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Porewater nutrient concentrations in control and fertilized plots in a Spartina alterniflora-dominated salt marsh, North Inlet, Georgetown, SC : 1993-2025
Porewater nutrient concentrations were measured as a component of a long-term project seeking to understand how salt marsh primary production and sediment chemistry respond to anthropogenic (e.g. eutrophication) and natural (e.g. sea-level rise) environmental change. Feedbacks between plants, sediments, nutrients and flooding were investigated with particular attention to mechanisms that keep marshes in equilibrium with sea level. Other data collected as part of the project include aboveground macrophyte biomass, plant density, marsh surface elevation and annual above ground primary productivity. These data have been used to develop the Marsh Equilibrium Model, an important tool for coastal resource managers. Sampling occurred at Spartina alterniflora-dominated salt marsh sites in North Inlet, a relatively pristine estuary near Georgetown, SC on the SE coast of the United States. North Inlet is a tidally-dominated, bar-built estuary, with a semi-diurnal mixed tide and a tidal range of 1.4m. The 25-km2 estuary is comprised of about 20.5 km2 of intertidal salt marsh and mudflats, and 4.5 km2 of open water. Sampling began at two locations in December 1993, and at three additional locations in January 1994. Sampling occurred approximately monthly at these 5 locations through 2025. Sampling occurred at a sixth location from 2006 to 2010. The site was a dieback site that had recovered by 2010. At the other sites, the study is on-going. Porewater was collected at multiple depths from diffusion samplers and was analyzed for sulfide, salinity, ammonium, phosphate, and iron concentrations. There are five sampling locations at three sites. Two locations are in the low marsh; three locations are in the high marsh. One high marsh location had control sampling plots in addition to plots fertilized with nitrogen and phosphorus.
Time series of in situ Uv-Vis absorbance spectra and high-frequency predictions of total and soluble Fe and Mn concentrations measured at multiple depths in Falling Creek Reservoir (Vinton, VA, USA) in 2020 and 2021
High-frequency measurements of light absorbance were collected at multiple depths in Falling Creek Reservoir (FCR; Vinton, VA, USA) using a s::can Spectrolyser UV-Visible spectrophotometer coupled with a multiplexor pumping system. The system pumps water samples from individual depths into a flow-through cuvette where the UV-vis absorbance spectra of the sample are measured by the spectrophotometer. The system used in our study collected measurements of light absorbance every 2.5 nm wavelengths from 200 nm to 732.5 nm (optical path length of 10 mm) approximately at an hourly time step for seven monitoring depths in the reservoir. Data was collected during two periods; the first deployment (16 October to 9 November 2020) was to observe changes in Fe and Mn concentrations before, during, and after reservoir fall turnover and the second deployment (26 May to 21 June 2021) was to observe the effects of engineered hypolimnetic oxygenation on Fe and Mn concentrations. Partial least squares regression models were developed to generate predictions of total and soluble Fe and Mn concentrations based on the correlation between absorbance spectra and sampling data.
Concentration of nutrients in water samples collected from the Upper Clark Fork River (Montana, USA) during water year 2019 (1 Oct 2018 - 30 Sept 2019)
The umbrella LTREB monitoring project generating these data is conducted separately and complementarily to the $200 million-dollar (USD) superfund project for ecological restoration of the Upper Clark Fork River (UCFR), associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the Upper Clark Fork River includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river's floodplain closest to contaminant sources. The UCFR Long Term Research in Environmental Biology (LTREB) project includes bi-weekly water quality monitoring across a 200-km gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The UCFR LTREB monitoring project is conducted within the first 200 km of the Upper Clark Fork River and associated tributaries located in western Montana. The current monitoring program began in 2017 and will be completed in the year 2023, with likely funding extension to 2028. Surface water samples represented in this data product are collected from fourteen sites along the mainstem of the UCFR, and one site representing a major tributary to the UCFR. Water samples are collected at each monitoring site in triplicate and filtered with a 0.7-µm glass fiber filter. Nutrient samples are analyzed using a spectrophotometric flow injection analyzer (AP2) for nitrate (NO3-N), soluble reactive phosphorus (SRP, as representative of PO4-P), and ammonium (NH4-N) concentrations reported in mg/L. The analysis-ready data of this dataset therefore represent Quality Assurance and Quality Control (QAQC) processed NH4-N, SRP, and NO3-N concentrations from fourteen sites along the mainstem of the UCFR and one tributary, collected in water year 2019 (1 Oct 2018 - 30 Sept 2019).
