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990 results for “quantification”
Data from: Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab
<p>HER2/ERBB2 evaluation is necessary for treatment decision-making in breast cancer (BC), however current methods have limitations and considerable variability exists. DNA copy number (CN) evaluation by droplet digital PCR (ddPCR) has complementary advantages for HER2/ERBB2 diagnostics. In this study, we developed a single-reaction multiplex ddPCR assay for determination of ERBB2 CN in reference to two control regions, CEP17 and a copy-number-stable region of chr. 2p13.1, validated CN estimations to clinical in situ hybridization (ISH) HER2 status, and investigated the association of ERBB2 CN with clinical outcomes. 909 primary BC tissues were evaluated and the area under the curve for concordance to HER2 status was 0.93 and 0.96 for ERBB2 CN using either CEP17 or 2p13.1 as reference, respectively. The accuracy of ddPCR ERBB2 CN was 93.7% and 94.1% in the training and validation groups, respectively. Positive and negative predictive value for the classic HER2 amplification and non-amplification groups was 97.2% and 94.8%, respectively. An identified biological "ultrahigh" ERBB2 ddPCR CN group had significantly worse survival within patients treated with adjuvant trastuzumab for both recurrence-free survival (hazard ratio, HR: 3.3; 95% CI 1.1–9.6; <em>p</em> = 0.031, multivariable Cox regression) and overall survival (HR: 3.6; 95% CI 1.1–12.6; <em>p</em> = 0.041). For validation using RNA-seq data as a surrogate, in a population-based SCAN-B cohort (NCT02306096) of 682 consecutive patients receiving adjuvant trastuzumab, the ultrahigh-ERBB2 mRNA group had significantly worse survival. Multiplex ddPCR is useful for ERBB2 CN estimation and ultrahigh ERBB2 may be a predictive factor for decreased long-term survival after trastuzumab treatment.</p>
Raw data and MTEX script for the article : "Quantification of grain boundary mobilities in natural olivine by annealing experiments and full-field modelling"
<p>This dataset contains the EBSD (.ctf) files of the different sample areas analyzed in the article : "Quantification of grain boundary mobilities in natural olivine by annealing experiments and full-field modelling" by J. Furstoss, S. Demouchy, A. Tommasi, E. Gardès, F. Barou and N. Marino, which is expected to be published in Tectonophysics. This repository also contains the Analyze.m MTEX script which has been used for the post-processing of the EBSD files. This script has to be run in matlab and outputs different figures and .csv files containing the raw data used in the article. For any questions please contact jfurstoss@orange.fr </p>
Exploring the impact of varied background on quantification of soil carbon content using microwave and millimeter wave signal reflectance
<p>The quantification of soil carbon content is paramount to the advancement of soil carbon management practices, serving as the bedrock for the development and implementation of various carbon-negative and carbon-neutral technologies. These technologies are crucial in the battle against climate change and in enhancing soil health to boost agricultural productivity. Therefore, we employ an innovative sensor technology comprised of a compact array, including 18 pairs of radar transmitters (TX) and receivers (RX) within a microwave radar array sensor, alongside a configuration of 20 TX and 20 RX pairs in a millimeter wave radar array sensor. For this kind of setup to work, the sensors need to be carefully tested to make sure they can capture changes in the soil's carbon content over time and space.</p> <p>This dataset presents an exhaustive series of raw data aimed at evaluating the efficacy of these two sensor technologies in detecting soil carbon content. A distinctive aspect of this study is the examination of sensor performance across four divergent backgrounds—glass, metal, sponge, and wood surfaces—to ascertain the influence of background material on radar wave reflectance and, consequently, measurement accuracy. Furthermore, the investigation extends to the analysis of sensing distance as a critical parameter for classification accuracy, with the microwave radar array sensor tested across distances ranging from 1 inch to 4 inches and the millimeter wave radar sensor evaluated at intervals of 2.5 inches, 5 inches, 7.5 inches, and 10 inches. By providing a comprehensive dataset on the performance evaluation of cutting-edge sensor technologies, this study aims to facilitate further advancements in the field of soil carbon management, ultimately supporting the global effort to combat climate change through innovative and sustainable agricultural practices.</p>
Datasets for airborne in-situ quantification of methane emissions from oil and gas production in Romania
<p>This dataset includes airborne in-situ measurements taken around target clusters and regions of oil and gas production sites in Romania, as well as two models outputs interpolated to the flight tracks during the ROMEO (ROmanian Methane Emissions from Oil and gas) campaign that took place in Romania in 2019. The dataset is used for the evaluation presented in the manuscript titled: "Airborne in-situ quantification of methane emissions from oil and gas production in Romania."</p>
Karim et al; Fig-S7A-IF Raw Image for quantification-Gal3
Open the record for dataset details and reuse information.
Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity – Peptide Quantifications
<p>Cognitive decline during aging represents a major societal burden, causing both personal and economic hardship in an increasingly aging population. There are a few well-known proteins that can misfold and aggregate in an age-dependent manner, such as amyloid β and α-synuclein. However, many studies have found that the proteostasis network, which functions to keep proteins properly folded, is impaired with age, suggesting that there may be many more proteins that incur structural alterations with age. Here, we used limited-proteolysis mass spectrometry (LiP-MS), a structural proteomic method, to globally interrogate protein conformational changes in a rat model of cognitive aging. Specifically, we compared soluble hippocampal proteins from aged rats with preserved cognition to those from aged rats with impaired cognition. We identified several hundred proteins as having undergone cognition-associated structural changes (CASCs). We report that CASC proteins are substantially more likely to be nonrefoldable than non-CASC proteins, meaning they typically cannot spontaneously refold to their native conformations after being chemically denatured. The potentially cofounding variable of post-translational modifications is systematically addressed, and we find that oxidation and phosphorylation cannot significantly explain the limited proteolysis signal. These findings suggest that noncovalent, conformational alterations may be general features in cognitive decline, and more broadly, that proteins need not form amyloids for their misfolded states to be relevant to age-related deterioration in cognitive abilities.</p> <p>This deposition provides processed peptide quantifications for all LC-MS/MS proteomics experiments conducted for this study.</p>
Data Set "Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification"
<p>Data set accompanying the publication "Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification"</p> <p>This dataset contains:</p> <p>- PDB files of the reactant and product starting structure</p> <p>- modified AMBER95 force field file</p> <p>- AMS fragment files for the ligands and ions</p> <p>- AMS input files for all geometry optimizations and single point calculations</p>
Quantification of Electric Fields in Fast Breakdown during Lightning Initiation from VHF-UHF Power Spectra
<p>The data support the manuscript entitled “Quantification of Electric Fields in Fast Breakdown during Lightning Initiation from VHF-UHF Power Spectra” that is submitted to GRL. These files can be opened by MATLAB. The data can be used freely for scientific purposes with appropriate citation.</p>
Precise quantification of behavioral individuality from 80 million decisions across 183,000 flies
<p>Data set associated with a study into distributions of individual behavioral measures. </p> <p> </p> <p>Manuscript abstract:<br> <br> Individual animals behave differently from each other. This variability is a component of personality and arises even when genetics and environment are held constant. Discovering the biological mechanisms underlying behavioral variability depends on efficiently measuring individual behavioral bias, a requirement that is facilitated by automated, high-throughput experiments. We compiled a large data set of individual locomotor behavior measures, acquired from over 183,000 fruit flies walking in Y-shaped mazes. With this data set we first conducted a “computational ethology natural history” study to quantify the distribution of individual behavioral biases with unprecedented precision and examine correlations between behavioral measures with high power. We discovered a slight, but highly significant, left-bias in spontaneous locomotor decision-making. We then used the data to evaluate standing hypotheses about biological mechanisms affecting behavioral variability, specifically: the neuromodulator serotonin and its precursor transporter, heterogametic sex, and temperature. We found a variety of significant effects associated with each of these mechanisms that were behavior-dependent. This indicates that the relationship between biological mechanisms and behavioral variability may be highly context dependent. Going forward, automation of behavioral experiments will likely be essential in teasing out the complex causality of individuality. </p>
Additional data for manuscript "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data"
<p>Additional data for manuscript "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data".</p> <p>Additional mitochondrial gene sequences for Danio rerio, Homo sapiens, and Mus musculus.</p>
Data package for Pozzolanic activity quantification of hollow glass microspheres
<p>Raw data of calengorimetry, TGA, UCS and XRD tests developed as part of the research published in Cement and Concrete Composites. The dataset is deposited in a .zip file in .txt or .xls(.xlsx) file format.</p> <p>Linked publication:</p> <p>C.M. Martín, N.B. Scarponi, Y.A. Villagrán, D.G. Manzanal, T.M. Piqué,<br> Pozzolanic activity quantification of hollow glass microspheres,<br> Cement and Concrete Composites,<br> Volume 118,<br> 2021,<br> 103981,<br> ISSN 0958-9465,<br> https://doi.org/10.1016/j.cemconcomp.2021.103981.<br> (https://www.sciencedirect.com/science/article/pii/S0958946521000500)</p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 35 Binding Site Data
