Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
518
datasets available to search
ShareScore release 0.9.0
Dataset results
518 results for “useful plants”
Object-based image analysis for monitoring plant invasions, can we use an open-source solution?
<p><strong>Introduction</strong></p> <p>This is a practical exercise testing possibilities of open-source solutions (FOSS) for object-based image analysis (OBIA) to monitor plant invasion using unoccupied aerial system (UAS, drone).</p> <p>The material is accompanying a chapter <strong><em>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier.</em></strong></p> <p>The material is meant for readers to run the workflow and detect invasion of giant hogweed on the UAS data themselves testing different FOSS solutions.</p> <p> </p> <p><strong>Data</strong></p> <p>• a subset of UAS-borne data (consumer camera) collected in Czech Republic during the flowering of a noxious invasive plant species giant hogweed (<em>Heracleum mantegazzianum</em>)</p> <p>• training dataset</p> <p>• eCognition rulebase (proprietary OBIA software)</p> <p>• a script for SegOptim package implemented in R</p> <p> </p> <p><strong>Description</strong></p> <p>The use case represents a simple application of OBIA approach based on the SegOptim package implemented in R.</p> <p>Four bands (RGBN) UAS image subset are available, capturing the central area of a heavily invaded location (CZ) by giant hogweed (Heracleum mantegazzianum). Thanks to the proper image timing, the invasive species is clearly observable as white objects (in RGB) representing the various stage of the blossom. Considering the complex shape of the flower heads, detection based on image segmentation outperforms pixel-based classification (Müllerová et al., 2017). Simple segmentation of input imagery is performed (for simplicity only the spectral bands are considered both for segmentation and feature space definition, however additional features such as vegetation indices or textural measures may be included), followed by supervised classification using training data. Finally, a visual comparison of result detection both from proprietary (eCognition) and open-source (SegOptim) implementation is provided, confirming comparable results.</p> <p>Based on #github("joaofgoncalves/SegOptim")</p> <p> </p> <p><strong>References</strong></p> <p>Gonçalves, J., Pôças, I., Marcos, B., Mücher, C. A., & Honrado, J. P. (2019). SegOptim—A new R package for optimizing object-based image analyses of high-spatial resolution remotely-sensed data. <em>International Journal of Applied Earth Observation and Geoinformation</em>, <em>76</em>, 218-230.</p> <p>Müllerová, J., Brůna, J., Bartaloš, T., Dvořák, P., Vítková, M. & Pyšek, P. (2017b). Timing Is Important: Unmanned Aircraft vs. Satellite Imagery in Plant Invasion Monitoring. Frontiers in Plant Science 8:1–13.</p> <p>Accompanying material for</p> <p>Müllerová, J. et al. (2023). Vegetation mapping and monitoring by unoccupied aerial systems – current state and perspectives. In: Manfreda, S. et Eyal B.D. (eds). Unmanned Aerial Systems for Monitoring Soil, Vegetation, and Riverine Environments. Elsevier</p>
Spanish wild plants traditionally used as medicine
<p>List of Spanish wild plant species with the ethnobotanical references in which they have been reported as medicinal and their cultural importance index (CI). Accompanied as well by data about origin (wild or cultivated), abundance, occupancy area, endemicity, conservation status, protection status. We also provide the complete list of references and legislation used.</p> <p>The excel file has five tabs: 1. Ethnobotanical references, 2. Medicinal species, 3. Legislation, 4. Protection, 5. Protection categories.</p>
How do young identify plants? Using the drawing method to explore early ethnobotanical knowledge in Madagascar
<p>Database from the article "How do young identify plants? Using the drawing method to explore early ethnobotanical knowledge in Madagascar"</p> <p>Please contact the author before using it for more details.</p> <p> </p>
The Prairie State: Using Ecological Niche Modeling to Predict Distributions of Early Land Plants
<p>This data includes raw data of over 12,000 occurrences were downloaded from the<strong> Consortium of Bryophyte Herbaria (<a href="http://www.bryophyteportal.org/portal">www.bryophyteportal.org/portal</a>), </strong>that were listed to be in Illinois and included longitude and latitude data. This data set was screened and cleaned to investigate species distribution models as well as generate models of selected bryophytes investigating future changes in distribution across climate change scenarios.</p>
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
<p>In the paper associated with this dataset, a workflow is presented which enables the identification of single-/low-copy nuclear molecular markers for a plant group of interest, by mining data from a small representative target capture experiment done using a commercial probe kit and Oxford Nanopore long-read sequencing. The proposed pipeline first assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low-copy. The approach can be applied to any probe set. As it relies on long reads, the contribution also provides template workflows for processing Nanopore-based target capture data. Identified loci can be used for NGS amplicon sequencing. For detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, the long-read assembly tool CANU is employed. The presented workflow can be useful for researchers dealing with reticulate or polyploidization phylogenetic histories in plants.</p> <p>The present dataset contains several documents supplementing the original paper. Its most important elements are a detailed description (alongside two graphical workflow figures) of all methods employed in the study, suitable for reproducing the steps of the workflow and also the wet-lab work. The workflow employs a collection of BASH, Python and R scripts which is available here, together with a detailed account on command line use in Linux. Also, reference sequences for the identified markers can be found as well as sequence alignments derived from the amplicon sequencing.</p>
