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644 results for “data visualization”
Data Visualization and Gendered Questions in Radiation Protection
<p>Recognition that age and biological sex are key factors in outcome of radiation exposure is reflected in the Discussion Paper on The Future of Radiological Protection. Use of a hypothetical "fixed" or universal exposure level in visualization of exposure outcomes in a large population such as the A bomb survivors, and application of a lifecycle model as compared to the population model are explored. The author is an evolutionary biologist with decades of national and global policy engagement, and she examines the efficacy of the idea of multiple standards from the perspective of the need for reparation.</p>
Data from: Effects of arousal and movement on secondary somatosensory and visual thalamus
<p>Neocortical sensory areas have associated primary and secondary thalamic nuclei. While primary nuclei transmit sensory information to cortex, secondary nuclei remain poorly understood. We recorded juxtasomally from secondary somatosensory (POm) and visual (LP) nuclei of awake mice while tracking whisking and pupil size. POm activity correlated with whisking, but not precise whisker kinematics. This coarse movement modulation persisted after facial paralysis and thus was not due to sensory reafference. This phenomenon also continued during optogenetic silencing of somatosensory and motor cortex and after lesion of superior colliculus, ruling out a motor efference copy mechanism. Whisking and pupil dilation were strongly correlated, possibly reflecting arousal. Indeed LP, which is not part of the whisker system, tracked whisking equally well, further indicating that POm activity does not encode whisker movement <em>per se.</em> The semblance of movement-related activity is likely instead a global effect of arousal on both nuclei. We conclude that secondary thalamus monitors behavioral state, rather than movement, and may exist to alter cortical activity accordingly.</p>
Data from: Research and exploratory analysis driven - time-data visualization (read-tv) software
<strong><em>read-tv</em></strong> <p>The main paper is about, <em>read-tv</em>, open-source software for longitudinal data visualization. We uploaded sample use case surgical flow disruption data to highlight <em>read-tv</em>'s capabilities. We scrubbed the data of protected health information, and uploaded it as a single CSV file. A description of the original data is described below.</p> Data source <p>Surgical workflow disruptions, defined as "<i>deviations from the natural progression of an operation thereby potentially compromising the efficiency or safety of care", </i>provide a window on the systems of work through which it is possible to analyze <u>mismatches between the work demands and the ability of the people to deliver the work</u>. They have been shown to be sensitive to different intraoperative technologies, surgical errors, surgical experience, room layout, checklist implementation and the effectiveness of the supporting team. The significance of flow disruptions lies in their ability to provide a hitherto unavailable perspective on the quality and efficiency of the system. This allows for a systematic, quantitative and replicable assessment of risks in surgical systems, evaluation of interventions to address them, and assessment of the role that technology plays in exacerbation or mitigation.</p> <p>In 2014, Drs Catchpole and Anger were awarded NIBIB R03 EB017447 to investigate flow disruptions in Robotic Surgery which has resulted in the detailed, multi-level analysis of over 4,000 flow disruptions. Direct observation of 89 RAS (robitic assisted surgery) cases, found a mean of 9.62 flow disruptions per hour, which varies across different surgical phases, predominantly caused by coordination, communication, equipment, and training problems.</p>
Visual stimuli elicit feedforward and feedback waves in mouse cortex (data and code)
<p>See the readme file for details of the information contained therein.</p> <p>There are also separate readme files for publicly available github repositories from Lyle Muller and the circular statistics toolbox (both for matlab). </p> <p>This dataset includes both the raw data and the analysis code used to process them in Aggarwal et al, Nature Communications, 2022. </p>
Data from: Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs
<p>Data from: Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs</p>
Data associated with the paper "Exploiting Color space geometry for visual stimulus design across animals"
<p>These are the pickled data files (pickled using pandas.DataFrame objects in Python) associated with the supplementary figures S4 and S7. </p> <p>* amp_1155: Data for S4B</p> <p>* amp_1156: Data for S4A</p> <p>* amp_518: Data for S7C-D</p> <p>* amp_529: Data for S7E-F</p>
Data for: The visual ecology of selective predation: Are unhealthy hosts less stealthy hosts?
