Reference map

SLIDO-4.5 is an Esri ArcGIS version 10.7 file geodatabase which can be downloaded here: https://www.oregon.gov/dogami/slido/Pages/data.aspx The geodatabase contains two feature datasets (a group of datasets within the geodatabase) containing six feature classes total, as well as two raster data sets, one individual table, and two individual feature classes. The original studies vary widely in scale, scope and focus which is reflected in the wide range of accuracy, detail, and completeness with which landslides are mapped. In the future, we propose a continuous update of SLIDO. These updates should take place: 1) each time DOGAMI publishes a new GIS dataset that contains landslide inventory or susceptibility data or 2) at the end of each winter season, a common time for landslide occurrences in Oregon, which will include recent historic landslide point data. In order to keep track of the updates, we will use a primary release number such as Release 4.0 along with a decimal number identifying the update such as 4.5.

For the purposes of training AI-based models to identify (map) road features in rural/remote tropical regions on the basis of true-colour satellite imagery, and subsequently testing the accuracy of these AI-derived road maps, we produced a dataset of 8904 satellite image ‘tiles’ and their corresponding known road features across Equatorial Asia (Indonesia, Malaysia, Papua New Guinea). Methods

1. INPUT 200 SATELLITE IMAGES

The main dataset shared here was derived from a set of 200 input satellite images, also provided here. These 200 images are effectively ‘screenshots’ (i.e., reduced-resolution copies) of high-resolution true-colour satellite imagery (~0.5-1m pixel resolution) observed using the Elvis Elevation and Depth spatial data portal (https://elevation.fsdf.org.au/), which here is functionally equivalent to the more familiar Google Earth. Each of these original images was initially acquired at a resolution of 1920x886 pixels. Actual image resolution was coarser than the native high-resolution imagery. Visual inspection of these 200 images suggests a pixel resolution of ~5 meters, given the number of pixels required to span features of familiar scale, such as roads and roofs, as well as the ready discrimination of specific land uses, vegetation types, etc. These 200 images generally spanned either forest-agricultural mosaics or intact forest landscapes with limited human intervention. Sloan et al. (2023) present a map indicating the various areas of Equatorial Asia from which these images were sourced.
IMAGE NAMING CONVENTION A common naming convention applies to satellite images’ file names: XX##.png where:

XX – denotes the geographical region / major island of Equatorial Asia of the image, as follows: ‘bo’ (Borneo), ‘su’ (Sumatra), ‘sl’ (Sulawesi), ‘pn’ (Papua New Guinea), ‘jv’ (java), ‘ng’ (New Guinea [i.e., Papua and West Papua provinces of Indonesia])

– denotes the ith image for a given geographical region / major island amongst the original 200 images, e.g., bo1, bo2, bo3…

1. INTERPRETING ROAD FEATURES IN THE IMAGES For each of the 200 input satellite images, its road was visually interpreted and manually digitized to create a reference image dataset by which to train, validate, and test AI road-mapping models, as detailed in Sloan et al. (2023). The reference dataset of road features was digitized using the ‘pen tool’ in Adobe Photoshop. The pen’s ‘width’ was held constant over varying scales of observation (i.e., image ‘zoom’) during digitization. Consequently, at relatively small scales at least, digitized road features likely incorporate vegetation immediately bordering roads. The resultant binary (Road / Not Road) reference images were saved as PNG images with the same image dimensions as the original 200 images.