GCNT-Plume: Long-term observation of global nuclear power plants thermal plumes using Landsat images and deep learning
<p>This repository contains the relevant code and data for the paper <strong>Long-term observation of global nuclear power plants thermal plumes using Landsat images and deep learning</strong><strong> </strong>(Wei et al, 2023, <em>Remote Sensing of Environment</em>).</p> <p>Specifically, the <strong>U-Net.zip</strong> file includes the associated codes for segmenting surface thermal plumes from nuclear power plants along the global coasts and the Great Lakes by using the U-Net model integrated with prior knowledge. The <strong>GCNT-Plume.zip</strong> file includes the occurrence footprints of core area plumes (the <strong>occurrence_all </strong>folder), raw water temperature increment (WST) images (the <strong>delta </strong>folder), mixed area plumes and annotations (the <strong>extractWithLocation </strong>folder), model-predicted core area plumes (the <strong>prediction*_*</strong> folders), the mixed/core area plumes and background areas in shapefile format (the <strong>sampleAnnotation* </strong>folders), and location information (the <strong>location.xlsx </strong>table). Please refer to the <strong>README.md </strong>file in the <strong>U-Net.zip</strong> file for more detailed information.</p>
Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants
Open the record for dataset details and reuse information.
Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
Open the record for dataset details and reuse information.
Data from: Frugivore traits predict plant-frugivore interactions using generalized joint attribute modeling
Open the record for dataset details and reuse information.
Data from: Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on plant functional groups
Open the record for dataset details and reuse information.
Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations
Open the record for dataset details and reuse information.
Phylogeny explains why less therapeutically redundant plant species are not necessarily facing greater use pressure
Open the record for dataset details and reuse information.
Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity
Open the record for dataset details and reuse information.
Pollen chemical and mechanical defences restrict host-plant use by bees
Open the record for dataset details and reuse information.
Threats of land use to the global diversity of vascular plants
Open the record for dataset details and reuse information.
Improving genomic prediction for plant disease using environmental covariates
Open the record for dataset details and reuse information.
American Residential Macrosystems - Presence/absence of plant species within land use groups in residential yards in six major metropolitan areas in the United States, 2017-2018
"This dataset includes presence/absence of plant species recorded in residential yards and nearby natural and interstitial areas (i.e.unmanaged vegetation areas in the residential/wildland interface) in six cities across the U.S. Baltimore, MD, Boston, MA, Los Angeles, CA, Miami, FL, Minneapolis-St. Paul, MN, and Phoenix, AZ. Yards were grouped in 4 categories based on fertilizer input frequency, landscaping style and their impact on hydrology: high-input lawns, low-input lawns, wildlife-certified yards and yards with low impact on hydrology (or rain gardens)."
Plant available NH4, NO3, and PO4 was determined at sites near ARC LTER Toolik acidic tundra and at a toposequence along the floodplain of the Sagavanirktuk River using 2 N KCL and weak HCL extracts, Arctic LTER 1987 to 2002
Plant available NH4, NO3, and PO4 was determined at sites near ARC LTER Toolik acidic tundra and at a toposequence along the floodplain of the Sagavanirktuk River using 2 N KCL and weak HCL extracts. This file complies data collected at different times from 1987 through 2001 and includes initial extracts taken for buried bag method of net nitrogen mineralization.
The effects of land-use history and the contemporary landscape on non-native plant invasion at local and regional scales in the French Broad Watersheds, 2007
Determining what factors explain the distribution of non-native invasive plants that can spread in forest-dominated landscapes could advance understanding of the invasion process and identify forest areas most susceptible to invasion. The researchers conducted roadside surveys to determine the presence and abundance of 15 non-native plant species known to invade forests in western North Carolina, USA. Prior to sampling, the researchers identified 15 non-native invasive plant species that were of concern in the study region. Generalized linear models were used to examine how contemporary and historic land use, landscape context, and topography influenced presence and abundance of the species at local and regional scales.
Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits
<p>Data for the preprint "Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits.”, by Legay N. , Grassein F., Arnoldi C., Segura R., Laîné P., Lavorel S., Clément J.C.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.