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Habitat mapping of coastal dunes with deep learning - Scripts & Data

Authors: Eva M. Lansu, Valérie C. Reijers, Freek Daniëls, Rebecca James, Marjolijn J. A. Christianen, Tjisse van der Heide   Abstract About one-third of the world's shoreline is defined by sandy coasts with developed dune ecosystems. These ecosystems drastically degraded them due to anthropogenic pressures. To develop strategic management that counteracts this degradation, it is essential to closely monitor ongoing habitat changes. Traditionally, coastal dune monitoring is based on field observations, which are labour intensive and costly. While automated analyses of aerial imagery could reduce monitoring efforts and enhance spatial coverage, to date, its application has remained limited to a single small-scale trial (<2 km2). Here, we trained a Convolutional Neural Network to map the Dutch coastal dunes (562 km2) at 25 cm resolution using six habitat classes: bare sand, shrubs, fresh water, grass, broadleaf trees, and needleleaf trees. Training the network on only RGB imagery resulted in predictions with 92% accuracy, 80% average recall and 70% precision. Model performance increased when the network was trained on all available data - RGB imagery, near-infrared, distance to sea, digital surface model, and canopy height - resulting in 95% accuracy, 88% averaged recall and 80% precision. Finally, we compared the predictions with 499 in-field observations across the Dutch coastal dunes and found 88% accuracy, 74% averaged recall and 62% precision. We used this model to create a map of the entire Dutch coastal dunes, which enables rapid and precise assessments of habitat diversity and extent. As habitat and species diversity are intrinsically linked, our results showcase how automated image analysis can enable biodiversity monitoring on a national scale. ============================================== Methods The analyses rely on the following datasets: <ul> <li>Orthophoto mosaics including a near-infrared band (from <a href="http://geotiles.nl/">http://geotiles.nl/</a>)</li> <li>Digital surface model and a digital terrain model (from <a href="https://www.ahn.nl/">https://www.ahn.nl/</a>)</li> <li>A land-use map (from <a href="https://lgn.nl/basiskaart">https://lgn.nl/basiskaart)</a></li> </ul>

Mapping data and computer code

Open the record for dataset details and reuse information.

30 m resolution Qinghai-Tibet Plateau quarterly leaf area index maps of 2023

Quarterly LAI maps of the Qinghai-Tibet Plateau are stored in folders divided into 5 × 5-degree blocks. The data files are in TIFF format, using the WGS84 coordinate system, with a uniform resolution of 30 meters. The naming convention for the files is: “LAI_Quarter_Longitude_Latitude”, e.g., LAI_1202_95_30.tif indicates the 2023 Q1 maximum LAI composite image for a block with the lower-left corner at 95°E longitude and 30°N latitude. Data usage instructions: The files can be opened with software such as ArcGIS, ENVI, and QGIS. Pixel valid values range from 0 to 8, while the background fill value is NaN. All block data has been compressed using LZW (Lempel-Ziv-Welch) lossless compression.

Performance regression testing initiatives: A systematic mapping - Replication Package

This repository contains the supporting material for the manuscript titled "Performance regression testing initiatives: A systematic mapping", currently under revision to the Journal of Information and Software Technology.  Repository Content: <ul> <li> Protocol Performance Regression Testing.xlsx: it includes the *protocol* specification, i.e., the data extraction process used for the selection of the studies and gathering all relevant information. The outcome of the systematic mapping consists of 68 *selected studies* and information supporting the answers to four research questions: *RQ1*, *RQ2*, *RQ3*, and *RQ4*; </li> <li> scripts.zip: it includes all the scripts used in the forward snowballing. Two additional files support the replication of the scripts: (1) README.md explains how to run the scripts; (2) requirements.txt file reports the installation prerequisites and their dependencies; </li> <li> SM-PRT-overview.xlsx: this spreadsheet reports the information about tools and replication packages, benchmark suites and subject systems adopted per study; </li> <li> README-SM-PRT-overview.md.docx: this file describes the columns of the spreadsheet above to facilitate the usage of the collected information. </li> </ul>

opencc-by-4.0Dec 2024View details →

An evidence map of research assessing the effects of timber harvesting on water quality, biotic and biodiversity indicators in running waters: Data and R code