2. IMAGE TILES AND REFERENCE DATA FOR MODEL DEVELOPMENT

The 200 satellite images and the corresponding 200 road-reference images were both subdivided (aka ‘sliced’) into thousands of smaller image ‘tiles’ of 256x256 pixels each. Subsequent to image subdivision, subdivided images were also rotated by 90, 180, or 270 degrees to create additional, complementary image tiles for model development. In total, 8904 image tiles resulted from image subdivision and rotation. These 8904 image tiles are the main data of interest disseminated here. Each image tile entails the true-colour satellite image (256x256 pixels) and a corresponding binary road reference image (Road / Not Road).
Of these 8904 image tiles, Sloan et al. (2023) randomly selected 80% for model training (during which a model ‘learns’ to recognize road features in the input imagery), 10% for model validation (during which model parameters are iteratively refined), and 10% for final model testing (during which the final accuracy of the output road map is assessed). Here we present these data in two folders accordingly:

'Training’ – contains 7124 image tiles used for model training in Sloan et al. (2023), i.e., 80% of the original pool of 8904 image tiles. ‘Testing’– contains 1780 image tiles used for model validation and model testing in Sloan et al. (2023), i.e., 20% of the original pool of 8904 image tiles, being the combined set of image tiles for model validation and testing in Sloan et al. (2023).

IMAGE TILE NAMING CONVENTION A common naming convention applies to image tiles’ directories and file names, in both the ‘training’ and ‘testing’ folders: XX##_A_B_C_DrotDDD where

XX – denotes the geographical region / major island of Equatorial Asia of the original input 1920x886 pixel image, as follows: ‘bo’ (Borneo), ‘su’ (Sumatra), ‘sl’ (Sulawesi), ‘pn’ (Papua New Guinea), ‘jv’ (java), ‘ng’ (New Guinea [i.e., Papua and West Papua provinces of Indonesia])

– denotes the ith image for a given geographical region / major island amongst the original 200 images, e.g., bo1, bo2, bo3…

A, B, C and D – can all be ignored. These values, which are one of 0, 256, 512, 768, 1024, 1280, 1536, and 1792, are effectively ‘pixel coordinates’ in the corresponding original 1920x886-pixel input image. They were recorded within the names of image tiles’ sub-directories and file names merely to ensure that names/directory were uniquely named)

rot – implies an image rotation. Not all image tiles are rotated, so ‘rot’ will appear only occasionally.

DDD – denotes the degree of image-tile rotation, e.g., 90, 180, 270. Not all image tiles are rotated, so ‘DD’ will appear only occasionally.

Note that the designator ‘XX##’ is directly equivalent to the filenames of the corresponding 1920x886-pixel input satellite images, detailed above. Therefore, each image tiles can be ‘matched’ with its parent full-scale satellite image. For example, in the ‘training’ folder, the subdirectory ‘Bo12_0_0_256_256’ indicates that its image tile therein (also named ‘Bo12_0_0_256_256’) would have been sourced from the full-scale image ‘Bo12.png’.

USGS Structures from The National Map (TNM) consists of data to include the name, function, location, and other core information and characteristics of selected manmade facilities across all US states and territories. The types of structures collected are largely determined by the needs of disaster planning and emergency response, and homeland security organizations. Structures currently included are: School, School:Elementary, School:Middle, School:High, College/University, Technical/Trade School, Ambulance Service, Fire Station/EMS Station, Law Enforcement, Prison/Correctional Facility, Post Office, Hospital/Medical Center, Cabin, Campground, Cemetery, Historic Site/Point of Interest, Picnic Area, Trailhead, Vistor/Information Center, US Capitol, State Capitol, US Supreme Court, State Supreme Court, Court House, Headquarters, Ranger Station, White House, and City/Town Hall. Structures data are designed to be used in general mapping and in the analysis of structure related activities using geographic information system technology. Included is a feature class of preliminary building polygons provided by FEMA, USA Structures. The National Map structures data is commonly combined with other data themes, such as boundaries, elevation, hydrography, and transportation, to produce general reference base maps. The National Map viewer allows free downloads of public domain structures data in either Esri File Geodatabase or Shapefile formats. For additional information on the structures data model, go to https://www.usgs.gov/ngp-standards-and-specifications/national-map-structures-content.

This is a general reference map of Canada and surrounding countries. The representation of political features on this map does not necessarily reflect the position of the Government of Canada on international issues of recognition, sovereignty or jurisdiction. Political status is as of 2009.