<p>Predators can strongly influence disease transmission and evolution, particularly when they prey selectively on infected hosts. Although selective predation has been observed in numerous systems, why predators select infected prey remains poorly understood. Here, we use a mathematical model of predator vision to test a longstanding hypothesis about the mechanistic basis of selective predation in a <em>Daphnia</em>-microparasite system, which serves as a model for the ecology and evolution of infectious diseases. Bluegill sunfish feed selectively on <em>Daphnia</em> infected by a variety of parasites, particularly in water uncolored by dissolved organic carbon. The leading hypothesis for selective predation in this system is that infection-induced changes in the transparency of <em>Daphnia</em> render them more visible to bluegill. Rigorously evaluating this hypothesis requires that we quantify the effect of infection on the visibility of prey from the predator's perspective, rather than our own. Using a model of the bluegill visual system, we show that three common parasites, <em>Metschnikowia bicuspidata</em>, <em>Pasteuria ramosa</em> and <em>Spirobacillus cienkowskii</em>, decrease the transparency of <em>Daphnia</em>, rendering infected <em>Daphnia</em> darker against a background of downwelling light. As a result of this increased brightness contrast, bluegill can see infected <em>Daphnia</em> at greater distances than uninfected <em>Daphnia</em> - between 19-33% further, depending on the parasite. <em>Pasteuria</em> and <em>Spirobacillus</em> also increase the chromatic contrast of <em>Daphnia</em>. These findings lend support to the hypothesis that selective predation by fish on infected <em>Daphnia</em> could result from the effects of infection on <em>Daphnia</em>'s visibility. However, contrary to expectations, the visibility of <em>Daphnia</em> was not strongly impacted by water color in our model. Our work demonstrates that models of animal visual systems can be useful in understanding ecological interactions that impact disease transmission.</p>
Training and test data, plus saved models for the paper "Top-down effects in an early visual cortex inspired hierarchical Variational Autoencoder" submitted to the SVRHM 2022 Workshop @ NeurIPS
<p>Each .pkl file contains a training or test dataset in the form of a Python dictionary (generated with Python 3.8.5) with the following fields:</p><ul><li>'train_images': 640,000 float32 images used for model training. 20px images contain 400 pixel intensities, 40px images contain 1600 pixel intensities each.</li><li>'train_labels': float32 labels for each image in 'train_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li><li>'test_images': 64,000 float32 images used for model testing. 20px images contain 400 pixel intensities, 40px images contain 1600 pixel intensities each.</li><li>'test_labels': float32 labels for each image in 'test_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li></ul><p>Each .zip file contains a saved model. Details on these are coming soon.</p><p>For more details, see the paper "Top-down effects in an early visual cortex inspired hierarchical Variational Autoencoder" published at the SVRHM 2022 Workshop @ NeurIPS (<a href="https://openreview.net/forum?id=8dfboOQfYt3">link</a>).</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 03
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One infected ciliated cell is visible in the center of the recorded area. Virus particles are visible within membrane-bound compartments of the cytoplasm. Spike visibility is poor and some virus particles appear compressed.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 04
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (negative control). The recorded area shows the profiles of four keratinocytes which are surrounded by heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus partricles are not visible.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 01
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). Two, more or less, intact ciliated cells are visible and surrounded by other cells or cellular debris. The ciliated cell in the upper right corner is infected with SARS-CoV-2. Virus particles are visible within membrane-bound compartments of the cytoplasm. Several double-membrane vesicles, which are typical compartments of the coronavirus replication machinery, are also detectable.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 02
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One ciliated cell is visible and surrounded by cellular debris. The ciliated cell is infected with SARS-CoV-2. Few virus particles are visible within membrane-bound compartments of the cytoplasm. Numerous virus particles are located at the cell surface intermingled between the cilia. The virus particles of this cell appear deformed and deviate from the oval/circular profile which is usually present.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
The visualization of the collected data corresponding to the following paper: "The development of a Self-Rated ICF-based questionnaire (HEAR-COMMAND Tool) to evaluate Hearing, Communication, and Conversation disability: multinational experts' and patients' perspectives"