Ecosystem metabolism and associated environmental data for a forested, meadow and reforested reach of White Clay Creek, Chester Co., Pennsylvania; 1971-1975 and 1997-2010
Ecosystem metabolism data for a 3rd-order Piedmont stream were collected during two periods: P1- April 1971 – Dec 1975, and P2- May 1997 – January 2010. Measures were made in a meadow and a forested reach during each period and in a reforested (formerly meadow) reach during the latter years of P2. During P1, measures were made by transferring streambed substrata to chambers in water jackets located on the streambank and measuring dissolved oxygen changes over diel periods. During P2, open system measures of dissolved O2 change were made for several days in warm and cold seasons, with reaeration determined from a propane injection experiment. Metabolism estimates were determined from diel curves of dissolved O2 change. Photosynthetically active radiation (PAR) and chlorophyll were measured concurrent with many measurements in P1 and all measures during P2, and temperature with all measures. Water chemistry parameters (NH4-N, NO3-N, PO4-P, SiO2, Cl, SO4, total alkalinity, pH) associated with each run are included in the data set, as are days since storm of various thresholds. Field procedures, analytical methods and data analyses are detailed in Bott, T.L. & J. D. Newbold, 2023. A multi-year analysis of factors affecting ecosystem metabolism in forested and meadow reaches of a Piedmont Stream. Hydrobiologia
Near-surface, soil, and air temperature data acquired across multiple locations on the San Joaquin Experimental Range, California, 2011-2017
These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies at the San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Temperature sensors were located at 23 sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. To characterize surface temperature variation within a site, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens. An additional 18 sensors were placed along three transects over the landscape running E-W. They were placed strategically to sample topographic inflection points (hill tops and valley bottoms) as well as north and south facing slopes. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor, using HOBO (Onset, www.onsetcomp.com) devices.
Weather station data acquired across multiple locations on the San Joaquin Experimental Range, California, 2011-2017
These weather station records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These weather station records are for studies at the San Joaquin Experimental Range (Lat 37.083, Long -119.716, elevation 210-520 m, www.fs.fed.us/psw/ef/san_joaquin/). Weather stations were located at six sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges, and valleys. Three full weather stations (north slope, south slope, and valley floor) monitored precipitation, wind, insolation, temperature, relative humidity, and soil moisture. Three micro stations (west slope, east slope, and ridge) measured soil moisture at -20 cm. Data was recorded on a 10-minute interval using HOBO (Onset, www.onsetcomp.com) devices.
Near-surface, soil, and air temperature data acquired across multiple locations in the Teakettle Experimental Forest, California, 2011-2017
These temperature records were collected as part of a larger study relating microclimates to tree seedling survival in southern California mountains. These temperature records are for studies at the Teakettle Experimental Forest (Lat 36.967, Long -119.017, elevation 2000-2800 m, www.fs.fed.us/psw/ef/teakettle/). Temperature sensors were located at 44 sites across the landscape. Sites were selected to sample topographic variation in surface and air temperatures within a narrow range of elevations on northeast to southwest-facing slopes, ridges and valleys. To characterize surface temperature variation within select sites, 21 sensors were arranged in an identical pattern around and in six, 5x5 m experimental gardens (see garden schematic for details). An additional 33 sites were located across the site by way of a stratified sampling scheme which targeted low, medium, and high elevation areas, low, medium, and high radiation areas, and cold air pooling areas. In June 2012, in order to concentrate sensors in a smaller study area (ease of access and to make this more similar to other sites, 22 sites were "retired," and 7 new sites were installed, for a total of 18 during the remainder of the study. Temperatures were recorded on a 10 or 20-minute interval, depending on the sensor. using HOBO (Onset, www.onsetcomp.com) devices.