Libraries data contains name and location data for selected manmade facilities. These data are designed to be used in general mapping and analysis of structure related activities using a geographic information system (GIS) For mapping purposes, structures can be used with other GIS data themes to produce general reference maps as a base map dataset

The INDIGO Change Detection Reference Dataset

Description

This graffiti-centred change detection dataset was developed in the context of INDIGO, a research project focusing on the documentation, analysis and dissemination of graffiti along Vienna's Donaukanal. The dataset aims to support the development and assessment of change detection algorithms.

The dataset was collected from a test site approximately 50 meters in length along Vienna's Donaukanal during 11 days between 2022/10/21 and 2022/12/01. Various cameras with different settings were used, resulting in a total of 29 data collection sessions or "epochs" (see "EpochIDs.jpg" for details). Each epoch contains 17 images generated from 29 distinct 3D models with different textures. In total, the dataset comprises 6,902 unique image pairs, along with corresponding reference change maps. Additionally, exclusion masks are provided to ignore parts of the scene that might be irrelevant, such as the background.

To summarise, the dataset, labelled as "Data.zip," includes the following:

• Synthetic Images: These are colour images created within Agisoft Metashape Professional 1.8.4, generated by rendering views from 17 artificial cameras observing 29 differently textured versions of the same 3D surface model.
• Change Maps: Binary images that were manually and programmatically generated, using a Python script, from two synthetic graffiti images. These maps highlight the areas where changes have occurred.
• Exclusion Masks: Binary images are manually created from synthetic graffiti images to identify "no data" areas or irrelevant ground pixels.

Image Acquisition

Image acquisition involved the use of two different camera setups. The first two datasets (ID 1 and 2; cf. "EpochIDs.jpg") were obtained using a Nikon Z 7II camera with a pixel count of 45.4 MP, paired with a Nikon NIKKOR Z 20 mm lens. For the remaining image datasets (ID 3-29), a triple GoPro setup was employed. This triple setup featured three GoPro cameras, comprising two GoPro HERO 10 cameras and one GoPro HERO 11, all securely mounted within a frame. This triple-camera setup was utilised on nine different days with varying camera settings, resulting in the acquisition of 27 image datasets in total (nine days with three datasets each).

Data Structure

The "Data.zip" file contains two subfolders:

• 1_ImagesAndChangeMaps: This folder contains the primary dataset. Each subfolder corresponds to a specific epoch. Within each epoch folder resides a subfolder for every other epoch with which a distinct epoch pair can be created. It is important to note that the pairs "Epoch Y and Epoch Z" are equivalent to "Epoch Z and Epoch Y", so the latter combinations are not included in this dataset. Each sub-subfolder, organised by epoch, contains 17 more subfolders, which hold the image data. These subfolders consist of:
  • Two synthetic images rendered from the same synthetic camera ("X_Y.jpg" and "X_Z.jpg")
  • The corresponding binary reference change map depicting the graffiti-related differences between the two images ("X_YZ.png"). Black areas denote new graffiti (i.e. "change"), and white denotes "no change". "DataStructure.png" provides a visual explanation concerning the creation of the dataset.
    
    The filenames follow the following pattern:
    • X - Is the ID number of the synthetic camera. In total, 17 synthetic cameras were placed along the test site
    • Y - Corresponds to the reference epoch (i.e. the "older epoch")
    • Z - Corresponds to the "new epoch"
      
• 2_ExclusionMasks: This folder contains the binary exclusion masks. They were manually created from synthetic graffiti images and identify "no data" areas or areas considered irrelevant, such as "ground pixels". Two exclusion masks were generated for each of the 17 synthetic cameras:
  • "groundMasks": depict ground pixels which are usually irrelevant for the detection of graffiti
  • "noDataMasks": depict "background" for which no data is available.
    

