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9,882 results for “Scale”
Spectral induced polarization of calcite precipitation: 2D experimental pore scale observation
<p>This data will be available after publication.</p>
Supplementary datasets for: Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution
<p>Microalgae are integral primary producers for global ecosystems whose genomes can be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This genome collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Marine species contained significantly more viral families in their genomes (<span>p-value = 8 x 10(-4))</span>. Viral sequences were identified from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and others integrated into algal genomes. Algal, viral-origin sequences were found to be expressed and to code for a wide variety of functions. Our results clarify the poorly characterized occurrences of viral elements in algal genomes and define a unified adaptive strategy for algal halotolerance.</p>
Raw data accompanying: Ground reaction forces in monitor lizards (Varanidae) and the scaling of locomotion in sprawling tetrapods
<p>Geometric scaling predicts a major challenge for legged, terrestrial locomotion.<b> </b>Locomotor support requirements scale identically with body mass (α M<sup>1</sup>), while force generation capacity should scale α M<sup>2/3</sup> as it depends on muscle cross-sectional area. Mammals compensate with more upright limb postures at larger sizes, but it remains unknown how sprawling tetrapods deal with this challenge. Varanid lizards are an ideal group to address this question because they cover an enormous body size range while maintaining a similar bent-limb posture and body proportions. This study reports the scaling of ground reaction forces and duty factor for varanid lizards ranging from 7 g 37 kg. Impulses (force x time) scaled roughly as predicted by the inverted pendulum model (α M<sup>0.99-1.34</sup>) while peak forces (α M<sup>0.73-1.00</sup>) scaled higher than expected. Duty factor scaled α M<sup>0.04 </sup>and was higher for the hindlimb than the forelimb. The proportion of vertical impulse to total impulse increased with body size, and impulses decreased while peak forces increased with speed. These results provide valuable data into how locomotor forces vary with body size and suggest how other, extinct, sprawling tetrapods may have dealt with the biomechanical challenges associated with generating sufficient locomotor forces at larger body sizes.</p>
Data from: Thalamus and focal to bilateral seizures: a multi-scale cognitive imaging study
<p><span><span><span><span><span><span><span><span><span><span><span><b><i>Objective</i></b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>To investigate the functional correlates of recurrent secondarily generalized seizures in temporal lobe epilepsy (TLE), using task-based fMRI as a framework to test for epilepsy-specific network rearrangements. As the thalamus modulates propagation of temporal-lobe onset seizures and promotes cortical synchronization during cognition, we hypothesized that occurrence of secondarily generalized, i.e. focal to bilateral tonic-clonic seizures (FBTCS), would relate to thalamic dysfunction, altered connectivity and whole-brain network centrality.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b><i>Methods</i></b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>FBTCS occur in a third of patients with TLE and are a major determinant of disease severity. In this cross-sectional study, we analyzed 113 patients with drug-resistant TLE (55 left/58 right), who performed a verbal fluency fMRI task that elicited robust thalamic activation. Thirty-three patients (29%) had experienced at least one FBTCS in the year preceding the investigation. We compared patients with TLE-FBTCS to those without FBTCS via a multi-scale approach, entailing analysis of SPM12-derived measures of activation, task-modulated thalamic functional connectivity (psychophysiological interaction), and graph-theoretical metrics of centrality. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b><i>Results</i></b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Individuals with TLE-FBTCS had less task-related activation of bilateral thalamus, with left-sided emphasis, and left hippocampus than those without FBTCS. In TLE-FBTCS, we also found greater task-related thalamotemporal and thalamo-motor connectivity, and higher thalamic degree and betweenness centrality. Receiver operating characteristic curves, based on a combined thalamic functional marker, accurately discriminated individuals with and without FBTCS.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b><i>Conclusions</i></b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>In TLE-FBTCS, impaired task-related thalamic recruitment coexists with enhanced thalamotemporal connectivity and whole-brain thalamic network embedding. Altered thalamic functional profiles are proposed as imaging biomarkers of active secondary generalization.</span></span></span></span></span></span></span></span></span></span></span></p>
