Structure measurements of individual woody and non-woody plants, mapped positions of qualifying woody and non-woody plants, and metadata required to draw inference from individual measurements at the plot scale.

NEON operates 81 field sites strategically located across 20 eco-climatic domains across the United States, including 47 terrestrial field sites and 34 freshwater aquatic field sites. When logistically possible, aquatic and terrestrial sites are colocated (i.e. in close proximity) to support understanding of linkages across terrestrial and aquatic ecosystems and their interactions with the atmosphere. Core sites The spatial design of the NEON program includes one core terrestrial and one core aquatic site in each of the 20 ecoclimate Domains (with the exception of D20, in Hawaii, which only has a core terrestrial site). These core sites were selected to represent wildlands or more pristine ecosystems with relatively limited human influence within each Domain. As such, many of these sites are in conservation areas or national parks. Gradient sites The gradient sites were selected to provide contrasts with the core sites and enable exploration of scientific questions of cause and effect specific to each Domain. A "gradient," in this case, is a range in a driving variable of ecological change that can be measured across a Domain, such as a gradient of nitrogen and dust deposition, permafrost, invasive species, precipitation, or land use. The gradient sites allow us to evaluate how these differences impact ecosystems within a Domain by comparison with the core wildland site.Aquatic instrument and observation systems are virtually identical between core sites and gradient sites. There are some differences in terrestrial instrumentation between sites (e.g., primary precipitation using a Double Fence Intercomparison Reference (DFIR), shortwave radiation, water vapor isotopes, and sun photometers), which are documented in each of the Data Product Page Descriptions on the NEON Data Portal. More site-specific details are included in the Sensor Position files associated with the data download expanded package. Some terrestrial observational sampling designs (e.g., mammal and mosquito sampling) differ between the core and gradient sites, which are documented within the associated data products' Science Designs and Protocols and Procedures, located on the data product landing pages of the NEON Data Portal.

Plant species cover-abundance and presence observed in multi-scale plots. Plant species and associated percent cover in 1m2 subplots and plant species presence in 10m2 and 100m2 subplots are reported from 400m2 plots. Archived plant vouchers and foliar tissue support the data and additional analyses.

NEON field and taxonomic and abundance data for the periphyton (DP1.20166.001), macroinvertebrate (DP1.20120.001), and zooplankton (DP1.20219.001) collection for all aqatic sites, as well as single aspirated air temperature for 15 sites, were downloaded from the NEON data portal. Provisional data, not included in the 2022 data release, are included in this upload. Data are from all 34 aquatic sites across the network. Data are from NEON sources only. NEON is sponsored by the National Science Foundation (NSF) and operated under a cooperative agreement by Battelle. This material is based in part upon work supported by NSF through the NEON Program. NEON (National Ecological Observatory Network). Periphyton, seston, and phytoplankton collection (DP1.20166.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). Macroinvertebrate collection (DP1.20120.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). Zooplankton collection (DP1.20219.001). https://data.neonscience.org (accessed March 12, 2022) NEON (National Ecological Observatory Network). (2022e). Single aspirated air temperature (DP1.00002.001). https://data.neonscience.org (accessed March 12, 2022) NEON field and taxonomic and abundance data for the periphyton (DP1.20166.001), macroinvertebrate (DP1.20120.001), and zooplankton (DP1.20219.001) collection were downloaded from the NEON data portal. Provisional data, not included in the 2021 data release, are included in this upload. Data are from all 34 aquatic sites across the network. Data are from NEON sources only. NEON is sponsored by the National Science Foundation (NSF) and operated under cooperative agreement by Battelle. This material is based in part upon work supported by NSF through the NEON Program.

 NEON (National Ecological Observatory Network). Periphyton, seston, and phytoplankton collection (DP1.20166.001). https://data.neonscience.org (accessed October 6, 2021)

 NEON (National Ecological Observatory Network). Macroinvertebrate collection (DP1.20120.001). https://data.neonscience.org (accessed October 6, 2021)

 NEON (National Ecological Observatory Network). Zooplankton collection (DP1.20219.001). https://data.neonscience.org (accessed October 6, 2021)

Teaching data set with elevation data from NEON project field sites in Domain 07. This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).

Soil physical and chemical properties from the top 30 cm of the profile from periodic soil core collections. Data are reported by horizon (mineral vs. organic). See initial characterization and megapit products for additional soil data.

This repository contains logged multisonde water quality data from National Ecological Observatory Network (NEON) lake sites. As of 1 May 2023 this data has not yet been ingested into NEON's data processing pipeline or published on the NEON data portal (data.neonscience.org). It is being provided to help fill these gaps until it can be ingested. This is raw, level 0 data which has not been QAQC'ed, and NEON makes no guarantees regarding its quality. Any questions regarding this data should be directed to the NEON staff listed in the Contacts.

