The establishment of a BES Multi-User Geodatabase (BES-MUG) allows for the storage, management, and distribution of geospatial data associated with the Baltimore Ecosystem Study. At present, BES data is distributed over the internet via the BES website. While having geospatial data available for download is a vast improvement over having the data housed at individual research institutions, it still suffers from some limitations. BES-MUG overcomes these limitations; improving the quality of the geospatial data available to BES researches, thereby leading to more informed decision-making. BES-MUG builds on Environmental Systems Research Institute's (ESRI) ArcGIS and ArcSDE technology. ESRI was selected because its geospatial software offers robust capabilities. ArcGIS is implemented agency-wide within the USDA and is the predominant geospatial software package used by collaborating institutions. Commercially available enterprise database packages (DB2, Oracle, SQL) provide an efficient means to store, manage, and share large datasets. However, standard database capabilities are limited with respect to geographic datasets because they lack the ability to deal with complex spatial relationships. By using ESRI's ArcSDE (Spatial Database Engine) in conjunction with database software, geospatial data can be handled much more effectively through the implementation of the Geodatabase model. Through ArcSDE and the Geodatabase model the database's capabilities are expanded, allowing for multiuser editing, intelligent feature types, and the establishment of rules and relationships. ArcSDE also allows users to connect to the database using ArcGIS software without being burdened by the intricacies of the database itself. For an example of how BES-MUG will help improve the quality and timeless of BES geospatial data consider a census block group layer that is in need of updating. Rather than the researcher downloading the dataset, editing it, and resubmitting to through ORS, access rules will allow the authorized user to edit the dataset over the network. Established rules will ensure that the attribute and topological integrity is maintained, so that key fields are not left blank and that the block group boundaries stay within tract boundaries. Metadata will automatically be updated showing who edited the dataset and when they did in the event any questions arise. Currently, a functioning prototype Multi-User Database has been developed for BES at the University of Vermont Spatial Analysis Lab, using Arc SDE and IBM's DB2 Enterprise Database as a back end architecture. This database, which is currently only accessible to those on the UVM campus network, will shortly be migrated to a Linux server where it will be accessible for database connections over the Internet. Passwords can then be handed out to all interested researchers on the project, who will be able to make a database connection through the Geographic Information Systems software interface on their desktop computer. This database will include a very large number of thematic layers. Those layers are currently divided into biophysical, socio-economic and imagery categories. Biophysical includes data on topography, soils, forest cover, habitat areas, hydrology and toxics. Socio-economics includes political and administrative boundaries, transportation and infrastructure networks, property data, census data, household survey data, parks, protected areas, land use/land cover, zoning, public health and historic land use change. Imagery includes a variety of aerial and satellite imagery. See the readme: http://96.56.36.108/geodatabase_SAL/readme.txt See the file listing: http://96.56.36.108/geodatabase_SAL/diroutput.txt

Have you ever wanted to create your own maps, or integrate and visualize spatial datasets to examine changes in trends between locations and over time? Follow along with these training tutorials on QGIS, an open source geographic information system (GIS) and learn key concepts, procedures and skills for performing common GIS tasks – such as creating maps, as well as joining, overlaying and visualizing spatial datasets. These tutorials are geared towards new GIS users. We’ll start with foundational concepts, and build towards more advanced topics throughout – demonstrating how with a few relatively easy steps you can get quite a lot out of GIS. You can then extend these skills to datasets of thematic relevance to you in addressing tasks faced in your day-to-day work.