A detailed dataset description (including detailed explanations of the data creation) is part of a journal paper currently in preparation. The paper will be linked here for further clarification as soon as it is available.

Licensing

Due to the nature of the three image types, this dataset comes with two licenses:

• Synthetic images:
  • These come with an In Copyright license (for the rights usage terms, see https://rightsstatements.org/page/InC/1.0/?language=en).
  • The copyright lies with:
    • the Ludwig Boltzmann Gesellschaft (https://d-nb.info/gnd/1024204324)
    • the TU Wien (https://d-nb.info/gnd/55426-1)
    • One or more anonymous graffiti creator(s) upon whose work these images are based.
  • The first two entities are also the licensor of these images.
    
• Change maps and masks:
  • These are openly licensed via CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)
  • In this case, the copyright lies with:
    • the Ludwig Boltzmann Gesellschaft (https://d-nb.info/gnd/1024204324)
    • the TU Wien (https://d-nb.info/gnd/55426-1)
  • Both institutes are also the licensor of these images.

Every synthetic image, change map and mask has this licensing information embedded as IPTC photo metadata. In addition, the images' IPTC metadata also provide a short image description, the image creator and the creator's identity (in the form of an ORCiD).

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If there are any questions, problems or suggestions for the dataset or the description, please do not hesitate to contact the corresponding author, Benjamin Wild.

This dataset is a series of digital map-posters accompanying the AdaptNRM Guide: Helping Biodiversity Adapt: supporting climate adaptation planning using a community-level modelling approach.

These represent supporting materials and information about the community-level biodiversity models applied to climate change. Map posters are organised by four biological groups (vascular plants, mammals, reptiles and amphibians), two climate change scenario (1990-2050 MIROC5 and CanESM2 for RCP8.5), and five measures of change in biodiversity.

The map-posters present the nationally consistent data at locally relevant resolutions in eight parts – representing broad groupings of NRM regions based on the cluster boundaries used for climate adaptation planning (http://www.environment.gov.au/climate-change/adaptation) and also Nationally.

Map-posters are provided in PNG image format at moderate resolution (300dpi) to suit A0 printing. The posters were designed to meet A0 print size and digital viewing resolution of map detail. An additional set in PDF image format has been created for ease of download for initial exploration and printing on A3 paper. Some text elements and map features may be fuzzy at this resolution.

Each map-poster contains four dataset images coloured using standard legends encompassing the potential range of the measure, even if that range is not represented in the dataset itself or across the map extent.

Most map series are provided in two parts: part 1 shows the two climate scenarios for vascular plants and mammals and part 2 shows reptiles and amphibians. Eight cluster maps for each series have a different colour theme and map extent. A national series is also provided. Annotation briefly outlines the topics presented in the Guide so that each poster stands alone for quick reference.

An additional 77 National maps presenting the probability distributions of each of 77 vegetation types – NVIS 4.1 major vegetation subgroups (NVIS subgroups) - are currently in preparation.

Example citations:

Williams KJ, Raisbeck-Brown N, Prober S, Harwood T (2015) Generalised projected distribution of vegetation types – NVIS 4.1 major vegetation subgroups (1990 and 2050), A0 map-poster 8.1 - East Coast NRM regions. CSIRO Land and Water Flagship, Canberra. Available online at www.AdaptNRM.org and https://data.csiro.au/dap/.

Williams KJ, Raisbeck-Brown N, Harwood T, Prober S (2015) Revegetation benefit (cleared natural areas) for vascular plants and mammals (1990-2050), A0 map-poster 9.1 - East Coast NRM regions. CSIRO Land and Water Flagship, Canberra. Available online at www.AdaptNRM.org and https://data.csiro.au/dap/.