Taxonomically identified mosquitoes and the plots and times from which they were collected

This shapefile displays the watershed boundaries for NEON's aquatic wadeable and non-wadeable stream and lake sites. The watershed boundary defines the perimeter of drainage areas formed by the terrain and other landscape characteristics. The pour point was selected nearest the downstream most sensor set, primarily NEON’s S2 sensor in wadeable streams, S1 or stream gauge in non-wadeable rivers, and the outlet sensor in lakes. For most of the sites NEON's 1 meter Elevation-LiDAR Digital Terrain Model (DTM) was used to derive the watersheds. In cases where NEON data did not provide complete watershed coverage, a 1/3 arc-second (10 meter) resolution Digital Elevation Model (DEM) raster, available from the U.S. Geological Survey (USGS) website, was utilized to provide full coverage of the watershed extent. A mosaic dataset was created to combine individual DTM or DEM tiles, and a local projection defined for the dataset. ArcGIS Pro software with the ArcHydro Tools [for] Pro were used to model and delineate the watershed. Attribute Table Information:DomainNum:NEON ecoclimatic domain number. DomainName: NEON ecoclimatic domain name.SiteName: NEON aquatic site name.SiteID: NEON four character site ID for the aquatic site.SiteType:Type of NEON site (e.g. core aquatic or relocatable aquatic).Science: Identifies the primary science theme as they relate to the NEON Grand Challenges (AD[01]) and if the aquatic site is a wadeable or non-wadeable stream, or lake.StateID: The 2 letter abbreviation for the state where the watershed is located.UTM_Zone: The local projected coordinate system for the aquatic site and model processing.WSAreaKm2: Watershed area in kilometers squared for watersheds derived from NEON’s 1 meter Elevation-LiDAR dataset.Source: States if the watershed was not derived from NEON data, these sites are supplemented with the 10 meter National Elevation Dataset.Area_NED: Watershed area in kilometers squared for sites where the watershed was derived from the 10 meter National Elevation Dataset.AOPLiDAR: Name of the Elevation-LiDAR DTM tile from the NEON data portal, includes site ID, year, and month the data was collected.AOP_Flight: Identifies the NEON AOP Flight Boundaries layer showing the extent and priority of airborne acquisition. AOPCoverag: Identifies percent coverage of the NEON AOP flight box over the aquatic watershed.TIS_Dist: Distance in kilometers from the aquatic site pour point to the corresponding terrestrial tower site.TIS_Bear: Bearing in degrees from the aquatic site pour point to the corresponding terrestrial tower site.TIS_WS: States if the corresponding terrestrial tower is within the aquatic watershed.HUC12Name: Name of the Hydrologic Unit Code with twelve digits based on the prominent water or physical feature(s) within the unit. Naming follows the conventions and rules outlined by the Geographic Names Information System (GNIS) order of priority and if the dominant feature is named in the HU10, the HU12 retains the twelve digit code as the name. HUC12: Hydrologic Unit Code with twelve digits based on the sixth-level (subwatershed) classification designated by the United States Geological Survey. NLCD_(number): Percentage of land cover classifications within the watershed from the National Land Cover Dataset (NLCD) (Table 2). NRCS_(Soil abbreviations): Percentage of soil classifications within the watershed from the Natural Resources Conservation Service (NRCS) (Table 3).

This collection contains air-dried soil samples collected during periodic soil sampling at NEON terrestrial sites (NEON sample class: sls_bgcSubsampling_in.bgcArchiveID). Soil biogeochemical samples are collected once every 5 years, with three unique sampling locations per plot and ten plots per site. Soil sampling is conducted to a maximum depth of 30 ± 1 cm where possible. When organic (O) and mineral (M) horizons are present within a single profile they are separated prior to analysis and archiving. However, other sub-horizons are not separated. Soil from the O horizon is homogenized and non-soil material is removed by hand (no sieving), whereas soil from the M horizon is homogenized and sieved to 2 mm. Prior to archiving, all soil samples are air-dried, then placed into glass jars and stored at room temperature. See links below for NEON data products that provide various physical, chemical, and biological measurements (pH, moisture, carbon and nitrogen content and stable isotopes, inorganic nitrogen pools and net transformation rates, microbial community composition and biomass) for these same soils. In addition, a more detailed characterization of the dominant soil types at each site, including taxonomy, texture, bulk density, and geochemical properties, occurred during the construction period of NEON through two projects. These data are available in NEON data products Soil physical and chemical properties, distributed initial characterization (DP1.10047.001) and Soil physical and chemical properties, Megapit (DP1.00096.001).