This project is a component of a broader effort focused on geothermal heating and cooling (GHC) with the aim of illustrating the numerous benefits of incorporating GHC and geothermal heat exchange (GHX) into community energy planning and national decarbonization strategies. To better assist private sector investment, it is currently necessary to define and assess the potential of low-temperature geothermal resources. For shallow GHC/GHX fields, there is no formal compilation of subsurface characteristics shared among industry practitioners that can improve system design and operations. Alaska is specifically noted in this work, because heretofore, it has not received a similar focus in geothermal potential evaluations as the contiguous United States. The methodology consists of leveraging relevant data to generate a baseline geospatial dataset of low-temperature resources (less than 150 degrees C) to compare and analyze information accessible to anyone trying to understand the potential of GHC/GHX and small-scale low-temperature geothermal power in Alaska (e.g., energy modelers, communities, planners, and policymakers). Importantly, this project identifies data related to (1) the evaluation of GHC/GHX in the shallow subsurface, and (2) the evaluation of low-temperature geothermal resource availability. Additionally, data is being compiled to assess repurposing of oil and gas wells to contribute co-produced fluids toward the geothermal direct use and heating and cooling resource potential. In this work we identified new data from three different datasets of isolated geothermal systems in Alaska and bottom-hole temperature data from oil and gas wells that can be leveraged for evaluation of low-temperature geothermal resource potential. The goal of this project is to facilitate future deployment of GHC/GHX analysis and community-led programs and update the low-temperature geothermal resources assessment of Alaska. A better understanding of shallow potential for GHX will improve design and operations of highly efficient GHC systems. The deployment and impact that can be achieved for low-temperature geothermal resources will contribute to decarbonization goals and facilitate widespread electrification by shaving and shifting grid loads. Most of the data uses WGS84 coordinate system. However, each dataset come from different sources and has a metadata file with the original coordinate system.

Geostatistics analyzes and predicts the values associated with spatial or spatial-temporal phenomena. It incorporates the spatial (and in some cases temporal) coordinates of the data within the analyses. It is a practical means of describing spatial patterns and interpolating values for locations where samples were not taken (and measures the uncertainty of those values, which is critical to informed decision making). This archive contains results of geostatistical analysis of COVID-19 case counts for all available US counties. Test results were obtained with ArcGIS Pro (ESRI). Sources are state health departments, which are scraped and aggregated by the Johns Hopkins Coronavirus Resource Center and then pre-processed by MappingSupport.com.

This update of the Zenodo dataset (version 6) consists of three compressed archives containing geostatistical analyses of SARS-CoV-2 testing data. This dataset utilizes many of the geostatistical techniques used in previous versions of this Zenodo archive, but has been significantly expanded to include analyses of up-to-date U.S. COVID-19 case data (from March 24th to September 8^th, 2020):

Archive #1: “1.Geostat. Space-Time analysis of SARS-CoV-2 in the US (Mar24-Sept6).zip” – results of a geostatistical analysis of COVID-19 cases incorporating spatially-weighted hotspots that are conserved over one-week timespans. Results are reported starting from when U.S. COVID-19 case data first became available (March 24^th, 2020) for 25 consecutive 1-week intervals (March 24th through to September 6th, 2020). Hotspots, where found, are reported in each individual state, rather than the entire continental United States.

Archive #2: "2.Geostat. Spatial analysis of SARS-CoV-2 in the US (Mar24-Sept8).zip" – the results from geostatistical spatial analyses only of corrected COVID-19 case data for the continental United States, spanning the period from March 24^th through September 8th, 2020. The geostatistical techniques utilized in this archive includes ‘Hot Spot’ analysis and ‘Cluster and Outlier’ analysis.

Archive #3: "3.Kriging and Densification of SARS-CoV-2 in LA and MA.zip" – this dataset provides preliminary kriging and densification analysis of COVID-19 case data for certain dates within the U.S. states of Louisiana and Massachusetts.

These archives consist of map files (as both static images and as animations) and data files (including text files which contain the underlying data of said map files [where applicable]) which were generated when performing the following Geostatistical analyses: Hot Spot analysis (Getis-Ord Gi*) [‘Archive #1’: consecutive weeklong Space-Time Hot Spot analysis; ‘Archive #2’: daily Hot Spot Analysis], Cluster and Outlier analysis (Anselin Local Moran's I) [‘Archive #2’], Spatial Autocorrelation (Global Moran's I) [‘Archive #2’], and point-to-point comparisons with Kriging and Densification analysis [‘Archive #3’].

The Word document provided ("Description-of-Archive.Updated-Geostatistical-Analysis-of-SARS-CoV-2 (version 6).docx") details the contents of each file and folder within these three archives and gives general interpretations of these results.

