</p> <p><strong>Author(s)</strong>: Théo, ASPERT</p> <p><strong>Contact email</strong>: theo.aspert@gmail.com</p> <p><strong>Affiliation</strong>: IGBMC, Université de Strasbourg</p> <p><strong>Funding bodies</strong>: This work was supported by the Agence Nationale pour la Recherche, the grant ANR-10-LABX-0030-INRT, a French State fund managed by the Agence Nationale de la Recherche under the frame program Investissements d'Avenir ANR-10-IDEX-0002-02.</p>
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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.