Changes to anthropogenic pressures on reach-scale rivers in South and Southeast Asia from 1990 to 2014
<p>The data documented the spatiotemporal anthropogenic pressures on reach-scale rivers across South and Southeast Asia from 1990-2014. The data used to produce the results reported in the manuscript "Changes to anthropogenic pressures on reach-scale rivers in South and Southeast Asia from 1990 to 2014".</p> <p>The attributes of the data are explained as follows:</p> <p>(1) "lengthkm": the length (km) of the river reach.</p> <p>(2) "order": stream order of the river reach, from Lin et al. (2019).</p> <p>(3) "nnCCI92": the anthropogenic pressures induced by irrigation in 1992.</p> <p>(4) "nnCCI00": the anthropogenic pressures induced by irrigation in 2000.</p> <p>(5) "nnCCI14": the anthropogenic pressures induced by irrigation in 2014.</p> <p>(6) "nnGHSL90": the anthropogenic pressures induced by human usage in 1990.</p> <p>(7) "nnGHSL00": the anthropogenic pressures induced by human usage in 2000.</p> <p>(8) "nnGHSL14": the anthropogenic pressures induced by human usage in 2014.</p> <p>(9) "sum90": the total anthropogenic pressures on river reaches in 1990.</p> <p>(10) "sum00": the total anthropogenic pressures on river reaches in 2000.</p> <p>(11) "sum14": the total anthropogenic pressures on river reaches in 2014.</p> <p>(12) "mean9014": the average anthropogenic pressures on river reaches from 1990-2014.</p> <p>(13)"domin14": dominant pressure indicator impacting river reaches in 2014. "1" for healthy rivers, "2" for "both human usage and irrigation", "3" for "irrigation", "4" for "human usage".</p> <p><strong>Version 2 updates the anthropogenic pressures on rivers considering the proportion of irrigation taken from groundwater.</strong></p>
A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak
<p>Yak is an important livestock for the people who lived in harsh and oxygen-deprived Qinghai-Tibetan Plateau and Hindu-Kush Himalayan Mountains. Although there is a yak genome be sequenced in 2012, the assembly is quite fragmented due to the limitation of Illumina sequencing technology. An accurate and complete reference genome is critical for studying genetic variation of a specie. Long-read sequences are more complete than short-read ones, and they have been successfully used for high-quality genome assembly in several species. Here, we present a high-quality assembly of the yak genome (PB_v1.0) at chromosome scale, which was constructed using long-read sequencing technology assisted by chromatin interaction technology. Compared to the previous yak genome assembly (BosGru_v2.0), the PB_v1.0 assembly has substantially improved chromosome sequence continuity, minimized repetitive structure ambiguity, and achieved gene model completeness. To intensively characterize genetic variation of yak, we generated de novo genome assemblies based on Illumina short reads of seven recognized domestic yak breeds from Tibet and Sichuan as well as one wild yak from Hoh Xil. By comparing these eight assemblies to the PB_v1.0 genome, we obtained a comprehensive map of yak genetic diversity at whole genome level and identified a few protein-coding genes that were absent from the PB_v1.0 assembly. Although wild yak suffered bottleneck effect, the genetic diversity of wild yak is still higher than that of domestic yak. By whole genome alignment, we identified breed-specific sequences and genes, this will help the breeds identification of yak.</p>
Setpoints obtained for generator G in large-scale study
<p>The attached JSON files contain the setpoints obtained for the generator G in the large-scale study.</p> <ul> <li>results_enwl_exp_1.json: results with the exponents set to 1.0</li> <li> results_enwl_exp_3.json: results with the exponents set to 3.0</li> </ul> <p>Each json file is a tree, where the first two levels indicate the network and feeder from the ENWL dataset. Per (network, feeder) dictionary, the following data is available</p> <ul> <li><strong>pg_swl</strong>: per-phase active power set-point obtained with the SWL formulation, in kW</li> <li><strong>qg_swl</strong>: per-phase reactive power set-point obtained with the SWL formulation, in kvar</li> <li><strong>pg_su</strong>: per-phase active power set-point obtained with the SU formulation, in kW</li> <li><strong>qg_su</strong>: per-phase reactive power set-point obtained with the SU formulation, in kvar</li> <li><strong>gen_bus</strong>: bus to which the generator is connected</li> </ul>
Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>
The dataset of figures for "The GPU version of LICOM3 under HIP framework and its large-scale application"
<p>A high-resolution (1/20°) global ocean general circulation model with Graphics processing units (GPUs) code implementations is developed based on the LASG/IAP Climate system Ocean Model version 3 (LICOM3) under Heterogeneous-compute Interface for Portability (HIP) framework. The dynamic core and physics package of LICOM3 are both ported to the GPU, and 3-dimensional parallelization is applied. The HIP version of the LICOM3 (LICOM3-HIP) is 42 times faster than what the same number of CPU cores dose, when 384 AMD GPUs and CPU cores are used. The LICOM3-HIP has excellent scalability; it can still obtain speedup of more than four on 9216 GPUs comparing to 384 GPUs. In this phase, we successfully performed a test of 1/20° LICOM3-HIP using 6550 nodes and 26200 GPUs, and at the grand scale, the model’s time to solution can still obtain an increasing, about 2.72 simulated years per day (SYPD). The high performance was due to putting almost all of computation processes inside GPUs, and thus greatly reduces the time cost of data transfer between CPUs and GPUs. At the same time, a 14-year spin-up integration following the phase 2 of Ocean Model Intercomparison Project (OMIP-2) protocol of surface forcing has been conducted, and the preliminary results have been evaluated. We found that the model results have little differences from the CPU version. Further comparison with observations and lower-resolution LICOM3 results suggests that the 1/20° LICOM3-HIP can not only reproduce the observations, but also produce much smaller scale activities, such as submesoscale eddies and frontal scales structures.</p>
Data from: Large-scale meta-analysis on rheumatoid arthritis across East Asian and European populations
<p><span><span><span><b>Objective:</b> Nearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly polygenic genetic architecture of RA. Here, we performed the largest-ever trans-ancestral meta-analysis with the aim to identify new RA loci and to better understand RA biology underlying genetic associations.</span></span></span></p> <p><span><span><span><b>Methods:</b> Genome-wide RA association summary statistics in three large case-control collections consisting of 311,292 individuals of Korean, Japanese, and European populations were used in an inverse-variance-weighted fixed-effects meta-analysis. Several computational analyses using public omics resources were conducted to prioritize causal variants and genes, RA variant-implicating features (tissues, pathways, and transcription factors), and potentially repurposable drugs for RA treatment. </span></span></span></p> <p><span><span><span><b>Results:</b> We identified 11 new RA susceptibility loci that explained 6.9% and 1.8% of the SNP-based heritability in East Asians and Europeans, respectively, and confirmed 71 known non-HLA susceptibility loci, identifying 90 independent association signals. The RA variants were preferentially located in binding sites of various transcription factors and in cell type-specific transcription-activation histone marks that simultaneously highlighted the importance of CD4<sup>+</sup> T-cell activation and the potential role of non-immune organs in RA pathogenesis. A total of 615 plausible effector genes, based on gene-based associations, expression-associated variants, and chromatin interaction, included targets of drugs approved for RA treatments and potentially repurposable drugs approved for other indications.</span></span></span></p> <p><span><span><span><b>Conclusion:</b> Our findings provide useful insights regarding RA genetic etiology and variant-driven RA pathogenesis.</span></span></span></p>
Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales
<p>Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β-diversity) along ecological gradients. Here, we characterize soil microbial β-diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β-diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β-diversities with respect to plant β-diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β-diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β-diversities were mostly related to plant β-diversity, while bacterial β-diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β-diversities with plant β-diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β-diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early-evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.</p>
Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples
<p>Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (<i>Rhincodon typus</i>) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant non-target species mackerel tuna<i> </i>(<i>Euthynnus affinis</i>), showing a clear relation between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from <i>E</i>. <i>affinis</i>. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and non-target sequences as well as presence of non-target species at the sampling site, is crucial to consider. Environmental DNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.</p>
Dataset for "Study on Reference Frames and Geographic Scale"
<p>The analysis code was written in RStudio.</p> <p>The user data folder contains six .csv flies:</p> <ul> <li>Separate_pointing_errors.csv: participants' performance in the onsite pointing task</li> <li>Pre-Questionnaire.csv: participants' responses to the pre-questionnaire</li> <li>Post_Questionnaire.csv: participants' responses to the post-questionnaire</li> <li>Reference_frame_preference.csv: categorizing participants based on their reference frame proclivities</li> <li>LookingDirection_seperate.csv: participants' looking directions during maze learning</li> <li>Separate_time_data.csv: participants' time spent at each location in the virtual maze</li> </ul> <p> </p>
easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data
<p>With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we present easyMF, a user-friendly web platform that aims to facilitate biological discovery from large-scale transcriptome data through matrix factorization (MF). The easyMF platform enables users with little bioinformatics experience to streamline transcriptome analysis from raw reads to gene expression and to decompose expression matrix from thousands of genes to a handful of metagenes. easyMF also offers a series of functional modules for metagene-based exploratory analysis with an emphasis on functional gene discovery. As a modular, containerized and open-source platform, easyMF can be customized to satisfy users’ specific demands and deployed as a web server for broad applications. easyMF is freely available at https://github.com/cma2015/easyMF. We demonstrated the application of easyMF with four case studies using 940 RNA sequencing datasets from maize (<em>Zea mays </em>L<em>.</em>).</p>
Link-operator parameterized boolean models from scale-free topologies
<p>See analysis on this dataset here: <a href="https://druglogics.github.io/brf-bias/random-scale-free-networks-analysis.html">https://druglogics.github.io/brf-bias/random-scale-free-networks-analysis.html</a></p>
Data for "Potential of mid-tropospheric water vapor isotopes to improve large-scale circulation and weather predictability"
<p>This contains simulation results of "Potential of mid-tropospheric water vapor isotopes to improve large-scale circulation and weather predictability".</p>
Estimating individual level plant traits at scale: input data
<p>This dataset includes the input data to ensure replicability of the results. This dataset include the (1) reflectance for individual tree crowns, extracted from field and algorithmically delineated crowns in 2 NEON sites (OSBS and TALL); (2) the associated measures of tree traits (N%, C%, P%, LMA). The folder should be decompressed inside of the root directory of the project in https://github.com/MarconiS/Estimating-individual-level-plant-traits-at-scale/ for correctly replicate the analysis.</p>
Large scale virtual screening for finding inhibitor against the main protease from herbal medicine for SARS-Cov2 therapy
<p>The pandemic COVID-19 caused by SARS-CoV-2 has raised global health concerns. However, there is still no targeted medicine available for treatment of this disease. It is reported that 3CLpro plays an important role for the life cycle of virus and this protein has also been proved as an effective drug target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Medicinal plantsare important resource for drug discovery. Therefore, we executed large scale virtual screening on the herbal medicine library and hoped to find a potential drug againstthe main protease. As a result, we obtained three available compounds derived from Chinese herbal medicines through the docking and binding free energy calculation.Then 100 ns molecular dynamic (MD) were employed to uncover the potential mechanisms which is helpful for further drug optimization.</p>
Developing hierarchical density-structured models to study the national-scale dynamics of an arable weed