California Department of Fish and Wildlife Adult Sturgeon Study, Sacramento-San Joaquin Watershed, 1954-2022
The Sacramento-San Joaquin Watershed, located in Central and Northern California, drains approximately 43,000 square miles and terminates at the Golden Gate Bridge. This watershed hosts numerous species of ecological, cultural, and recreational importance, including White (Acipenser transmontanus) and Green Sturgeon (Acipenser medirostris). Sturgeon were severely overfished in the late 1800s and early 1900s, prompting a closure of the recreational and commercial sturgeon fishery in 1917 by the California Department of Fish and Game (CDFG; Now California Department of Fish and Wildlife, CDFW). The fishery remained closed until 1954, when a recreational fishery was once again allowed by the CDFG. A single year of surveying was conducted by the CDFG in 1954 to monitor the new fishery and a semi-regular survey was established in 1967. Since then, CDFW has systematically surveyed subadult and adult White and Green Sturgeon as part of the Adult Sturgeon Study, with annual surveys conducted between 2005 and 2022. Capturing adult sturgeon using 3.7m deep drifted trammel nets in areas including Suisun Bay, Grizzly Bay, and San Pablo Bay, these efforts have been supplemented by angler-contributed data, collected through mail returns and river/bay creel surveys. Tagging practices involve individually coded ½” Petersen-disk tags, with reward values introduced in 1974 to encourage angler cooperation and enhance tag return rate accuracy. The adoption of PIT (Passive Integrated Transponder) tags began in 2007 and has been consistently employed since 2019. These data provide insights into tag return rates, recaptures, and mortalities, supporting the estimation of abundance and harvest rates. This comprehensive dataset enriches our understanding of sturgeon population dynamics and is crucial for monitoring California sturgeon.
Densities and cover data for intertidal organisms from an LTREB project in the Gulf of Maine, USA, from 1996 to 2023.
Experimental clearings in macroalgal (Ascophyllum nodosum) stands were made in 1996 to determine if mussel beds and macroalgal stands on protected intertidal shores in New England represent alternative community states. Uncleared control plots and four sizes of circular clearings (1m, 2m, 4m and 8m in diameter), which mimicked ice scour events, were established in A. nodosum stands at 12 sites on Swan’s Island, Maine, USA. The purpose of these datasets is to provide access to data on densities and percentage cover in the 60 experimental plots from 1996 to 2023. Earlier versions of the data prior to 2007 can be found in Ecological Archives ( E087-047 and E089-032). The current EDI version includes corrections of errors in the versions in Ecological Archives. Data include densities of mussels (Mytilus edulis), an herbivorous limpet (Testudinalia testudinalis), herbivorous snails (Littorina littorea, Littorina obtusata), a predatory snail (Nucella lapillus), a barnacle (Semibalanus balanoides), and fucoid algae (Ascophyllum nodosum and Fucus vesiculosus), and percentage cover by mussels, barnacles, fucoids and other sessile organisms. Research was funding by NSF's LTREB program.
