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INTERPNT Software for Mapping Trees Using Distance Measurements
The INTERPNT method can be used to produce accurate maps of trees based solely on tree diameter and tree-to-tree distance measurements. For additional details on the technique please see the published paper (Boose, E. R., E. F. Boose and A. L. Lezberg. 1998. A practical method for mapping trees using distance measurements. Ecology 79: 819-827). Additional information is contained in the documentation that accompanies the program. The Abstract from the paper is reproduced below. "Accurate maps of the locations of trees are useful for many ecological studies but are often difficult to obtain with traditional surveying methods because the trees hinder line of sight measurements. An alternative method, inspired by earlier work of F. Rohlf and J. Archie, is presented. This "Interpoint method" is based solely on tree diameter and tree-to-tree distance measurements. A computer performs the necessary triangulation and detects gross errors. The Interpoint method was used to map trees in seven long-term study plots at the Harvard Forest, ranging from 0.25 ha (200 trees) to 0.80 ha (889 trees). The question of accumulation of error was addressed though a computer simulation designed to model field conditions as closely as possible. The simulation showed that the technique is highly accurate and that errors accumulate quite slowly if measurements are made with reasonable care (e.g., average predicted location errors after 1,000 trees and after 10,000 trees were 9 cm and 15 cm, respectively, for measurement errors comparable to field conditions; similar values were obtained in an independent survey of one of the field plots). The technique requires only measuring tapes, a computer, and two or three field personnel. Previous field experience is not required. The Interpoint method is a good choice for mapping trees where a high level of accuracy is desired, especially where expensive surveying equipment and trained personnel are not available."
Estimating Forest Productivity Using Carbon Isotopes in Tree Rings at Harvard Forest 1992-2010
We investigated relationships between tree-ring δ13C and growth, and flux tower estimates of gross primary productivity (GPP) at Harvard Forest from 1992 to 2010. Seasonal variations of derived photosynthetic isotope discrimination (Δ13C) and leaf intercellular CO2 concentration (ci) showed significant increasing trends for the dominant deciduous and coniferous species. Δ13C was positively correlated to growing-season GPP and is primarily controlled by precipitation and soil moisture indicating that site conditions maintained high stomatal conductance under increasing atmospheric CO2 levels. Increasing Δ13C over the 1992-2010 period is attributed to increasing annual and summer water availability identified at Harvard Forest and across the region. Higher Δ13C is coincident with an enhancement in growth and ecosystem-level net carbon uptake. This work suggests that tree-ring δ13C could serve as a measure of forest GPP and be used to improve the calibration and predictive skill of ecosystem and carbon cycle models.
Land-Use Impacts on Ecosystem Services Provisioning in Massachusetts 2001-2011
Meeting fundamental human needs while also maintaining ecosystem function and services is the central challenge of sustainability science. In the densely populated state of Massachusetts, USA, abundant forests and other natural land cover convey a range of ecosystem services. However, after more than a century of reforestation following an agrarian past, Massachusetts is again losing forests, this time to housing and commercial development. We used land-cover maps, ecosystem process models, and land-use data bases to map changes (2001, 2006, 2011) in eight ecosystem service variables and to identify “hotspots,” or areas that produce a high value of five or more services, at three policy-relevant spatial scales. Water-related services (clean water provisioning and flood regulation) experienced local declines in response to shifting land uses, but changed little when measured at the state-level. General habitat quality for terrestrial species declined state-wide during the study period as a consequence of forest loss. In contrast, climate regulation (carbon storage) and cultural services (outdoor recreation) increased, driven by continued forest biomass accrual and land protection, respectively. Timber harvest volume had high inter-annual variability, but no temporal trend. The scale at which hotspots are delineated greatly affects their quantity and spatial configuration, with a higher density in eastern Massachusetts and 10–12% more hotspots overall when they are identified at a town scale as compared to a watershed or state scale. Ecosystem service hotspots cover a small percentage of land area in Massachusetts (2.5–3.5% of the state), but are becoming more abundant as urbanization concentrates ecosystem service provisioning onto a diminished natural land base. This suggests that while ecosystem service hotspots are valuable targets for conservation, more are not necessarily better since hotspot proliferation can reflect the bifurcation of the landscape into servic
CBC02 Winter-spring survival and response of birds to variable climate using mist-net captures at Konza Prairie
This dataset includes captures of small-bodied landbirds captured via passive mist-netting efforts. The objectives are to (a) initiate a long-term survey of the non-breeding birds of the site, (b) understand the behavioral and physiological mechanisms that allow birds to cope with the unpredictable, variable, and often harsh conditions during winter months, and (c) provide a training platform for students. The collection of this dataset is fully integrated into the teaching of “Wild Bird Research” (an undergraduate hands-on research course in the Division of Biology) and less formal instruction in bird research methods for graduate students. Additionally, the banding efforts have benefited from the engagement of Konza Prairie docents and frequently hosts class visits and other visitors interested in witness bird banding operations.