<p class="BodyText1">Population dynamics can be highly variable in the face of environmental heterogeneity, and understanding this variation is central in the study of ecology. Robust management decisions require that we understand how populations respond to management at a range of scales, and under a broad suite of conditions. Population models are potentially valuable tools in addressing this challenge. However, without adequate data, models can fail to produce useful results. Populations of arable weeds are particularly problematic in this respect, as they are widespread and their dynamics are extremely variable. Owing to the inherent cost of collecting data, most studies of weed population dynamics are derived from localized experiments under a small range of environmental conditions, limiting the extent to which variance in population dynamics can be measured. Density-structured models provide a route to rapid, large-scale analysis of population dynamics, and can expand the scale of ecological models that are directly tied to data. Here we extend previous density-structured models to include environmental heterogeneity, variation in management, and to account for inter-population variation. We develop, parameterize and test hierarchical density-structured models for a common agricultural weed, black-grass (<i>Alopecurus myosuroides</i>). We model the dynamics of this species in response to crop management, using survey data gathered over 4 years from 364 fields across a network of 45 UK farms. We show that hierarchical density-structured models provide a substantial improvement over their non-hierarchical counterparts. Using these models, we demonstrate that several alternative crop-rotations are effective in reducing weed densities. Rotations with high wheat prevalence exhibit the most severe infestations, and diverse rotations generally have lower weed densities. However, a key outcome is that in many cases the effect of crop rotation is small compared to the high variability arising from spatio-temporal heterogeneity. This result highlights the need to monitor and model population dynamics across large spatial and temporal scales in order to account for variation in the drivers of plant dynamics. Our framework for data collection and modelling provides a means to achieve this.</p>
Large-scale patterns of green turtle trophic ecology in the eastern Pacific Ocean
<p><span><span><span><span><span><span><span><span><span><span><span>Trophic position and niche width are fundamental components of a species' ecology, reflecting resource use, and influencing key demographic parameters such as somatic growth, maturation, and survival. The present data file contains results of stable isotope analysis (stable-carbon, δ<sup>13</sup>C; stable-nitrogen, δ<sup>15</sup>N values) that was conducted on bulk skin tissue of 718 green sea turtles (<i>Chelonia mydas</i>) distributed among 16 foraging areas in the eastern Pacific from the US to Chile, a range spanning ~10,000 km. These study sites </span></span></span></span></span></span></span></span></span></span></span>were distributed across a latitudinal range from 33.736 °N to 23.098°S in the Eastern Pacific (Site Code): Long Beach, USA (LB); San Diego Bay, USA (SDB); north Gulf of Ulloa, Mexico (NGU); Magdalena Bay, Mexico (BMA); Los Angeles Bay, Mexico (BLA); Infiernillo Channel, Mexico (CIN); Navachiste Bay, Mexico (NAV); Dulce Gulf, Costa Rica (DUL); Cocos Island, Costa Rica (COC); Gorgona Island, Colombia (GOR); Punta Espinosa, Galapagos Islands, Ecuador (IGP); Bahia Elizabeth, Galapagos Islands, Ecuador (IGE); Caleta Derek, Galapagos Islands, Ecuador (IGD); oceanic waters, Peru (PPE); Pisco Paracas Bay, Peru (PAR); and Mejillones Bay, Chile (MEJ). <span><span><span><span><span><span><span><span><span><span><span>Substantial variability in bulk tissue δ<sup>13</sup>C and δ<sup>15</sup>N values was found within and among sites. These data were also used to calculate the isotope niche space (used as a proxy for ecological niche space) using the Bayesian ellipse approach, and we found that isotope niche space varied among sites, likely influenced by the diversity of prey types and relative input of terrestrial- vs. marine-derived nutrients. In addition to providing additional spatial resolution for δ<sup>13</sup>C and δ<sup>15</sup>N isoscapes in the eastern Pacific, especially in coastal habitats, this study and resultant dataset further establish stable isotope analysis as an effective tool to study the trophic ecology of sea turtles across a variety of food webs and habitats. </span></span></span></span></span></span></span></span></span></span></span></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.