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 35 binding sites.</p>
Quantification of the effects of chimerism: datasets
<p>To aid in exploring the effects of chimerism on read mapping, differential expression analysis and <em>de novo</em>assembly, a base set of 26,680 transcripts containing all sequences ranging in length of between 300 and 5000 nt present within the fruit fly cDNA library was created from Ensembl release-100 (https://www.ensembl.org/info/data/ftp/index.html) [1]. These transcripts along with the complete cDNA library from which they were compiled are located within the <strong><em>BaseSetTranscripts</em>.zip</strong> file.</p> <p>This base set of transcripts was used as a reference for simulating reads as required within subsequent sections of our paper (titled: <em>Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly.</em>). Such simulations often involved hundreds of replicate iterations due to the nature of the study, as well as for the associated creation of modified base sets containing varying portions of chimerism. Parameter values used for read simulations and modified reference sets used within iterations are described in detail within the paper (F1000 <em>paper link to be provided when available.).</em></p> <p>To explore the effects of chimerism on the detection of differentially expressed transcripts ten read datasets, each consisting of five million read-pairs, were simulated using CSReadGen [2] from the base set as described section 2.2 of the manuscript. These are located within the <strong><em>DEReads.zip</em></strong> file. Using these reads differential expression analysis was repeated iteratively, where during each iteration ChimSim [3] was used to create a modified base set to be used as a reference. Within each modified base set created a portion of the transcripts present were made chimeric. The portions of chimerism introduced ranged from 5% to 95% chimeric in steps of five. These modified base sets are located within the d <em><strong>DEChimSimRefs.zip</strong> </em>file. In each case a titles file has also been provided that indicates which transcripts within the base set were made chimeric (if any, e.g. at 0% chimerism this file is empty) and the manner in which chimeras was introduced in accordance to the three types discussed in the paper. For example in the file titled chimeric_refs_0.1_SEQS.fasta 10% of the sequences are chimeric and the file titled chimeric_refs_0.1_TITLES.txt indicates which these are and the type of chimerism introduced.</p> <p>The base set was then used to simulate ten data sets consisting of ten million read-pairs that were each assembled using CStone [4], Trinity [5] and rnaSPAdes [6]. Parameters for read simulations are once again described in detail within our paper (Section 2.3). The assemblies produced by each assembler are contained within the <strong><em>DeNovoAssemblies_SimulatedData.zip</em></strong> file. The two whole body read datasets from Pang et al. [7], following filtering by Trimmomatic [8] as described in our paper, are within the files <em><strong>Reads_RealData_WholeBody_1.zip</strong></em> and <em><strong>Reads_RealData_WholeBody_2.zip</strong></em>, as are the assemblies produced by each of the three assemblers when using these reads as input (<em><strong>DeNovoAssemblies_RealData.zip</strong></em>).</p> <p>Related software to this project are:<br> 1. <a href="http://sourceforge.net/projects/cstone/">CStone</a> <br> 2. <a href="http://sourceforge.net/projects/csreadgen/">CSReadGen</a><br> 3. <a href="https://sourceforge.net/projects/cview/">CView</a><br> 4. <a href="https://sourceforge.net/projects/chimsim/">ChimSim</a> <<br> 5. <a href="https://sourceforge.net/projects/tvscript/">TVScript</a></p> <p>A related poster discussing the the identification of chimerism during assembly is available <a href="https://zenodo.org/record/6022494#.YgY-ji2cbGI">here</a> (DOI: <a href="https://doi.org/10.5281/zenodo.6022493">10.5281/zenodo.6022493</a>) and one discussing the effects of chimerism is available <a href="https://zenodo.org/record/6023171#.YgZmCC2cZQL">here</a> (DOI: <a href="https://doi.org/10.5281/zenodo.6023170">10.5281/zenodo.6023170</a>).</p> <p>General details of the project are available <a href="https://cibio.up.pt/en/projects/de-novo-based-sequence-assembly-of-next-generation-sequence-data-without-chimeras-improved-annotation-gene-expression-profiles-and-haplotype-br-reconstruction/">here</a>.</p> <p> </p> <p><strong>References</strong></p> <p>1. Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2020;48: D682–D688. doi:10.1093/NAR/GKZ966</p> <p>2. Archer J. CSReadGen website. 2020. Available: https://sourceforge.net/projects/csreadgen/</p> <p>3. Linheiro, Raquel; Archer J. ChimSim website. 2021. Available: https://sourceforge.net/projects/chimsim/</p> <p>4. Linheiro R, Archer J. CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. Pertea M, editor. PLOS Comput Biol. 2021;17: e1009631. doi:10.1371/JOURNAL.PCBI.1009631</p> <p>5. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011 297. 2011;29: 644–652. doi:10.1038/nbt.1883</p> <p>6. Bushmanova E, Antipov D, Lapidus A, Prjibelski AD. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. Gigascience. 2019;8: 1–13. doi:10.1093/GIGASCIENCE/GIZ100</p> <p>7. Pang TL, Ding Z, Liang SB, Li L, Zhang B, Zhang Y, et al. Comprehensive Identification and Alternative Splicing of Microexons in Drosophila. Front Genet. 2021;12. doi:10.3389/fgene.2021.642602</p> <p>8. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114–2120. doi:10.1093/BIOINFORMATICS/BTU170</p>