This dataset contains Spatial Transcriptomics (ST) data matching with Matrix Assisted Laser Desorption/Ionization - Mass Spetrometry Imaging (MALDI-MSI). This data is complementary to data contained in the same project. FIles with the same identifiers in the two datasets originated from the very same tissue section and can be combined in a multimodal ST-MSI object. For more information about the dataset please see our manuscript posted on BioRxiv (doi: https://doi.org/10.1101/2023.01.26.525195). This dataset includes ST data from 19 tissue sections, including human post-mortem and mouse samples. The spatial transcriptomics data was generated using the Visium protocol (10x Genomics). The murine tissue sections come from three different mice unilaterally injected with 6-OHDA. 6-OHDA is a neurotoxin that when injected in the brain can selectively destroy dopaminergic neurons. We used this mouse model to show the applicability of the technology that we developed, named Spatial Multimodal Analysis (SMA). Using our technology on these mouse brain tissue sections we were able to detect both dopamine with MALDI-MSI and the corresponding gene expression with ST. This dataset includes also one human post-mortem striatum sample that was placed on one Visium slide across the four capture areas. This sample was analyzed with a different ST protocol named RRST (Mirzazadeh, R., Andrusivova, Z., Larsson, L. et al. Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nat Commun 14, 509 (2023). https://doi.org/10.1038/s41467-023-36071-5), where probes capturing the whole transcriptome are first hybridized in the tissue section and then spatially detected. Each tissue section contained in the dataset has been given a unique identifier that is composed of the Visium array ID and capture area ID of the Visium slide that the tissue section was placed on. This unique identifier is included in the file names of all the files relative to the same tissue section, including the MALDI-MSI files published in the other dataset included in this project. In this dataset you will find the following files for each tissue section: - raw files: these are the read one fastq files (containing the pattern *R1*fastq.gz in the file name), read two fastq files (containing the pattern *R1*fastq.gz in the file name) and the raw microscope images (containing the pattern Spot.jpg in the file name). These are the only files needed to run the Space Ranger pipeline, which is freely available for any user (please see the 10x Genomics website for information on how to install and run Space Ranger); - processed data files: we provide processed data files of two types: a) Space Ranger outputs that were used to produce the figures in our publication; b) manual annotation tables in csv format produced using Loupe Browser 6 (csv tables with file names ending _RegionLoupe.csv, _filter.csv, _dopamine.csv, _lesion.csv, _region.csv patterns); c) json files that we used as input for Space Ranger in the cases where the automatic tissue detection included in the pipeline failed to recognize the tissue or the fiducials. Using these processed files the user can reproduce the figures of our publication without having to restart from the raw data files. The MALDI-MSI analyses preceding ST was performed with different matrices in different tissue section. We used 1) 9-aminoacridine (9-AA) for detection of metabolites in negative ionization mode, 2) 2,5-dihydroxybenzoic acid (DHB) for detection of metabolites in positive ionization mode, 3) 4-(anthracen-9-yl)-2-fluoro-1-ethylpyridin-1-ium iodide (FMP-10), which charge-tags molecules with phenolic hydroxyls and/or primary amines, including neurotransmitters. The information about which matrix was sprayed on the tissue sections and other information about the samples is included in the metadata table. We also used three types of control samples: - standard Visium: samples processed with standard Visium (i.e. no matrix spraying, no MALDI-MSI, protocol as recommended by 10x Gemomics with no exeptions) - internal controls (iCTRL): samples not sprayed with any matrix, neither processed with MALDI-MSI, but located on the same Visium slide were other samples were processed with MALDI-MSI - FMP-10-iCTRL: sample sprayed with FMP-10, and then processed as an iCTRL. This and other information is provided in the metadata table.

Replication data for the turnout example in Chapter 5 of Spatial Analysis for the Social Sciences.