Monitoring juvenile Chinook salmon outmigration using rotary screw traps on Deer and Mill creeks
The California Department of Fish and Wildlife (CDFW) conducts juvenile salmonid emigration monitoring on Mill and Deer Creek (Tehama County, CA) annually from October through June using rotary screw traps (RSTs). Data from this monitoring is used to estimate juvenile spring-run Chinook salmon (Oncorhynchus tshawytscha) (spring-run) abundance and passage, identify yearling outmigration timing and alert resource agencies of juvenile spring-run presence in the lower Sacramento-San Joaquin Delta. This data will be included in the development of a juvenile production estimate (JPE) for spring-run Chinook salmon in the Sacramento River as required by Condition of Approval 7.5.2 of Incidental Take Permit No. 2081-2019-006-00 (ITP) issued by CDFW to California Department of Water Resources (DWR) for the long-term operation of the State Water Project. Salmonid data collected from the Mill and Deer RSTs, among other datasets, is also used by the Salmon Monitoring Team (SaMT) to understand the movement of juvenile salmon in the Sacramento River Watershed to estimate the number of winter-run and spring-run Chinook salmon that have entered the Sacramento-San Joaquin Delta (Delta). SaMT is a real-time operations monitoring team required by Condition of Approval 8.1.2 of the ITP which meets weekly from October through June, to provide advice for real-time management of SWP operations to DWR, CDFW, and the Water Operation Management Team (WOMT) to minimize take of winter-run and spring-run Chinook salmon in the Delta.
Juvenile salmonid rotary screw trap data from Battle and Clear Creeks, Shasta and Tehama Counties, California.
Clear Creek The U.S. Fish and Wildlife Service continued its juvenile salmonid monitoring project in Clear Creek, Shasta County, California, that began in December 1998 using a rotary screw trap (RST) located at river mile (RM) 1.7. This monitoring project has three primary objectives: (1) calculate annual juvenile passage indices for Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout/steelhead O. mykiss (we use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories because of the difficulties in differentiating the anadromous and resident forms in the field) for inter-year comparisons and analyses of the effectiveness of stream restoration activities; (2) obtain juvenile salmonid life history information including size, timing, and potential factors limiting survival; and (3) collect biological samples from juvenile salmonids. Chinook Salmon run classifications show that all Chinook Salmon runs known to the Sacramento River were captured; however, due to overlapping spawning times of spring-run and fall-run Chinook Salmon it was problematic to index the juvenile passage using only the RST at RM 1.7. Since 2003 a separation weir has been used to isolate adult spring-run Chinook Salmon from adult fall-run Chinook Salmon; therefore, a second RST was added above the weir at RM 8.4. Battle Creek The U.S. Fish and Wildlife Service continued its juvenile salmonid monitoring project in Battle Creek, Shasta and Tehama Counties, California, that began in December 1998 using a RST located at river mile (RM) 6.2. The upper Battle Creek RST objectives are to (1) calculate annual juvenile passage indices for spring-run, late-fall run, and winter-run Chinook Salmon; Rainbow Trout/steelhead O. mykiss (we use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories because of the difficulties in differentiating the anadromous and resident forms in the field); (
Long-term (1935-2019) tree population data from remeasurements of a large network of permanent study plots in old-growth forest, Dukes Research Natural Area, Marquette Co., MI, USA
The Dukes Research Natural Area (Hiawatha National Forest, Marquette Co., MI) amounts to ca. 100 ha of minimally disturbed original forests, including a mix of mesic 'hemlock-northern hardwood' types and peaty wetlands dominated by several species of swamp conifers and black ash (Fraxinus nigra). The RNA hosts a regular grid of 250 0.2-acre (~0.08 ha) permanent monitoring (CFI) plots. This package includes tree censuses for subsets of CFI plots conducted in 1935, 1948, and 1974-1980, and repeated censuses with mapped stems from 1989 to 2019. This 84-year record constitutes one of the longest repeated-measurement, permanent-plot data-sets for old-growth temperate forest.