These are the data and R code that accompany the Forest Ecology and Management publication titled "An evidence map of research assessing the effects of timber harvesting on water quality, biotic and biodiversity indicators in running waters".

opennotspecifiedNov 2024View details →

MAP. Distribution of Chinese Skleroprotopus species. Star, S. confucius; triangle, S. laticoxalis laticoxalis; square, S. laticoxalis longus; circle, S. membranipedalis; hexagon, S. securifer sp. nov.; diamond, S. serratus. in The millipede genus Skleroprotopus Attems, 1901 (Diplopoda, Julida, Mongoliulidae) in China, with description of a new species

MAP. Distribution of Chinese Skleroprotopus species. Star, S. confucius; triangle, S. laticoxalis laticoxalis; square, S. laticoxalis longus; circle, S. membranipedalis; hexagon, S. securifer sp. nov.; diamond, S. serratus.

opencc-by-4.0Dec 2024View details →

Data for "Updated maps of major oxides and Mg# on the lunar surface"

In this study, we added CE-6 lunar soil sample, and used high spatial resolution SELENE (Kaguya) Multiband Imager (MI) spectra data of 59 m/pixel, combined with a deep learning inversion model based on the one-dimensional convolutional neural network (1D-CNN), to present new maps of the major oxides (Al2O3, CaO, FeO, MgO, TiO2) and Mg # (Mg/ (Mg + Fe) in mole percent) values.

Single-nucleotide-resolution genomic maps of O6-methylguanine from the glioblastoma drug temozolomide

Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. We analyzed O6-MeG formation and repair with regards to sequence contexts and functional genomic regions in a glioblastoma-derived cell line and evaluated the impact of MGMT expression. O6-MeG signatures were highly similar to mutational signatures from patients previously treated with temozolomide. Furthermore, MGMT did not preferentially repair O6-MeG with respect to sequence context, chromatin state or gene expression level, however, may protect oncogenes from mutations. Finally, we found an MGMT-independent strand bias in O6-MeG accumulation in highly expressed genes. These data provide high resolution insight on how O6-MeG formation and repair are impacted by genome structure and nucleotide sequence. Further, O6-MeG-seq is expected to enable future studies of DNA modification signatures as diagnostic markers for addressing drug resistance and preventing secondary cancers.

opencc-by-4.0Aug 2024View details →

ALCC: Temporally consistent annual land cover maps over China from 1985 to 2022 based on an ensemble change detection method

We develope  a consistent annual land cover product for China (ALCC)  from 1985 to 2022. First, change areas for each year was detected baesd on an ensemble change detection method combing CCDC, BFASTm, and Chow Test. Then, stable training samples were derived from both CLCD and CLUDs. The Random Forest classifier was locally trained and used to classify change areas year by year. Finally, ALCC was generated by updating land cover classification results for change areas and remaining class label the same as the base map forthe unchanged areas. ALCC achieved a mean overall accuracy of 81.11±0.67% nationwide and exceeded 72.00% across seven geographical regions.

50k Maps of Burma--additional 11--20250104

98 50k maps of Burma

openmit-licenseMar 2024View details →

Evaluation of Cas13d as a tool for genetic interaction mapping

This zenodo upload contains the scripts for the calculation of tau values and genetic interaction scores (GI) in knockdown experiments with Cas13d. In addition to the scripts for determining the tau values and GI scores (Calculate_tau_and_GI.zip), the script for creating the plots used and the reference files for the publication “On the utility of Cas13d for genetic interaction mapping” are also provided. Further information can be found in the README.

opencc-by-4.0Jul 2024View details →

Dataset for mapping 'visual university studies' journal articles published in English from 1992 to 2023

