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4,694 results for “data analysis”
Data from: Functional diversity of phyllostomid bats in an urban-rural landscape: a scale-dependent analysis
<p>Urbanization is one of the most pervasive landscape transformational processes responsible for novel selection agents promoting functional community homogenization. Bats may persist in those human environments, but the mechanisms responsible for their adaptability and the spatial scales in which landscape imposes environmental filtering remain poorly studied in the Neotropics. We tested the hypothesis that landscape composition interacts with the spatial scale to affect the functional diversity of phyllostomids in an urban-rural gradient. Based on functional traits, we calculated indices of functional richness, divergence, evenness, community-weighted means of morphological traits, and classified species into functional groups. We evaluated the changes of those variables in response to forest, grassland, and urbanized areas at 0.5, 1.25 and, 2 km scales. The number of functional groups, functional richness, and functional evenness tended to be higher in areas far from cities and with higher forest cover, whereas functional divergence increased in more urbanized areas. Our results show that the mean value of wing loading in the assemblage was negatively associated to landscape transformation at several spatial scales. However, environmental filtering driven by grass cover was particularly robust at the 500 m scale, affecting big-sized species with long pointed wings. Retaining natural forest in cattle ranging systems at ~12 km<sup>2</sup> appears to favor bat abundance evenness among functional types in the urban-rural landscape. Recognizing the scale of the effect on phyllostomid functional responses appears to be a fundamental issue for elucidating the spatial extent to which phyllostomid conservation planning in urban-rural landscapes should be addressed.</p>
Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis
<p><span>Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes are subject to reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, empirical evidence shows contradictory effects of anthropogenic disturbances on the genetic diversity of terrestrial species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and preserved areas (317 paired comparisons) to investigate general responses to different disturbance type. We found significant negative effects of disturbance on genetic diversity (effect size: -0.45), in which the loss of structural connectivity was the most detrimental disturbance type. The choice of the genetic parameter has an influence on the detection of the effect (direction and magnitude), and consequently the studies using number of effective alleles did not detect genetic erosion, while all other indices, especially allelic richness, revealed negative responses to disturbances. Yet, only studies performed with transferred or both transferred and specific microsatellites showed negative responses to disturbances. The general effect was more detrimental in animal than plant populations. Only plant species with biotic pollination and seed dispersal mode, self-incompatible reproductive system, and shrubs showed negative responses to disturbances. Despite all heterogeneity among studies, we found an overall negative effect of disturbance on genetic diversity of terrestrial populations, which suggests that the remaining populations inhabiting anthropogenic landscapes have a reduced evolutionary potential being more prone to local extinction.</span></p>
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Data from: Global prevalence and burden of HIV-associated neurocognitive disorder: a meta-analysis
<p>Objectives: We aimed to characterise the prevalence and burden of HAND and assess associated factors in the global population with HIV.</p> <p>Methods: We searched PubMed and Embase for cross-sectional or cohort studies reporting the prevalence of HAND or its subtypes in HIV-infected adult populations from Jan 1, 1996, to May 15, 2020, without language restrictions. Two reviewers independently undertook the study selection, data extraction, and quality assessment. We estimated pooled prevalence of HAND by a random effects model and evaluated its overall burden worldwide.</p> <p>Results: Of 5588 records identified, we included 123 studies involving 35513 participants from 32 countries. The overall prevalence of HAND was 42·6% (95% CI: 39·7-45·5), and did not differ with respect to diagnostic criteria used. The prevalence of asymptomatic neurocognitive impairment (ANI), mild neurocognitive disorder (MND) and HIV-associated dementia (HAD) were 23·5% (20·3-26·8), 13·3% (10·6-16·3) and 5·0% (3·5-6·8) according to the Frascati criteria, respectively. The prevalence of HAND was significantly associated with the level of CD4 nadir, with a prevalence of HAND higher in low CD4 nadir groups (mean/median CD4 nadir <200: 45·2%, 40·5-49·9) versus high CD4 nadir group (mean/median CD4 nadir ≥200: 37·1%, 32·7-41·7). Worldwide, we estimated that there were roughly 16145400 (95% CI 15046300-17244500) cases of HAND in HIV-infected adults, with 72% in sub-Saharan Africa (11571200 cases, 95% CI 9600000-13568000).</p> <p>Conclusions: Our findings suggest that people living with HIV have a high burden of HAND in the ART era, especially in sub-Saharan Africa and Latin America. Earlier initiation of ART and sustained adherence to maintain a high level CD4 cell count and prevent severe immunosuppression is likely to reduce the prevalence and severity of HAND.</p>
Data accompanying the dissertation "Genre Analysis and Corpus Design: 19th Century Spanish American Novels (1830-1910)" (part of data-nh)
<p>This dataset includes research data that resulted from the analysis of the bibliography Bib-ACMé (see https://github.com/cligs/bibacme) and the corpus Conha19 (see https://github.com/cligs/conha19) as part of the work on the dissertation "Genre Analysis and Corpus Design: 19th Century Spanish American Novels (1830-1910)" by Ulrike Henny-Krahmer. Both the bibliography and the corpus include novels from Argentina, Cuba, and Mexico published between 1830 and 1910 which were analyzed by subgenre on the levels of metadata and text (see the dissertation for details).</p> <p>The dataset is part of "data-nh" (see https://github.com/cligs/data-nh), which is the whole collection of research data accompanying the above-mentioned dissertation.</p>