North Temperate Lakes LTER Northern Highland Lake District Land Use - Land Cover 1930s
Land use/land cover was interpreted from historical aerial photographs for riparian buffer zones surrounding 50 lakes in Vilas County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
North Temperate Lakes LTER Northern Highland Lake District Land Use - Land Cover 1960s
Land use/land cover was interpreted from historical aerial photographs for riparian buffer zones surrounding 50 lakes in Vilas County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
North Temperate Lakes LTER Northern Highland Lake District Land Use - Land Cover 1990s
Land use/land cover was interpreted from historical aerial photographs for riparian buffer zones surrounding 50 lakes in Vilas County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
North Temperate Lakes LTER Yahara Lakes District Land Use - Land Cover 1930s
Land use/land cover was interpreted from historical aerial photographs for selected watersheds in Dane County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
North Temperate Lakes LTER Yahara Lakes District Land Use - Land Cover 1960s
Land use/land cover was interpreted from historical aerial photographs for selected watersheds in Dane County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
North Temperate Lakes LTER Yahara Lakes District Land Use - Land Cover 1990s
Land use/land cover was interpreted from historical aerial photographs for selected watersheds in Dane County, Wisconsin. Photography from the 1930s, 1960s, and 1990s were interpreted, resulting in land use/land cover data for three time periods.
PIE LTER surveys of salt marsh breeding birds using point counts in Rowley and Newbury, Massachusetts
This data set contains the results of point count surveys of breeding birds in the salt marshes of the Plum Island Estuary. Surveys have been carried out each year in June beginning in 2004 and are ongoing. Currently six circles of 100 m radius are being surveyed. Three of the circles are in plots that had been regularly hayed and three in unhayed plots. Currently only one of the plots is regularly hayed. 85 species recorded as of 2020. Most frequently encountered are Agelaius phoeniceus, Ammospiza caudacuta, Tringa semipalmata.
Survey of small mammals using trapping data on all Virginia Coast Reserve barrier islands south of Parramore Island (inclusive) 1975-1978
During 1975 and 1977 live-trapping surveys of small-mammals of the Virginia Barrier Islands were conducted. Primary species encountered were Oryzomys palustris, Mus musculus, Micrutus pennsylvanicus, Rattus norvegicus, Cryptotis parva, and Peromyscus leucopus. Data is presented as primary trapping records giving the date of capture, island, species, sex and reproductive condition of the captured animal. Each animal was tagged to allow individual identification upon recapture. Each island was typically trapped for 8 days in two 4-day sessions.
Migratory shorebird habitat use, diet, and prey selection on mudflats in the Virginia barrier island and lagoon system, 2023-2024
Migratory shorebirds require access to heterogenous resources during migration. Understanding how shorebirds utilize different foraging substrates and food resources across the coastal landscape is important for informing conservation. We compared shorebird habitat use and invertebrate prey communities between barrier island and mudflat foraging substrates. We counted shorebirds and collected prey samples at random points on sand, peat, and mudflat substrates during spring migration (May 14 - June 2), 2023 - 2024. We opportunistically collected fecal samples on mudflats in our study area and used fecal DNA metabarcoding with 18S (invertebrates) and 23S (biofilm) primers to describe the diets of dunlin (Calidris alpina), red knots (Calidris canutus rufa) and semipalmated sandpipers (Calidris pusilla). We then used network null modeling to determine if our focal species were selectively consuming invertebrates on mudflats. Peat banks were the most heavily used intertidal substrate and mudflats supported similar shorebird abundances and species richness to sand. Dunlin and semipalmated sandpipers were more abundant on peat and mudflats, while red knots were more abundant on sand and peat. Invertebrate density was highest on peat banks and similar between mudflat and sand substrate, though mudflats supported a more diverse prey community. Amphipod crustaceans, blue mussels (Mytilus edulis), and polychaete worms were main prey consumed by all species on mudflats. Dunlin and semipalmated sandpipers fed primarily on crustaceans whereas red knots mainly fed on bivalves. All species consumed biofilm and a high proportion of diatoms were observed in fecal samples collected from semipalmated sandpipers. Red knots and dunlin selectively consumed bivalves on mudflats while semipalmated sandpipers showed no dietary preferences. Managing staging sites to preserve a diversity of intertidal habitats is critical for meeting the variable foraging requirements of migratory shorebirds.
Reconstructing Faces from fMRI Patterns using Deep Generative Neural Networks.