This dataset has been delivered incrementally. Please check that you are accessing the latest version of the dataset. Lineage: The map posters show case the scientific data. The data layers have been developed at approximately 250m resolution (9 second) across the Australian continent to incorporate the interaction between climate and topography, and are best viewed using a geographic information system (GIS). Each data layers is 1Gb, and inaccessible to non-GIS users. The map posters provide easy access to the scientific data, enabling the outputs to be viewed at high resolution with geographical context information provided.

Maps were generated using layout and drawing tools in ArcGIS 10.2.2

A check list of map posters and datasets is provided with the collection.

Map Series: 7.(1-77) National probability distribution of vegetation type – NVIS 4.1 major vegetation subgroup pre-1750 #0x

8.1 Generalised projected distribution of vegetation types (NVIS subgroups) (1990 and 2050)

9.1 Revegetation benefit (cleared natural areas) for plants and mammals (1990-2050)

9.2 Revegetation benefit (cleared natural areas) for reptiles and amphibians (1990-2050)

10.1 Need for assisted dispersal for vascular plants and mammals (1990-2050)

10.2 Need for assisted dispersal for reptiles and amphibians (1990-2050)

11.1 Refugial potential for vascular plants and mammals (1990-2050)

11.1 Refugial potential for reptiles and amphibians (1990-2050)

12.1 Climate-driven future revegetation benefit for vascular plants and mammals (1990-2050)

12.2 Climate-driven future revegetation benefit for vascular reptiles and amphibians (1990-2050)

Point locations of schools in Maine. Structures data contains name and location data for selected manmade facilities. These data are designed to be used in general mapping and analysis of structure related activities using a geographic information system (GIS) For mapping purposes, structures can be used with other GIS data themes to produce general reference maps as a base map dataset.

The Water Framework Directive (WFD) sets out the basic principles for sustainable water policy. Its purpose is to establish a framework for the protection of inland surface waters, transitional waters, coastal waters and groundwater. The WFD aims to achieve good water status. The body of water is the elementary territorial division of aquatic environments intended to be the WFD assessment unit. A reference for water bodies is established for all waters in the Seine Normandy basin. It allows the development of the WFD management plan to achieve good water status.

This data concerns the Master Plan for Water Management 2022-027 (SDAGE) of the Seine Normandy Basin. It lists the surface water bodies: river body, transitional water body, coastal water body, body of water body water body

A river water body is a distinct and significant part of surface waters such as a river, river or canal, part of a river, river or canal. A transitional water body is a distinct and significant part of surface waters located near the mouths of rivers or rivers, which are partly salty because of their proximity to coastal waters but which remain fundamentally influenced by fresh water currents. A coastal water body is a distinct and significant part of the surface waters between the baseline used to measure the breadth of territorial waters and a distance of one nautical mile. A body of water body of water is a distinct and significant part of surface waters such as a lake, a reservoir.

For more information, you can consult the document of the Sander dedicated to water body repositories: http://www.sandre.eaufrance.fr/urn.php? urn=urn:sandre:dictionnaire:MDO:FRA:::ressource:1.3:::pdf

Abstract

This dataset and its metadata statement were supplied to the Bioregional Assessment Programme by a third party and are presented here as originally supplied.

Dataset contains framework layers compiled for representation on state reference map, scale 1:1.5 million. Line and polygon features only. Road, rail, waterbody and watercourse themes included. State coastline not included.

Purpose

Can be used as a framework layer for whole of state mapping or for a generalised framework for regional mapping. Not suitable for analysis.

Dataset History

Information was compiled and digitised in generalised form from 1:250 000 scale hard copy maps. The individual CAD files were combined into seamless form and converted to Lambert Conformal Conic projection, standard parallels 29 degrees and 35 degrees S, central meridian 135 degrees E. Subsequently the information was converted to GIS format and re-projected to the state standard LCC projection.

Dataset Citation

SA Department of Environment, Water and Natural Resources (2015) Topography - State Refence Map - ARC. Bioregional Assessment Source Dataset. Viewed 26 May 2016, http://data.bioregionalassessments.gov.au/dataset/b6f2d7af-7fbb-4bf5-9051-b725d51b270a.