Data and Source codes for: Real-time Radial Tagging for Quantification of Left Ventricular Torsion
<p> </p> <p>Magnetic Resonance Imaging measurement raw data, simulation, and reconstruction codes used in our paper about ‘Real-time Radial Tagging for Quantification of Left Ventricular Torsion' (DOI:10.1002/mrm.29169).</p> <p> </p> <p> </p> <p> </p>
Data for Quantification and classification of grainflow morphology on natural dunes
<p><strong>Overview:</strong></p> <p>The attached file, “GrainflowMorphologyCharacteristics.xlsx”, includes the grainflow morphometric attributes used in the article “Quantification and classification of grainflow morphology on natural dunes” by Zhang, Pei; Sherman, Douglas J.; Pelletier, Jon D.; Ellis, Jean T.; Farrell, Eugene J.; Li, Bailiang, published in <em>Earth Surface Processes and Landforms</em>.</p> <p><strong>Key to variables (unit):</strong></p> <p>Date: date of data collection at Jericoacoara, Brazil.</p> <p>Dunes: “S” indicates samples from the smaller dune (21.3 m high), and “L” indicates samples from the larger dune (54.5 m high). Details of the metrics may be found in the associated publication (https://doi.org/10.1002/esp.5348).</p> <p><span class="math-tex">\(\bar{l_{g}}\)</span> (m): average length</p> <p><span class="math-tex">\(\bar{w_{g}}\)</span> (m): average width</p> <p><span class="math-tex">\(r_{t}\)</span> : rectangularity</p> <p><span class="math-tex">\(TRI\)</span>: triangularity</p> <p><span class="math-tex">\(e_{g}\)</span>: elongation</p> <p>Type: classified types</p>
Datasets and scripts from: Sensory-based quantification of male colour patterns in Trinidadian guppies reveals no support for parallel phenotypic evolution in multivariate trait space
<p>Parallel evolution, in which independent populations evolve along similar phenotypic trajectories, offers insights into the repeatability of adaptive evolution. Here, we revisit a classic example of parallelism, that of repeated evolution of brighter males in the Trinidadian guppy (<em>Poecilia reticulata</em>). In guppies, colonisation of low predation habitats is associated with emergence of 'more colourful' phenotypes since predator-induced viability selection for crypsis weakens while sexual selection by female preference for conspicuousness remains strong. Our study differs from previous investigations in three respects. First, we adopt a multivariate phenotyping approach to characterise parallelism in multi-trait space. Second, we use ecologically-relevant colour traits defined by the visual systems of the two selective agents (i.e. guppy, predatory cichlid). Third, we estimate population genetic structure to test for adaptive (parallel) evolution against a model of neutral phenotypic divergence. We find strong phenotypic differentiation that is inconsistent with a neutral model but very limited support for the predicted pattern of greater conspicuousness at low predation. Effects of predation regime on each trait were in the expected direction, but weak, largely non-significant, and explained little among-population variation. In multi-trait space, phenotypic trajectories of lineages colonising low from high predation regimes were not parallel. Our results are consistent with reduced predation risk facilitating adaptive differentiation, potentially by female choice, but suggest that this proceeds in independent directions of multi-trait space across lineages. Pool-sequencing data also revealed SNPs showing greater differentiation than expected under neutrality, among which some are found in genes contributing to colour pattern variation, presenting opportunities for future genetic study.</p>
Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids
<p>Water temperature is the major controlling factor that shapes the physiology, behavior, and ultimately, survival of aquatic ectotherms. Here we examine temperature effects on the survival of Chinook salmon (<em>Oncorhynchus tshawytscha</em>), a species of high economic and conservation importance. We implement a framework to assess how incremental changes in temperature impact survival across populations that is based on thermal performance models for three freshwater life stages of Chinook salmon. These temperature-dependent models were combined with local spatial distribution and phenology data to translate spatial-temporal stream temperature data into maps of life stage-specific physiological performance in space and time. Specifically, we converted temperature-dependent performance (i.e., energy used by pre-spawned adults, mortality of incubating embryos, and juvenile growth rate) into a common currency that measures survival in order to compare thermal effects across life stages. Based on temperature data from two abnormally warm and dry years for three managed rivers in the Central Valley, California, temperature-dependent mortality during pre-spawning holding was higher than embryonic mortality or juvenile mortality prior to smolting. However, we found that local phenology and spatial distribution helped to mitigate negative thermal impacts. In a theoretical application, we showed that high temperatures may inhibit successful reintroduction of threatened Central Valley spring-run Chinook salmon to two rivers where they have been extirpated. To increase Chinook salmon population sizes, especially for the threatened and declining spring-run, our results indicate that adults may need more cold-water holding habitat than currently available in order to reduce pre-spawning mortality stemming from high temperatures. To conclude, our framework is an effective way to calculate thermal impacts on multiple salmonid populations and life stages within a river over time, providing local managers the information to minimize negative thermal impacts on salmonid populations, particularly important during years when cold-water resources are scarce.</p>
Supplementary data and information for 'Electron-Beam-Induced Carbon Contamination in STEM-in-SEM: Quantification and Mitigation'
<p>This repository contains supplementary data and information for the journal article "Electron-beam-induced carbon contamination in STEM-in-SEM: Quantification and mitigation" (https://doi.org/10.1093/micmic/ozac003).</p> <p>It provides comprehensive documentation of the thickness evaluation procedure based on STEM images. The thickness evaluation procedure is packed into a PYTHON library that can run using the provided exemplary images. It can also be adapted and applied to other images and individual settings, as described in the documentation file PythonTDL_Documentation.pdf. K. Adrion prepared the library based on the scripts written by her and M. Hugenschmidt, which were used for evaluating contamination thicknesses in the before-mentioned publication and on a conference poster: https://doi.org/10.5445/IR/1000135526.</p>
Raw data for 'Electron-Beam-Induced Carbon Contamination in STEM-in-SEM: Quantification and Mitigation'
<p>This repository contains the raw data of the figures in the journal article 'Electron-Beam-Induced Carbon Contamination in STEM-in-SEM: Quantification and Mitigation' (https://doi.org/10.1093/micmic/ozac003)</p>
eDNA quantification to evaluate bullfrog management
<p><span>Biological invasions contribute now more than ever to the global homogenization of fauna and flora. Large-scale monitoring programs are therefore needed to detect incipient invasions and to evaluate management interventions. As conventional monitoring methods are constrained by large costs, environmental DNA (eDNA)-based methods are increasingly recognized as valuable monitoring tools. However, accurately estimating species abundance from eDNA concentrations in natural systems remains challenging and consequently hinders their integration in management applications. Here, we used droplet digital PCR (ddPCR) in eDNA surveys to estimate the abundance of invasive American bullfrogs (<em>Lithobates catesbeianus</em>). We first introduced bullfrog tadpoles in natural ponds to assess the relationship between abundances and eDNA concentrations under field conditions. Next, we combined eDNA sampling with fyke netting in naturally colonized ponds to investigate whether bullfrog eDNA concentrations can estimate bullfrog capture success and conventional abundance measures obtained via depletion sampling. Finally, we evaluated eradication measures by comparing bullfrog eDNA concentrations before and after fyke netting. We found a strong linear relationship between the numbers of introduced tadpoles and eDNA concentrations (r<sup>2</sup> = 0.988). Bullfrog eDNA concentrations were not only linearly related to the catch-per-unit-effort (r<sup>2 </sup>= 0.739), but also to conventional abundance estimates (r<sup>2</sup> = 0.716), particularly when eDNA concentrations were standardized for pond area (r<sup>2</sup> = 0.834) and volume (r<sup>2 </sup>= 0.888). Bullfrog tadpoles were only captured when eDNA concentrations exceeded 1.5 copies µL<sup>-1</sup>, indicating that quantitative eDNA analyses enable the localization of breeding ponds. We found a significant reduction in eDNA concentrations after fyke netting proportional to the number of captured bullfrogs. These results demonstrate that eDNA quantification is a reliable tool that accurately estimates bullfrog abundance in natural lentic systems. We show that quantitative eDNA analyses can complement the toolbox of natural resource managers and facilitate the coordination of eradication campaigns targeting alien invasive species.</span></p>
ScienceDex guides
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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.