Bathymetry of lake bottoms and non-wadeable streams for detecting environmental change as well as for determining lake morphology, estimating primary productivity, habitat features, and water quality.

Abstract

The NeonTreeCrowns dataset is a set of individual level crown estimates for 100 million trees at 37 geographic sites across the United States surveyed by the National Ecological Observation Network’s Airborne Observation Platform. Each rectangular bounding box crown prediction includes height, crown area, and spatial location.

How can I see the data?

A web server to look through predictions is available through idtrees.org

Dataset Organization

The shapefiles.zip contains 11,000 shapefiles, each corresponding to a 1km^2 RGB tile from NEON (ID: DP3.30010.001). For example "2019_SOAP_4_302000_4100000_image.shp" are the predictions from "2019_SOAP_4_302000_4100000_image.tif" available from the NEON data portal: https://data.neonscience.org/data-products/explore?search=camera. NEON's file convention refers to the year of data collection (2019), the four letter site code (SOAP), the sampling event (4), and the utm coordinate of the top left corner (302000_4100000). For NEON site abbreviations and utm zones see https://www.neonscience.org/field-sites/field-sites-map.

The predictions are also available as a single csv for each file. All available tiles for that site and year are combined into one large site. These data are not projected, but contain the utm coordinates for each bounding box (left, bottom, right, top). For both file types the following fields are available:

Height: The crown height measured in meters. Crown height is defined as the 99th quartile of all canopy height pixels from a LiDAR height model (ID: DP3.30015.001)

Area: The crown area in m2 of the rectangular bounding box.

Label: All data in this release are "Tree".

Score: The confidence score from the DeepForest deep learning algorithm. The score ranges from 0 (low confidence) to 1 (high confidence)

How were predictions made?

The DeepForest algorithm is available as a python package: https://deepforest.readthedocs.io/. Predictions were overlaid on the LiDAR-derived canopy height model. Predictions with heights less than 3m were removed.

How were predictions validated?

Please see

Weinstein, B. G., Marconi, S., Bohlman, S. A., Zare, A., & White, E. P. (2020). Cross-site learning in deep learning RGB tree crown detection. Ecological Informatics, 56, 101061.

Weinstein, B., Marconi, S., Aubry-Kientz, M., Vincent, G., Senyondo, H., & White, E. (2020). DeepForest: A Python package for RGB deep learning tree crown delineation. bioRxiv.

Weinstein, Ben G., et al. "Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks." Remote Sensing 11.11 (2019): 1309.

Were any sites removed?

Several sites were removed due to poor NEON data quality. GRSM and PUUM both had lower quality RGB data that made them unsuitable for prediction. NEON surveys are updated annually and we expect future flights to correct these errors. We removed the GUIL puerto rico site due to its very steep topography and poor sunangle during data collection. The DeepForest algorithm responded poorly to predicting crowns in intensely shaded areas where there was very little sun penetration. We are happy to make these data are available upon request.

Contact

We welcome questions, ideas and general inquiries. The data can be used for many applications and we look forward to hearing from you. Contact ben.weinstein@weecology.org.

To standardize NEON organismal data for major taxonomic groups, we first systematically reviewed NEON’s documentations for each taxonomic group. We then discussed as a group and with NEON staff to decide how to wrangle and standardize NEON organismal data. See Li et al. 2022 for more details. All R code to process NEON data products can be obtained through the R package ‘ecocomDP’. Once the data are in ecocomDP format, we further processed them to convert them into long data frames with code on Github (https://github.com/daijiang/neonDivData/tree/master/data-raw), which is also archived here.

These samples are associated with NEON prototype dataset: NEON Decommissioned Site data: Root sampling, chemistry, and isotopes (Megapit) from D04 MAME site (a36e6ce2-d845-13e9-c881-c1d4e5881a53) DOI: 10.48443/j1hp-f273 NEON (National Ecological Observatory Network). NEON Decommissioned Site data: Root sampling, chemistry, and isotopes (Megapit) from D04 MAME site, v1 (10.48443/j1hp-f273). https://doi.org/10.48443/j1hp-f273. Dataset accessed from https://data.neonscience.org on July 7, 2021

The National Ecological Observatory Network (NEON; https://www.neonscience.org) collects water temperature measurements from its seven lake sites using a temperature chain consisting of thermistors measuring at various depths throughout the water column. This data is published as part of the water temperature at specific depth in surface water data product (DP1.20264.001). During 2021, a misconfiguration resulted in gaps in this data.