Discrete water temperature, flow, solar radiation, chlorophyll-a and inundation, Sacramento-San Joaquin Delta, CA, 1999-2019
The objective of our study is to better understand the factors affecting chlorophyll-a production within a floodplain and its transport downstream to determine how lateral connectivity influences longitudinal connectivity. The Yolo Bypass is an engineered floodplain of the Sacramento River that inundates during periods of high outflow via overtopping weirs. Water traveling through the Yolo Bypass flows parallel to the Sacramento River and re-connects to the mainstem at the southern extent of the floodplain. Several monitoring programs in the Sacramento San-Joaquin Delta and Yolo Bypass collect discrete and continuous water quality data, including chlorophyll measurements. For this study, we synthesized available flow, water temperature, chlorophyll and inundation data between March 1999 to December 2019 and modeled the effects of environmental variables and inundation on chlorophyll-a production in the floodplain, the mainstem, and downstream of the floodplain/mainstem.
Metabolism dataset: one year of high-frequency temperature, dissolved oxygen, wind, photosynthetically active radiation observations and low-frequency nutrient data for 58 lakes in the Global Lake Ecological Observatory Network
Understanding controls on primary productivity is essential for describing ecosystems and their responses to environmental change. Lake primary production is strongly controlled by inputs of nutrients and colored dissolved organic matter. While past studies have developed mathematical models of this nutrient-color paradigm, broad empirical tests of these models are scarce. We compiled data from 58 diverse and globally distributed and mostly temperate lakes to test such a model and improve understanding and prediction of the controls on lake primary production. These lakes varied widely in size (0.02-2300 km2), pelagic gross primary production (20-8000 mg C m-2 d-1), and other characteristics. The data package includes high-frequency dissolved oxygen, water temperature, wind speed, and solar radiation data as well as daily estimates of GPP and ER derived from those data. In addition, the data package includes median in-lake and stream concentrations of dissolved organic carbon and total phosphorus for a subset of 18 of those lakes.
USFWS Adult White Sturgeon Monitoring, San Joaquin River, 2012-2025
Overview The Central Valley Project Improvement Act (CVPIA) funds habitat improvement work and associated monitoring in the Central Valley of California to increase salmonid populations in furtherance of meeting CVPIA fish doubling goals. This data package contains three datasets for adult White Sturgeon (Acipenser transmontanus) monitoring in the San Joaquin River (SJR) conducted by the US Fish and Wildlife Service, Lodi Fish and Wildlife Office. The primary purpose for this sampling was to capture White Sturgeon and implant acoustic telemetry tags for a tracking project. Therefore, the data are useful for determining when and where White Sturgeon were captured, but they should not be used to determine actual distribution or abundance. SJR_Adult_WST_Set Data This dataset contains data from a sampling program using various methods to catch adult White Sturgeon in the San Joaquin River. Sets were made at targeted locations primarily from March-May in 2012-2024 (other dates were occasionally sampled). SJR_Adult_WST_Catch Data This dataset contains data for individual fish caught via gillnets, trammel nets, setlines, or angling in the San Joaquin River. Species and fork length were recorded for all fish. For White Sturgeon, girth, maturation, tag, and surgery information are provided. SJR_Fish_Taxonomy Data This dataset contains data for fish codes used in the Catch datafile. For each species that was captured, the Species codes are listed with the corresponding Interagency Ecological Program code, common name, taxonomy (Phylum, Class, Order, Family, Genus, and Species), and whether or not the species is native to the region.