This dataset includes the information on the 208 items that were selected, following a systematised search and sift, of journal articles published in English from 1992 to 2023. Belluigi led the systematised search process, supported through the research assistance of Leanne York (shown as Researcher 1) and Yvonne Moynihan (Researcher 2).   <div> Databases, which relate to ‘education’ or ‘sociology’, were searched including: British Education Index, Child Development and Adolescent Studies, Educational Administration Abstracts, ERIC, Frontier, Routledge, Sage, Scielo, Social Science Citation Index, Sociological Abstracts, Springer, Taylor and Francis, Tertiary Education and Management. Additional sources were double checked for papers too: Higher Education Special Interest Group (HESIG) of the Comparative and International Education Society (CIES) list of ‘Higher Education Journals’ (<a href="https://www.higheredsig.org/higher-education-journals">https://www.higheredsig.org/higher-education-journals</a>), Journal of Critical Scholarship on Higher Education and Student Affairs, SOTL in the South.  </div> Below are the search terms used, though Boolean operators were dependent on the search platform (Library at Queen’s University Belfast; data bases; journal platforms; Google Scholar et cetera), and other selection criteria.  <table> <tbody> <tr> <td> Search terms and criteria </td> </tr> <tr> <td> Terms </td> <td> higher education OR university OR academ* OR campus OR student </td> </tr> <tr> <td> AND </td> </tr> <tr> <td> visual* OR image OR photo* OR film* OR performance OR architecture* OR cultural infrastructure OR picture* OR snapshot OR iconography OR art </td> </tr> <tr> <td> Date range published </td> <td> 1992 – 2023 End of the Cold War to current 21 year period </td> </tr> <tr> <td> Language </td> <td> Inclusion: Englishes (translations and publications) </td> </tr> <tr> <td> Resource type </td> <td> Inclusion: Articles Exclusions: Books; chapters; data sets; dissertations; media; reports </td> </tr> <tr> <td> Focus </td> <td> university; academic citizens; events; social life on and of campus; Exclusions: teaching OR learning methods; research methods; general creative art practice; general student methodological practice; academic evaluation; student assessment; marketing </td> </tr> </tbody> </table>

opengpl-3.0-or-laterNov 2024View details →

Mapping the Landscape of Open Source Health Economic Models: A Systematic Database Review and Analysis

Health economic models are crucial for health technology assessment (HTA) to evaluate the value of medical interventions. Open source models (OSMs), where source code and calculations are publicly accessible, enhance transparency, efficiency, credibility, and reproducibility. This study systematically reviews databases to map the landscape of available OSMs in health economics.

South Asia Index Maps--latest updates

Index maps for Survey of India maps with scales of 253/250k, 126k, and 63/50k.

50k Maps of Burma--additional 6--20241029

97 50k maps of Burma

opencc-zeroOct 2021View details →

dryad32/100

Map of the proportion of threatened endemic species per country in relation with environmental and socioeconomic drivers

This dataset is a shapefile representing the proportion of threatened endemic species (both plants and animals) in 247 countries along with associated environmental and socioeconomic drivers. The geographic coordinate system is World Geodetic System 1984 (EPSG: 4326).

opennotspecifiedNov 2021View details →

FIGURES 117−118. Distribution maps for Sparianthina spp. 117 in The Neotropical genera Guadana Rheims, 2010 and Sparianthina Banks, 1929 (Araneae: Sparassidae: Heteropodinae)

FIGURES 117−118. Distribution maps for Sparianthina spp. 117 (Sparianthina adisi, Sparianthina boyaca sp. n., Sparianthina gaita, Sparianthina milleri, Sparianthina parang); 118 (Sparianthina deltshevi, Sparianthina pumilla, Sparianthina saaristoi, Sparianthina selenopoides, Sparianthina soca sp. n.).

opennotspecifiedNov 2021View details →

FIGURES 81−82. Distribution maps for Guadana spp. 81 in The Neotropical genera Guadana Rheims, 2010 and Sparianthina Banks, 1929 (Araneae: Sparassidae: Heteropodinae)

FIGURES 81−82. Distribution maps for Guadana spp. 81 (Guadana alpahuayo sp. n., Guadana amendoim sp. n., Guadana arawak sp. n., Guadana manauara, Guadana mapia sp. n., Guadana muirapinima sp. n.); 82 (Guadana neblina, Guadana panguana, Guadana quillu, Guadana tambopata, Guadana ucayali sp. n., Guadana urucu).

opennotspecifiedNov 2021View details →

MAP 1 in Notes on the genus Messageria Bavay & Dautzenberg, 1904, with descriptions of a new speciesand anew subspecies (Gastropoda: Caenogastropoda:Cyclophoroidea Alycaeidae)

MAP 1. Distributions of Messageria Bavay & Dautzenberg, 1904 (Area 1), Laotia Saurin, 1953 (Area 2) and Helicomorpha Möllendorff, 1890 (Area 3).