Our model is a full-annual-cycle population model {hostetler2015full} that tracks groups of bat surviving through four seasons: breeding season/summer, fall migration, non-breeding/winter, and spring migration. Our state variables are groups of bats that use a specific maternity colony/breeding site and hibernaculum/non-breeding site. Bats are also accounted for by life stages (juveniles/first-year breeders versus adults) and seasonal habitats (breeding versus non-breeding) during each year, This leads to four states variable (here depicted in vector notation): the population of juveniles during the non-breeding season, the population of adults during the non-breeding season, the population of juveniles during the breeding season, and the population of adults during the breeding season, Each vector's elements depict a specific migratory pathway, e.g., is comprised of elements, {non-breeding sites}, {breeding sites}The variables may be summed by either breeding site or non-breeding site to calculate the total population using a specific geographic location. Within our code, we account for this using an index column for breeding sites and an index column for non-breeding sides within the data table. Our choice of state variables caused the time step (i.e. (t)) to be 1 year. However, we recorded the population of each group during the breeding and non-breeding season as an artifact of our state-variable choice. We choose these state variables partially for their biological information and partially to simplify programming. We ran our simulation for 30 years because the USFWS currently issues Indiana Bat take permits for 30 years. Our model covers the range of the Indiana Bat, which is approximately the eastern half of the contiguous United States (Figure \ref{fig:BatInput}). The boundaries of our range was based upon the United States boundary, the NatureServe Range map, and observations of the species. The maximum migration distance was 500-km, which was based upon field observations reported in the literature \citep{gardner2002seasonal, winhold2006aspects}. The landscape was covered with approximately 33,000, 6475-ha grid cells and the grid size was based upon management considerations. The U.S.~Fish and Wildlife Service considers a 2.5 mile radius around a known maternity colony to be its summer habitat range and all of the hibernaculum within a 2.5 miles radius to be a single management unit. Hence the choice of 5-by-5 square grids (25 miles(^2) or 6475 ha). Each group of bats within the model has a summer and winter grid cell as well as a pathway connecting the cells. It is possible for a group to be in the cell for both seasons, but improbable for females (which we modeled). The straight line between summer and winter cells were buffered with different distances (1-km, 2-km, 10-km, 20-km, 100-km, and 200-km) as part of the turbine sensitivity and uncertainty analysis. We dropped the largest two buffer sizes during the model development processes because they were biologically unrealistic and including them caused all populations to go extinct all of the time. Note a 1-km buffer would be a 2-km wide path. An example of two pathways are included in Figure \ref{fig:BatPath}. The buffers accounts for bats not migrating in a straight line. If we had precise locations for all summer maternity colonies, other approaches such as Circuitscape \citep{hanks2013circuit} could have been used to model migration routes and this would have reduced migration uncertainty.

This dataset consists of cartographic data in digital line graph (DLG) form for the northeastern states (Connecticut, Maine, Massachusetts, New Hampshire, New York, Rhode Island and Vermont). Information is presented on two planimetric base categories, political boundaries and administrative boundaries, each available in two formats: the topologically structured format and a simpler format optimized for graphic display. These DGL data can be used to plot base maps and for various kinds of spatial analysis. They may also be combined with other geographically referenced data to facilitate analysis, for example the Geographic Names Information System.

This dataset contains the road and plot data used for the geospatial analysis example showcased in "Fostering Open Science at WSL with the EnviDat Environmental Data Portal", a contribution to the 5th Open Source Geospatial Research and Education Symposium (OGRS), 2018. The example uses Jupyter Notebook to calculate road densities in the neighbourhood of sample plot locations with Python. Road data were extracted from OpenStreetMap, while the point data (sample plots) were generated manually.

An example of voter data with real, Zip4, Street Segment, Census Block Group, and Zip centroid details.

This dataset constitutes an introduction to plotting and mapping and the essential concepts of spatial data management and modeling. And data ready for several examples of regression and classification algorithms (Multiple Linear Regression, Generalized Linear Models, CART and Random Forest), also exploring classic interpolation methods (Inverse Distance Weighting and Kriging).