Data Package for the 2022 Great Lakes Winter Grab
WARNINGS: 1. For Ice Thickness data, please use data in "WinterGrab_snow_ice_properties" file instead of data in Table 2 of the manuscript published in Limnology and Oceanography Letters! 2: In "WinterGrab_phytoplankton_abundance_McKay", EC1 has two sets of data records because it was sampled both on 2/28 and 3/10, both records are included in this data. --- The data package contains the results from a multi-institutional winter limnology sampling campaign on the Laurentian Great Lakes. Researchers from 19 institutions sampled 49 locations in all five of the Great Lakes over a period of 24 days in February-March 2022. This dataset contains information on diverse physical, chemical, and biological parameters. Great Lakes Winter Grab ArcGIS Storymap showing all locations of sampling sites and select photos: https://storymaps.arcgis.com/stories/8ff1c332dd944ba9a744dc0e0fc18906
Nitrogen fixation (acetylene reduction) and denitrification (acetylene block) data from streams across ecoclimatic domains in the United States, 2017-2019
We conducted a cross-ecoregion study to test the hypothesis that N-fixation and denitrification would co-occur in streams and rivers across a range of reactive N concentrations. Between 2017 and 2019, we sampled 30 streams in 13 ecoregions, using chambers to quantify N-fixation using acetylene reduction and denitrification using acetylene block. 25 of the study streams were part of the National Ecological Observatory Network or the StreamPULSE network, which provided data on water temperature, light, nutrients, discharge and metabolism. Although N-fixation and denitrification occur under contrasting environmental conditions, we found that they co-occurred in ca. 40% of stream ecosystems surveyed, and microbes capable of carrying out each process were found in all surveyed streams. This dataset includes the chamber data used to calculate nitrogen fixation and denitrification rates, stream substrate information used to scale rates from substrate to whole-reach scale, and a variety of reach-to-landscape scale covariates used to evaluate predictors of rates across the study streams.
Within-plant coexistence of viruses across nitrogen and phosphorus supply rates
Most species can be coinfected by multiple pathogens that may interact through shared resources (i.e., resource competition) or the host immune system (i.e., apparent competition). Community theory developed for free-living organisms suggests that coinfecting pathogens can persist if they satisfy the mutual invasion criterion of coexistence, establishing infections in hosts that are already infected. Furthermore, the likelihood of coexistence may depend on host nutrition which can affect shared resources and host immunity. Here we apply the novel approach of combining a dynamical model and experimental mutual invasibility trials to explore the effects of host nutrient supply on the coexistence of two viral plant pathogens. We focus on among-pathogen interactions mediated by shared resources. First, we used a model to generate hypotheses about how nitrogen (N) and phosphorus (P) supply rates affect the ability of two plant viruses to invade established infections of the other virus. Then, we experimentally manipulated the N and P supplied to oats (Avena sativa) in a growth chamber experiment and tested mutual invasion of two RNA viral pathogens, BYDV-PAV and CYDV-RPV. Nutrient supplies ranged from rates that barely kept hosts alive up to high, but sub-toxic, rates. Model simulations suggested that the viruses were more likely to invade established infections either when they could replicate at lower N and P concentrations or when plant N and P concentrations increased due to a combination of nutrient supply rates and resident virus nutrient use. In the experiment, each virus successfully invaded hosts infected by the other and had consistent growth rates across N and P supply rates. Our results suggest that BYDV-PAV and CYDV-RPV can coexist across a wide range environmental nutrient supply, which is consistent with the high levels of co-occurrence of these two viruses in field populations.
Stream Storm Sample Data from White Clay Creek (WCC) Watershed in 2021
These data were collected to explore Nitrogen update dynamics in the water column of small streams during storm events. Data was collected using a combination of passive sampling and grab sampling of suspended sediments from the stream channel. Analysis of samples include: dissolved and total chemistry, suspended sediment load, biological and microbiological characteristics, and Nitrogen uptake rates.
Ice timing (formation or ice-on and clearance or ice-off) for Yellowstone Lake, Wyoming, USA (1927-2022)
Lakes are sentinels of environmental change. In cold climates, lake ice phenology–the timing and duration of ice cover during winter–is a key control on ecosystem function. Ice phenology appears to be driven by a complex interplay between physical characteristics and climatic conditions. Under climate change, lakes are generally freezing later, melting out earlier, and experiencing a shorter duration of ice cover; however, few long-term records exist for large, high-elevation lakes which may be particularly vulnerable to climate impacts. Here, we provide an ice phenology data over the last century (1927-2022) for North America’s largest high-elevation lake—Yellowstone Lake.
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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.