Data from: Association between metabolic syndrome components and the risk of developing nephrolithiasis: Bayesian meta-analysis and meta-regression with dose-response analysis
<p>Nephrolithiasis has shifted to be a systemic disease. As opposed to an isolated urinary metabolic problem, it became determined that nephrolithiasis turned into considerably related to link with systemic diseases such as hypertension, obesity, dyslipidemia, and insulin resistance. The interplay between these four factors defines MetS (metabolic syndrome). In this review we aim to clarify the associations of metabolic syndrome and its components to kidney stone incident. Online databases of EMBASE, MEDLINE, and Google Scholar were searched up to October 2020 to identify observational studies examining the association between metabolic syndrome components and kidney stone incident. Bayesian Random-Effects Meta-Analysis and Meta-Regression were performed to observe the association. Linear dose-response analyses were conducted to shape the direction of the association. Data analysis was performed using STATA, and R statistics. This dataset contains supplementary material and figures as additional analysis of the study.</p>
Comparative analysis of angiogenesis models: MATLAB data files
<p>This data set contains the MATLAB files that were used to generate figures located in the article "Comparative analysis of angiogenesis models" (J. Math. Biol, in press). The article's abstract may be found below. </p> <p>Although discrete approaches are increasingly employed to model biological phenomena, it remains unclear how complex, population-level behaviours in such frameworks arise from the rules used to represent interactions between individuals. Discrete-to-continuum approaches, which are used to derive systems of coarse-grained equations describing the mean-field dynamics of a microscopic model, can provide insight into such emergent behaviour. Coarse-grained models often contain nonlinear terms that depend on the microscopic rules of the discrete framework, however, and such nonlinearities can make a model difficult to mathematically analyse. By contrast, models developed using phenomenological approaches are typically easier to investigate but have a more obscure connection to the underlying microscopic system. To our knowledge, there has been little work done to compare solutions of phenomenological and coarse-grained models. Here we address this problem in the context of angiogenesis (the creation of new blood vessels from existing vasculature). We compare asymptotic solutions of a classical, phenomenological "snail-trail" model for angiogenesis to solutions of a nonlinear system of partial differential equations (PDEs) derived via a systematic coarse-graining procedure (Pillay, 2017). For distinguished parameter regimes corresponding to chemotaxis-dominated cell movement and low branching rates, both continuum models reduce at leading order to identical PDEs within the domain interior. Numerical and analytical results confirm that pointwise differences between solutions to the two continuum models are small if these conditions hold, and demonstrate how perturbation methods can be used to determine when a phenomenological model provides a good approximation to a more detailed coarse-grained system for the same biological process.</p>
Data and analysis
<p>Data and analysis scripts for the paper:</p> <p>Qubits made by advanced semiconductor manufacturing</p> <p>by A.M.J. Zwerver,<em> et al.</em></p>
Data for "Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox"
<p>Data for the SIAMCAT manuscript</p>
Data for taxonomic analysis
<p>The data included in this repository was used for the taxonomic analysis.</p> <p>(1) silva-138-99-nb-classifier.qza: The classifier was used for analysis in qiime 2 (2020.8 core distribution)</p> <p>(2) ref_prok_rep_genomes: Metagenome data for blast+ queries (updates, 2020-06-19; accessed on July 15, 2020).</p> <p>(3) NCBI_taxdump.zip: Taxa dump data for lineage extractions.</p>
Data from: Habitat restoration benefits wild bees: a meta-analysis
1.Pollinator conservation is of increasing interest in light of managed honeybee (Apis mellifera) declines, and declines in some species of wild bees. Much work has gone into understanding the effects of habitat enhancements in agricultural systems on wild bee abundance, richness, and pollination services. However, the effects of ecological restoration targeting "natural" ecological endpoints (e.g., restoring former agricultural fields to historic vegetation types or improving degraded natural lands) on wild bees have received relatively little attention, despite their potential importance for countering habitat loss. 2.We conducted a meta-analysis to evaluate the effects of ecological restoration on wild bee abundance and richness, focusing on unmanaged bee communities in lands restored and managed to increase habitat availability and quality. Specifically, we assessed bee abundance and/or richness across studies comparing restored vs. unrestored treatments and studies investigating effects of specific habitat restoration techniques, such as burning, grazing, invasive plant removal and seeding. 3.We analysed 28 studies that met our selection criteria: these represented 11 habitat types and 7 restoration techniques. Nearly all restorations associated with these studies were performed without explicit consideration of habitat needs for bees or other pollinators. The majority of restorations targeted plant community goals, which could potentially have ancillary benefits for bees. 4.Restoration had overall positive effects on wild bee abundance and richness across multiple habitat types. Specific restoration actions, tested independently, also tended to have positive effects on wild bee richness and abundance. 5.Synthesis and applications. We found strong evidence that ecological restoration advances wild bee conservation. This is important given that habitat loss is recognized as a leading factor in pollinator decline. Pollinator responses to land management are rarely evaluated in non-agricultural settings and so support for wild bees may be an underappreciated benefit of botanically focused management. Future restoration projects that explicitly consider the needs of wild bees could be more effective at providing nesting, foraging and other habitat resources. We encourage land managers to design and evaluate restoration projects with the habitat needs of wild bee species in mind.
Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
Data from: A method for analysis of phenotypic change for phenotypes described by high-dimensional data
The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects—data called 'high-dimensional data'—researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables potentially reduces effect sizes for comparative analyses, yet test statistics require more observations than variables. This problem is exacerbated with data that describe 'multidimensional' phenotypes, whereby a description of phenotype requires high-dimensional data. For example, landmark-based geometric morphometric data use the Cartesian coordinates of (potentially) many anatomical landmarks to describe organismal shape. Collectively such shape variables describe organism shape, although the analysis of each variable, independently, offers little benefit for addressing biological questions. Here we present a nonparametric method of evaluating effect size that is not constrained by the number of phenotypic variables, and motivate its use with example analyses of phenotypic change using geometric morphometric data. Our examples contrast different characterizations of body shape for a desert fish species, associated with measuring and comparing sexual dimorphism between two populations. We demonstrate that using more phenotypic variables can increase effect sizes, and allow for stronger inferences.
Data from: Multiple benefits drive helping behavior in a cooperatively breeding bird: an integrated analysis
Several hypotheses exist to explain the seemingly altruistic helping behavior of cooperative breeders, although the general utility of these hypotheses remains unclear. While the potential importance of inclusive fitness benefits (kin selection) is traditionally widely appreciated, it is increasingly recognized that direct benefits may be more important than assumed. We use an integrative two-step framework to assess support for current hypotheses in purple-crowned fairy-wrens, a species where subordinates vary in relatedness to breeders and helping increases productivity. After establishing that assumptions of pay-to-stay and social prestige hypotheses (predicting that helping functions as 'paying rent' to stay on the territory or as a signal of individual quality, respectively) were not met, and that parentage by subordinates is extremely rare, we tested whether subordinates adjusted nestling feeding rates following the predictions of the kin selection and group augmentation hypotheses. Benefits of kin selection result from investment in relatives, and group augmentation benefits accrue when subordinates invest more in their own future helpers, for example when they have a better chance of inheriting the breeding position. We found that subordinates fed siblings more than unrelated nestlings, indicating that kin selection could facilitate cooperation. Moreover, the effect of relatedness on feeding effort varied depending on the probability of inheriting a breeding position, suggesting that active group augmentation can explain investment by unrelated subordinates. This statistical interaction would have gone undetected had we not considered both factors simultaneously, illustrating that a focus on single hypotheses could lead to underestimation of their importance in explaining cooperative breeding.
Data from: Retrospective stable isotope analysis reveals ecosystem responses to river regulation over the last century
Disruption of natural flow regimes, nutrient pollution, and other consequences of human population growth and development have impacted most major rivers of the world. Alarming losses of aquatic biodiversity and biotic homogenization coincide with human-caused river alteration, but effects on aquatic ecosystem processes are not as well documented. This is because unaltered systems for comparison are scarce, and some ecosystem-wide effects may take decades to manifest. We evaluated aquatic ecosystem responses to extensive river-floodplain engineering and nutrient addition in the Rio Grande of southwestern North America as revealed by changes in trophic structure of, and resource availability to, the fish community. Stable Isotope Analysis (SIA) was conducted on museum-preserved fishes collected over a 70-year period of intensive river management and exponential human population growth. Trophic complexity and resource heterogeneity for fish consumers (measured as 'isotopic niche breadth') decreased following sediment deprivation and channelization, and these effects persist into the present. Increased nutrient inputs led to δ15N enrichment in the entire fish community at all affected sites, and a shift to autochthonous sources of carbon at the most proximal site downstream of wastewater release probably via 'bottom-up' transfer. Overall, retrospective SIA of apex consumers suggests radical change and functional impairment of a floodplain river ecosystem already marked by significant biodiversity loss.