The USGS National Hydrography Dataset (NHD) service from The National Map is a comprehensive set of digital spatial data that encodes information about naturally occurring and constructed bodies of surface water (lakes, ponds, and reservoirs), paths through which water flows (canals, ditches, streams, and rivers), and related entities such as point features (springs, wells, stream gages, and dams). The information encoded about these features includes classification and other characteristics, delineation, geographic name, position and related measures, a "reach code" through which other information can be related to the NHD, and the direction of water flow. The network of reach codes delineating water and transported material flow allows users to trace movement in upstream and downstream directions. In addition to this geographic information, the dataset contains metadata that supports the exchange of future updates and improvements to the data. The NHD is available nationwide in two seamless datasets, one based on 1:24,000 (or larger) scale and referred to as high resolution NHD, and the other based on 1:100,000 scale and referred to as medium resolution NHD. The NHD from The National Map supports many applications, such as making maps, geocoding observations, flow modeling, data maintenance, and stewardship. The NHD is commonly combined with other data themes, such as boundaries, elevation, structures, and transportation, to produce general reference base maps. The National Map download client allows free downloads of public domain NHD data in either Esri File Geodatabase or Shapefile formats. For additional information on the NHD, go to https://www.usgs.gov/national-hydrography/national-hydrography-dataset. See https://apps.nationalmap.gov/help/ for assistance with The National Map viewer, download client, services, or metadata. Data Refreshed January, 2024.

DEPRECATED: This layer has not been maintained and is outdated. We recommend using the NG911 Address Points layer, filtered to shows schools, as a more current data layer.Point locations of schools in Maine. Structures data contains name and location data for selected manmade facilities. These data are designed to be used in general mapping and analysis of structure related activities using a geographic information system (GIS) For mapping purposes, structures can be used with other GIS data themes to produce general reference maps as a base map dataset.

This map is designed to be used as a basemap by GIS professionals and as a reference map by anyone. The map includes administrative boundaries, cities, water features, physiographic features, parks, landmarks, highways, roads, railways, and airports overlaid on land cover and shaded relief imagery for added context. The map provides coverage for the world down to a scale of ~1:72k. Coverage is provided down to ~1:4k for the following areas: Australia and New Zealand; India; Europe; Canada; Mexico; the continental United States and Hawaii; South America and Central America; Africa; and most of the Middle East. Coverage down to ~1:1k and ~1:2k is available in select urban areas. This basemap was compiled from a variety of best available sources from several data providers, including the U.S. Geological Survey (USGS), U.S. Environmental Protection Agency (EPA), U.S. National Park Service (NPS), Food and Agriculture Organization of the United Nations (FAO), Department of Natural Resources Canada (NRCAN), GeoBase, Agriculture and Agri-Food Canada, Garmin, HERE, Esri, OpenStreetMap contributors, and the GIS User Community. For more information on this map, including our terms of use, visit us online at http://goto.arcgisonline.com/maps/World_Topo_Map