 The multisonde used to measure water quality (DP1.20288.001) also collects water temperature measurements that can potentially be used to fill these gaps. This data is not published by NEON as part of the Level 1 water quality data product because it is not as accurate as the temperature chain derived measurements. The calibration of the multisonde temperature sensor is also factory set and cannot be adjusted. 

 This data package contains the Level 0 multisonde water temperature data for NEON lake sites in 2021. This is raw data that has not been QA/QC'ed. NEON makes no guarantees about the accuracy of this data.

Geomorphology maps characterize aquatic reaches (approximately 1,000 meters in stream length) within wadeable streams at NEON aquatic sites. Raw survey data is collected with high-resolution total station survey equipment at each NEON wadeable stream site. Survey maps and channel metrics are produced and calculated using raw survey data geo-referenced to a global coordinate system. Geomorphology surveys are conducted at each site once every five years or immediately following a storm event deemed to have significantly altered stream morphology within the aquatic reach. Geomorphology surveys conducted immediately after a stochastic event will assess event magnitude by quantifying changes in channel geometry, bed composition, and biological habitat.Download these data from the NEON data portal.

This dataset contains an inventory for the paper entitled "ecocomDP: A flexible data design pattern for ecological community survey data" (O'Brien et al), submitted to Ecological Informatics. The paper describes an approach for harmonizing and reformatting community survey data such as organism abundance or cover measurements. Data currently using this data model and workflow approach are from the repository of the Environmental Data Initiative (EDI), the Long Term Ecological Research (LTER) Network, and the National Ecological Observatory Network (NEON). Data were assembled for this analysis in late 2020. The inventory is composed of two tables, describing data from EDI (including LTER) and data from NEON. The EDI inventory includes information for 70 datasets: identifiers for both the original and converted datasets, and basic coverage information such as temporal coverage (range of years and a measurement of sampling evenness), spatial coverage (maximum bounding coordinates and area of the "bounding box"), and taxonomic coverage (taxonomic classes). The NEON inventory contains information from 11 continent-wide NEON data products, divided into individual field sites to be more spatially compatible with EDI and LTER data. Taxonomic coverage is by group (e.g., algae, birds) rather than explicit taxonomic classes. Spatial coverage is the area of a field sampling site polygon. Temporal coverage includes the same minimum and maximum sampling years and temporal evenness measures as for the EDI data plus a count of months during that period when sampling occurred. At the time of data download, NEON data was considered provisional, however identifiers are persistent and now deliver final, "released" data.

 Also included in the data package is a script to reformat inventory data and create Figure 3 of the paper.

Unclassified three-dimensional point cloud by flightline and classified point cloud by 1 km tile, provided in LAZ format. Classifications follow standard ASPRS definitions. All point coordinates are provided in meters. Horizontal coordinates are referenced in the appropriate UTM zone and the ITRF00 datum. Elevations are referenced to Geoid12A.

This dataset contains partial pressure and molar concentration of dissolved carbon dioxide, methane, and nitrous oxide in 34 streams, rivers, and lakes calculated from headspace equilibration samples collected by the National Ecological Observatory Network (NEON). All input data were collected by NEON and is available on the NEON data portal at https://data.neonscience.org. Specifically, in situ dissolved gas concentrations were calculated from the air and headspace mixing ratios provided by the NEON Dissolved gases in surface water data product (DP1.20097.001), adjusted for sample and water temperature (DP1.20097.001, DP1.20264.001, DP1.20053.001), barometric pressure (DP1.20097.001, DP1.00004.001), and alkalinity (DP1.20093.001). The final set of inputs is found in the file, input_file, and the processing scripts are available at https://github.com/kellyaho/NEON-GHG-processing. The file, output_file, contains the raw outputs from running the input_file through the processing scripts. There are three outputs for each gas for each sample, one for each of three different pre-equilibration headspace mixing ratios (paired atmospheric samples, loess smoothing of atmospheric samples, and site-specific median). The file, GHG_final, contains the final dataset. This GHG_final uses the outputs from output_file calculated with paired atmospheric samples, and substitutes 0.01 μatm, 0.001 μM, 0.001 μatm, and 0.001 μM for any negative instances of pCH4, [CH4], pN2O, and [N2O], respectively. See methods for more detail. Please cite the NEON data inputs (listed below), in addition to this dataset, when using the data. NEON is sponsored by the National Science Foundation (NSF) and operated under cooperative agreement by Battelle. This material is based in part upon work supported by NSF through the NEON Program.

California permit requirements necessitated a more thorough identification of beetle pitfall samples than is typical of this protocol. These invertebrate bycatch samples therefore have occurrence associations that indicate their contents in both the NEON Biorepository and main NEON data portals. See NEON prototype dataset 9bc959c-148b-aaad-aa35-2d0805327428 available here.