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21 000 transcript contigs with significant expression in our samples, showing high homology to exonic sequences in avian draft genomes. From these, we identified >31 000 high-quality SNPs and > 2500 simple sequence repeats (SSRs). We also analysed expression patterns in our data to identify potential candidate genes related to differences in male and female behaviour, identifying over 200 nonoverlapping putative autosomal transcripts that show significant expression differences between males and females. Gene ontology analysis revealed that female-biased transcripts were significantly enriched for cerebral functions related to learning, cognition and memory, and male-biased transcripts were mostly enriched for terms related to neural function such as neuron projection and synapses. This data set provides one of the first de novo transcriptome assemblies from non-normalized short-read next-generation data and outlines an effective strategy for measuring sequence and expression variability simultaneously without the aid of a reference genome.
Data from: Genetic analysis of the peatmoss Sphagnum cribrosum (Sphagnaceae) indicates independent origins of an extreme infra-specific morphology shift
Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a unique morphological variant (the "waveform"), found at only two lakes in North Carolina, has a branching architecture that is extremely differentiated from anything otherwise known in Sphagnum, though the plants are microscopically indistinguishable from S. cribrosum. At one site where the two morphologies co-occur, sixty years of field observations demonstrate the persistence of each morphology, even where the two forms grow intermixed. We conducted a reciprocal transplant experiment in which waveform and normal plants maintained their divergent morphologies for eight months. We sampled populations throughout the range and conducted genetic and phylogenetic analyses with microsatellite markers and DNA sequences to investigate the genetic context of the waveform morphology within S. cribrosum. Haplotype networks from DNA sequences showed the two waveform populations are separated by 11 substitutions across three loci. Microsatellite analyses using non-parametric clustering and admixture models also indicated genetic dissimilarity between genotypes with waveform morphology at the two lakes. Both molecular datasets suggest that the waveform morphology had at least two independent origins despite proximity of the two lakes where it uniquely occurs. Given the clonal nature of the waveform, it is unlikely to form a cohesive evolutionary lineage deserving of taxonomic status. The analysis also revealed a genetically diverse population in Georgia as the potential source of variation found in all other populations of S. cribrosum.
Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers
Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for analyzing this dominant marker may not be entirely clear in the context of species delimitation. In this study, we use AFLPs and mtDNA to investigate cryptic speciation in the Trimeresurus macrops complex that belongs to a taxonomically difficult lineage of Asian pitvipers. We analyze AFLPs using population genetic, phylogenetic, multivariate statistical, and Bayes Factor Delimitation methods. A gene tree from three mtDNA markers provided additional evidence. Our results show that the inferences about species boundaries that can be derived from population genetic analysis of AFLPs have certain limitations. In contrast, four multivariate statistical analyses produced clear clusters that are consistent with each other, as well as with Bayes Factor Delimitation results, and with mtDNA and total evidence phylogenies. Furthermore, our results concur with allopatric distributions and patterns of variation in individual morphological characters previously identified in the three proposed species: T. macrops sensu stricto, T. cardamomensis, and T. rubeus. Our study provides evidence for reproductive isolation and genetic distinctiveness that define these taxa as full species. In addition, we re-emphasize the importance of examining congruence of results from multiple methods of AFLP analysis for inferring species diversity.
Data from: Multivariate ratio analysis reveals Trigonoderus pedicellaris Thomson (Hymenoptera, Chalcidoidea, Pteromalidae) as a valid species
We demonstrate by multivariate ratio analysis (MRA) the validity of two female colour morphs as separate species in what was previously regarded as a single species, Trigonoderus cyanescens (Förster, 1841) (Hymenoptera: Pteromalidae). As a result, T. pedicellaris Thomson, 1878 stat.r., is resurrected from synonymy under T. cyanescens and T. filatus binubilatus Erdős, 1960 syn.n. is synonymized with T. cyanescens. More than 20 characters were measured as part of two MRA dataset analyses. The first analysis excluded all measurements related to the gaster, whereas the second included gaster length, gaster breadth and seventh gaster tergite breadth. The first analysis revealed that the best separating morphometric ratios for the two species are head breadth:metatibia length and OOL:parastigma length, whereas the second analysis revealed OOL:gaster length as the second best separating ratio. The measurement error of all characters was below the admissible level of 30%. Gaster length proved to be a good character for separating the two groups, showed the lowest measurement error, and its percentage coefficient of variation was not greater than for other characters. This indicates that gaster length should not be discarded out-of-hand as a morphometric character in Pteromalidae. The variables that gave the best separating ratios included different body parts; therefore we suggest that the body of a specimen should be taken as a whole for use in MRA analyses, where each distance measurement can interact freely with any other. A key, figures and re-descriptions of T. cyanescens and T. pedicellaris are provided.
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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.