Introduction and Rationale: Due to our increasing understanding of the role the surrounding landscape plays in ecological processes, a detailed characterization of land cover, including both agricultural and natural habitats, is ever more important for both researchers and conservation practitioners. Unfortunately, in the United States, different types of land cover data are split across thematic datasets that emphasize agricultural or natural vegetation, but not both. To address this data gap and reduce duplicative efforts in geospatial processing, we merged two major datasets, the LANDFIRE National Vegetation Classification (NVC) and USDA-NASS Cropland Data Layer (CDL), to produce an integrated land cover map. Our workflow leveraged strengths of the NVC and the CDL to produce detailed rasters comprising both agricultural and natural land-cover classes. We generated these maps for each year from 2012-2021 for the conterminous United States, quantified agreement between input layers and accuracy of our merged product, and published the complete workflow necessary to update these data. In our validation analyses, we found that approximately 5.5% of NVC agricultural pixels conflicted with the CDL, but we resolved a majority of these conflicts based on surrounding agricultural land, leaving only 0.6% of agricultural pixels unresolved in our merged product. Contents: Spatial data Attribute table for merged rasters Technical validation data Number and proportion of mismatched pixels Number and proportion of unresolved pixels Producer's and User's accuracy values and coverage of reference data Resources in this dataset:Resource Title: Attribute table for merged rasters. File Name: CombinedRasterAttributeTable_CDLNVC.csvResource Description: Raster attribute table for merged raster product. Class names and recommended color map were taken from USDA-NASS Cropland Data Layer and LANDFIRE National Vegetation Classification. Class values are also identical to source data, except classes from the CDL are now negative values to avoid overlapping NVC values. Resource Title: Number and proportion of mismatched pixels. File Name: pixel_mismatch_byyear_bycounty.csvResource Description: Number and proportion of pixels that were mismatched between the Cropland Data Layer and National Vegetation Classification, per year from 2012-2021, per county in the conterminous United States.Resource Title: Number and proportion of unresolved pixels. File Name: unresolved_conflict_byyear_bycounty.csvResource Description: Number and proportion of unresolved pixels in the final merged rasters, per year from 2012-2021, per county in the conterminous United States. Unresolved pixels are a result of mismatched pixels that we could not resolve based on surrounding agricultural land (no agriculture with 90m radius).Resource Title: Producer's and User's accuracy values and coverage of reference data. File Name: accuracy_datacoverage_byyear_bycounty.csvResource Description: Producer's and User's accuracy values and coverage of reference data, per year from 2012-2021, per county in the conterminous United States. We defined coverage of reference data as the proportional area of land cover classes that were included in the reference data published by USDA-NASS and LANDFIRE for the Cropland Data Layer and National Vegetation Classification, respectively. CDL and NVC classes with reference data also had published accuracy statistics. Resource Title: Data Dictionary. File Name: Data_Dictionary_RasterMerge.csv

We have developed ProjecTILs, a computational approach to project new data sets into a reference map of T cells, enabling their direct comparison in a stable, annotated system of coordinates. Because new cells are embedded in the same space of the reference, ProjecTILs enables the classification of query cells into annotated, discrete states, but also over a continuous space of intermediate states. By comparing multiple samples over the same map, and across alternative embeddings, the method allows exploring the effect of cellular perturbations (e.g. as the result of therapy or genetic engineering) and identifying genetic programs significantly altered in the query compared to a control set or to the reference map. We illustrate the projection of several data sets from recent publications over two cross-study murine T cell reference atlases: the first describing tumor-infiltrating T lymphocytes (TILs), the second characterizing acute and chronic viral infection.To construct the reference TIL atlas, we obtained single-cell gene expression matrices from the following GEO entries: GSE124691, GSE116390, GSE121478, GSE86028; and entry E-MTAB-7919 from Array-Express. Data from GSE124691 contained samples from tumor and from tumor-draining lymph nodes, and were therefore treated as two separate datasets. For the TIL projection examples (OVA Tet+, miR-155 KO and Regnase-KO), we obtained the gene expression counts from entries GSE122713, GSE121478 and GSE137015, respectively.Prior to dataset integration, single-cell data from individual studies were filtered using TILPRED-1.0 (https://github.com/carmonalab/TILPRED), which removes cells not enriched in T cell markers (e.g. Cd2, Cd3d, Cd3e, Cd3g, Cd4, Cd8a, Cd8b1) and cells enriched in non T cell genes (e.g. Spi1, Fcer1g, Csf1r, Cd19). Dataset integration was performed using STACAS (https://github.com/carmonalab/STACAS), a batch-correction algorithm based on Seurat 3. For the TIL reference map, we specified 600 variable genes per dataset, excluding cell cycling genes, mitochondrial, ribosomal and non-coding genes, as well as genes expressed in less than 0.1% or more than 90% of the cells of a given dataset. For integration, a total of 800 variable genes were derived as the intersection of the 600 variable genes of individual datasets, prioritizing genes found in multiple datasets and, in case of draws, those derived from the largest datasets. We determined pairwise dataset anchors using STACAS with default parameters, and filtered anchors using an anchor score threshold of 0.8. Integration was performed using the IntegrateData function in Seurat3, providing the anchor set determined by STACAS, and a custom integration tree to initiate alignment from the largest and most heterogeneous datasets.Next, we performed unsupervised clustering of the integrated cell embeddings using the Shared Nearest Neighbor (SNN) clustering method implemented in Seurat 3 with parameters {resolution=0.6, reduction=”umap”, k.param=20}. We then manually annotated individual clusters (merging clusters when necessary) based on several criteria: i) average expression of key marker genes in individual clusters; ii) gradients of gene expression over the UMAP representation of the reference map; iii) gene-set enrichment analysis to determine over- and under- expressed genes per cluster using MAST. In order to have access to predictive methods for UMAP, we recomputed PCA and UMAP embeddings independently of Seurat3 using respectively the prcomp function from basic R package “stats”, and the “umap” R package (https://github.com/tkonopka/umap).