Database created for replication of GeoStoryTelling. Our life stories evolve in specific and contextualized places. Although our homes may be our primarily shaping environment, our homes are themselves situated in neighborhoods that expose us to the immediate “real world” outside home. Indeed, the places where we are currently experiencing, and have experienced life, play a fundamental role in gaining a deeper and more nuanced understanding of our beliefs, fears, perceptions of the world, and even our prospects of social mobility. Despite the immediate impact of the places where we experience life in reaching a better understanding of our life stories, to date most qualitative and mixed methods researchers forego the analytic and elucidating power that geo-contextualizing our narratives bring to social and health research. From this view then, most research findings and conclusions may have been ignoring the spatial contexts that most likely have shaped the experiences of research participants. The main reason for the underuse of these geo-contextualized stories is the requirement of specialized training in geographical information systems and/or computer and statistical programming along with the absence of cost-free and user-friendly geo-visualization tools that may allow non-GIS experts to benefit from geo-contextualized outputs. To address this gap, we present GeoStoryTelling, an analytic framework and user-friendly, cost-free, multi-platform software that enables researchers to visualize their geo-contextualized data narratives. The use of this software (available in Mac and Windows operative systems) does not require users to learn GIS nor computer programming to obtain state-of-the-art, and visually appealing maps. In addition to providing a toy database to fully replicate the outputs presented, we detail the process that researchers need to follow to build their own databases without the need of specialized external software nor hardware. We show how the resulting HTML outputs are capable of integrating a variety of multi-media inputs (i.e., text, image, videos, sound recordings/music, and hyperlinks to other websites) to provide further context to the geo-located stories we are sharing (example https://cutt.ly/k7X9tfN). Accordingly, the goals of this paper are to describe the components of the methodology, the steps to construct the database, and to provide unrestricted access to the software tool, along with a toy dataset so that researchers may interact first-hand with GeoStoryTelling and fully replicate the outputs discussed herein. Since GeoStoryTelling relied on OpenStreetMap its applications may be used worldwide, thus strengthening its potential reach to the mixed methods and qualitative scientific communities, regardless of location around the world. Keywords: Geographical Information Systems; Interactive Visualizations; Data StoryTelling; Mixed Methods & Qualitative Research Methodologies; Spatial Data Science; Geo-Computation.

Replication data for the poverty rates example in Chapter 4 of Spatial Analysis for the Social Sciences.

The dataset and the validation are fully described in a Nature Scientific Data Descriptor https://www.nature.com/articles/s41597-019-0265-5

If you want to use this dataset in an interactive environment, then use this link https://mybinder.org/v2/gh/GeographerAtLarge/TravelTime/HEAD

The following text is a summary of the information in the above Data Descriptor.

The dataset is a suite of global travel-time accessibility indicators for the year 2015, at approximately one-kilometre spatial resolution for the entire globe. The indicators show an estimated (and validated), land-based travel time to the nearest city and nearest port for a range of city and port sizes.

The datasets are in GeoTIFF format and are suitable for use in Geographic Information Systems and statistical packages for mapping access to cities and ports and for spatial and statistical analysis of the inequalities in access by different segments of the population.

These maps represent a unique global representation of physical access to essential services offered by cities and ports.

The datasets travel_time_to_cities_x.tif (where x has values from 1 to 12) The value of each pixel is the estimated travel time in minutes to the nearest urban area in 2015. There are 12 data layers based on different sets of urban areas, defined by their population in year 2015 (see PDF report).

travel_time_to_ports_x (x ranges from 1 to 5)

The value of each pixel is the estimated travel time to the nearest port in 2015. There are 5 data layers based on different port sizes.

Format Raster Dataset, GeoTIFF, LZW compressed Unit Minutes

Data type Byte (16 bit Unsigned Integer)

No data value 65535

Flags None

Spatial resolution 30 arc seconds

Spatial extent

Upper left -180, 85

Lower left -180, -60 Upper right 180, 85 Lower right 180, -60 Spatial Reference System (SRS) EPSG:4326 - WGS84 - Geographic Coordinate System (lat/long)

Temporal resolution 2015

Temporal extent Updates may follow for future years, but these are dependent on the availability of updated inputs on travel times and city locations and populations.