<p>These two PDF files include the data collected for a study conducted by Afghah et.al, 2022. They include the responses of the participant in this study to a newly developed self-rated ICF-based questionnaire. One file includes the responses to 30 demographic questions and the other one 88 ICF-based questions. The presented data were collected in Germany, the USA, and Egypt as well as overall data.</p> <p>The design of the questionnaire is described here:<br> Afghah, T., Alfakir, R., Meis, M., van Leeuwen, L. M., Kramer, S. E., Hammady, M., Youssif, M., & Wagener, K. C. (2021). The development of a Self-Rated ICF-based questionnaire (HEAR-COMMAND Tool) to evaluate hearing, communication, and conversation disability: multinational experts' and patients' perspectives. Zenodo. https://doi.org/10.5281/zenodo.5534360.</p> <p>This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project ID: 352015383 – SFB 1330, C4.</p>
Data from "Asymmetric visual capture of virtual sound sources in the distance dimension"
<p>This repository will contain raw and processed data used and described in:</p> <p><strong>Zahorik P (2022) Asymmetric visual capture of virtual sound sources in the distance dimension. Front. Neurosci. 16:958577. doi: 10.3389/fnins.2022.958577</strong></p>
Data for: Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes
<p>Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (<em>lws</em>) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. <em>Lws</em> is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no <em>lws</em> expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased <em>lws</em> expression) only emerged in association with algivory but never with zooplanktivory. Higher <em>lws</em> expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 07
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises three stitched image montages recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (control). Ciliated cells and extracellular material, such as vesicles and needle-like crystals, are visible, but no coronavirus particles.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 06
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises three stitched image montages recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (control). Ciliated cells and extracellular material, such as vesicles and needle-like crystals, are visible, but no coronavirus particles.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Pergola: boosting visualization and analysis of longitudinal data by unlocking genomic analysis tools - C. elegans unc-16 and N2 motion behavior dataset
<p>Dataset contains <em>Caenorhabditis</em> <em>elegans </em>motor behaviors originally used in this publication <a href="https://www.nature.com/articles/nmeth.2560">10.1038/nmeth.2560</a> and downloaded from the available <a href="http://wormbehavior.mrc-lmb.cam.ac.uk/">DB</a> which points to Zenodo. The dataset consists in two worm strains, 20 individuals from a mutant unc-16 strain with reduced mobility and 40 individuals from a control N2 strain. The behavioral measures derived from each individual worm trajectory were available in a HDF5-formatted file (Hierarchical Data Format Version 5) that has been included in this dataset.</p> <p>The data set consist in:</p> <p>- a "mappings" folder containing all the mappings used by the pergola in the pipeline to convert data.</p> <p>- a "N2" folder containing the 40 HDF5 files with the measures derived from the N2 worms.</p> <p>- a "N2" folder containing the 20 HDF5 files with the measures derived from the unc-16 worms.</p>
Data for "Impact of early visual experience on later usage of color cues"
<div> <div>This repository contains the code and data underlying the paper "Impact of early visual experience on later usage of color cues" (Vogelsang et al., Science, 2024).</div> </div>
Climate Hazards Data Integration and Visualization for the Climate Adaptations Solutions Accelerator through School-Community Hubs
<p><strong>Community engagement in planning is essential for effective and just climate adaptation. However, historically underserved communities are often difficult to reach through traditional means of soliciting public input. The Climate Adaptation Solutions Accelerator (CASA) through School-Community Hubs project identifies public schools as promising sites for building both community engagement and community capacity for climate adaptation. To serve in this role, schools need information about the intersecting threats climate change poses to the communities they serve. The Climate Hazard Dashboard for California Schools is a platform that maps the current and future risks associated with five climate hazards, including wildfire, extreme heat days, wildfire extreme precipitation, flooding, and sea level rise, for the nearly 10,000 public schools serving Kindergarten through Grade 12 students in California. Each hazard is mapped and visualized at the school level, providing an accessible way for administrators, teachers, students, and neighborhoods to explore data reflecting the climate hazards they face, at a scale relevant to their communities. The dashboard also provides an aggregate summary hazard metric. </strong></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.