This data set, part of the NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) Program, consists of three as-complete-as-possible mosaic maps of velocities on the Antarctic ice sheet for the time periods 1995–2001, 2007–2009, and 2014–2017. The maps are posted at 450 m in the WGS 84/Antarctic Polar Stereographic projection. In addition to ice velocity, the data set provides maps of velocity error and standard deviation; counts of velocity estimates used per pixel; date ranges; and masks that delineate the ice fronts and grounding lines for the each period.

The Forest BD Version 2 is a reference database for forest space and semi-natural environments. It is the geographical reference for the description of forest species. It describes forest and natural plant formations by an approach to soil cover reflecting a description of the stand’s cover density, composition and dominant essence, for elements over 5 000 m² (i.e. 0.5 hectares). The Forest BD version 2 is a reference tool for the forest-wood sector, the environment, spatial planning and sustainable development (management, fire, resource, supply, certification, etc.) and acts in support of various projects (land planning, resource assessment and environmental quality, risk prevention, knowledge of biodiversity and ecological continuity, description of landscapes and natural environments, etc.).

The reference rating corresponds to the rating of the water body modelled to the right of an existing project or construction plus a safety factor, called “hydraulic revanche” and a value of 20 cm. Thus “out of water” of a construction will result in a first floor rating greater than or equal to that reference rating as indicated on the regulatory zoning mapping. It is displayed in NGF-IGN 69 meter, i.e. in meter in the official leveling network in metropolitan France, which is attached to the Marseilles tidegrapher. These odds are reported perpendicular to the river axis at regular intervals on the regulatory zoning map. At a given location, the reference rating is the value immediately upstream or at the right of the place in question. Between two reference ratings, the applicable rating will be calculated by linear interpolation between the two known ratings shown on the plane.

The USGS Transportation downloadable data from The National Map (TNM) is based on TIGER/Line data provided through U.S. Census Bureau and supplemented with HERE road data to create tile cache base maps. Some of the TIGER/Line data includes limited corrections done by USGS. Transportation data consists of roads, railroads, trails, airports, and other features associated with the transport of people or commerce. The data include the name or route designator, classification, and location. Transportation data support general mapping and geographic information system technology analysis for applications such as traffic safety, congestion mitigation, disaster planning, and emergency response. The National Map transportation data is commonly combined with other data themes, such as boundaries, elevation, hydrography, and structures, to produce general reference base maps. The National Map viewer allows free downloads of public domain transportation data in either Esri File Geodatabase or Shapefile formats. For additional information on the transportation data model, go to https://www.usgs.gov/core-science-systems/national-geospatial-program/national-map.