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Modeling an auditory stimulated brain under altered states of consciousness using the generalized ising model
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Hand-selective visual regions represent how to grasp 3D tools for use: brain decoding during real actions
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MiRoR15-P1-Tools used to assess the quality of peer review reports: a methodological systematic review
<p>Database, data extraction form, R codes and protocol related to: Superchi C, González JA, Solà I, Cobo E, Hren D, Boutron I. <em>Tools used to assess the quality of peer review reports: a methodological systematic review</em>. BMC Med Res Methodol. 2019;19(48):1–14. DOI: <a href="https://doi.org/10.1186/s12874-019-0688-x">https://doi.org/10.1186/s12874-019-0688-x</a></p> <p> </p>
P-S waves 3D velocity model of Los Humeros area from earthquake based travel-time tomography using CAT3D software (OGS)
<p>The dataset contains the 3D velocity model (VP (m/s), VS (m/s) and VP/VS) obtained from the tomographic inversion of seismological data in the area of Los Humeros (Mexico). The model was performed in the frame of the GEMex project (Mexico‐Europe Cooperation for research of enhanced geothermal systems and super-hot geothermal systems, WP5 ‘Detection of deep structures’, Jousset et al., D5.3, 2019).</p> <p>The inversion used 2661 P arrivals and 2272 S arrivals associated to 395 earthquakes recorded by 37 stations. The picking data was provided by Toledo et al., 2019.</p> <p>The inversion was performed by CAT3D software, a tomographic tool developed by OGS, which uses the SIRT method (Simultaneous Iterative Reconstruction Technique, Stewart, 1993) as inversion algorithm and the ray tracing procedure based on minimum time principle (Böhm et al., 1999). The velocities used as initial model for tomography were provided by the interpolated values obtained from the velocity analysis of four 2D seismic lines acquired inside the same investigated area by the tomographic inversion (See GEMex deliverable D5.3).</p> <p>The 3D velocity model is defined by a 3D grid of 61 nodes in X, 69 nodes in Y and 29 nodes in Z, equally spaced by 250 m in all directions. The total dimensions of the model is 15x17x7 km and the borders positions are (m) (WGS 84/UTM ZONE 14N):</p> <p>Xmin = 655000, Xmax = 670000</p> <p>Ymin = 2168000, Ymax = 2185000</p> <p>Zmin = -3000, Zmax = 4000</p>
Fe chemical speciation collected using trace metal rosette in the Southern Ocean during the austral summer of 2016/2017, on board the Antarctic Circumnavigation Expedition.
<p><strong>Dataset abstract</strong></p> <p>Fe chemical speciation of filtered seawater data are presented in this dataset, resulting from samples collected from a trace metal rosette on board the Antarctic Circumnavigation Expedition (ACE). During the austral summer of 2016/2017, seawater samples were collected from the Atlantic and Indian Ocean sectors of the Southern Ocean and dissolved Fe concentration, iron-binding organic ligands concentration and the conditional stability constant of Fe’ are presented here.</p> <p><strong>Dataset contents</strong></p> <ul> <li>ace_fe_chemical_speciation.csv, data file, comma-separated values</li> <li>figure1.pdf, metadata, portable document format</li> <li>data_file_header.txt, metadata, text</li> <li>README.txt, metadata, text</li> </ul> <p><strong>Dataset license</strong></p> <p>This Fe chemical speciation dataset from ACE is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/</p>
TCOM-CFC11 : TOMCAT CTM and Occultation Mesurement based daily zonal mean CFC-11 stratospheric profiles constructed using machine leaning (2000-2023)
<h3>TOMCAT CTM and Occultation measurement-based Stratospheric CFC11 (TCOM-CFC11) profile data data set </h3> <h3>Sandip S. Dhomse </h3> <p>School of Earth and Envio, University of Leeds, Leeds, UK</p> <p>National Centre for Earth Observations, University of Leeds, Leeds, UK</p> <p> email: s.s.dhomse@leeds.ac.uk</p> <p> </p> <h3>Methodology: TOMCAT simulation is performed at T64L32 resolution for the 2000-2024 time period. Collocated CFC11 (CFCl3) profiles are divided in five latitude bins: SH polar (90S-50S), SH mid-lat (70S-20S), tropics (40S-40N), NH mid-lat (20N-70N) and NH polar (50N-90N). Initially, model-measurement differences are calculated for each zonal bins (51 height levels, 10km to 60km). Separate XGBoost regression models are trained for the differences between TOMCAT and measurements at each level for a given latitude bin. XGBoost model is then used to estimate error corrections for all the TOMCAT grids. Estimated corrections for a given model grid that are added to the original TOMCAT simulated daily (at 1.30 local time) CFC-11 profiles. Height resolved data are then interpolated on 28-pressure levels (300 - 0.1hPa). For overlapping latitude bins, we use averages and then calculate daily zonal mean values. For more details see attached presentation.</h3> <h3>Dataset also includes two files containing daily mean zonal mean CFC11 profiles on height (10-60 km) and pressure (300-0.1 hPa) levels (8766 days/64 latitudes):</h3> <h3>zmcfc11_TCOM_hlev_T2Dz_2000-2024_V1.1.nc – height level data (10 to 60 km)</h3> <h3>zmcfc11_TCOM_plev_T2Dz_2000-2024_V1.1.nc – pressure level data (300 to 0.1 hPa)</h3> <h3>Daily 3D profiles on height and pressure levels would be made available on request. Xarrays “resample” can be used to get monthly means.</h3> <h3> </h3> <h3> </h3>
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.