Methodology Travel time to the nearest city or port was estimated using an accumulated cost function (accCost) in the gdistance R package (van Etten, 2018). This function requires two input datasets: (i) a set of locations to estimate travel time to and (ii) a transition matrix that represents the cost or time to travel across a surface.

The set of locations were based on populated urban areas in the 2016 version of the Joint Research Centre’s Global Human Settlement Layers (GHSL) datasets (Pesaresi and Freire, 2016) that represent low density (LDC) urban clusters and high density (HDC) urban areas (https://ghsl.jrc.ec.europa.eu/datasets.php). These urban areas were represented by points, spaced at 1km distance around the perimeter of each urban area.

Marine ports were extracted from the 26th edition of the World Port Index (NGA, 2017) which contains the location and physical characteristics of approximately 3,700 major ports and terminals. Ports are represented as single points

The transition matrix was based on the friction surface (https://map.ox.ac.uk/research-project/accessibility_to_cities) from the 2015 global accessibility map (Weiss et al, 2018).

Code The R code used to generate the 12 travel time maps is included in the zip file that can be downloaded with these data layers. The processing zones are also available.

Validation The underlying friction surface was validated by comparing travel times between 47,893 pairs of locations against journey times from a Google API. Our estimated journey times were generally shorter than those from the Google API. Across the tiles, the median journey time from our estimates was 88 minutes within an interquartile range of 48 to 143 minutes while the median journey time estimated by the Google API was 106 minutes within an interquartile range of 61 to 167 minutes. Across all tiles, the differences were skewed to the left and our travel time estimates were shorter than those reported by the Google API in 72% of the tiles. The median difference was −13.7 minutes within an interquartile range of −35.5 to 2.0 minutes while the absolute difference was 30 minutes or less for 60% of the tiles and 60 minutes or less for 80% of the tiles. The median percentage difference was −16.9% within an interquartile range of −30.6% to 2.7% while the absolute percentage difference was 20% or less in 43% of the tiles and 40% or less in 80% of the tiles.

This process and results are included in the validation zip file.

Usage Notes The accessibility layers can be visualised and analysed in many Geographic Information Systems or remote sensing software such as QGIS, GRASS, ENVI, ERDAS or ArcMap, and also by statistical and modelling packages such as R or MATLAB. They can also be used in cloud-based tools for geospatial analysis such as Google Earth Engine.

The nine layers represent travel times to human settlements of different population ranges. Two or more layers can be combined into one layer by recording the minimum pixel value across the layers. For example, a map of travel time to the nearest settlement of 5,000 to 50,000 people could be generated by taking the minimum of the three layers that represent the travel time to settlements with populations between 5,000 and 10,000, 10,000 and 20,000 and, 20,000 and 50,000 people.

The accessibility layers also permit user-defined hierarchies that go beyond computing the minimum pixel value across layers. A user-defined complete hierarchy can be generated when the union of all categories adds up to the global population, and the intersection of any two categories is empty. Everything else is up to the user in terms of logical consistency with the problem at hand.

The accessibility layers are relative measures of the ease of access from a given location to the nearest target. While the validation demonstrates that they do correspond to typical journey times, they cannot be taken to represent actual travel times. Errors in the friction surface will be accumulated as part of the accumulative cost function and it is likely that locations that are further away from targets will have greater a divergence from a plausible travel time than those that are closer to the targets. Care should be taken when referring to travel time to the larger cities when the locations of interest are extremely remote, although they will still be plausible representations of relative accessibility. Furthermore, a key assumption of the model is that all journeys will use the fastest mode of transport and take the shortest path.

Multiplexed imaging technologies provide insights into complex tissue architectures. However, challenges arise due to software fragmentation with cumbersome data handoffs, inefficiencies in processing large images (8 to 40 gigabytes per image), and limited spatial analysis capabilities. To efficiently analyze multiplexed imaging data, we developed SPACEc, a scalable end-to-end Python solution, that handles image extraction, cell segmentation, and data preprocessing and incorporates machine-learning-enabled, multi-scaled, spatial analysis, operated through a user-friendly and interactive interface. The demonstration dataset was derived from a previous analysis and contains TMA cores from a human tonsil and tonsillitis sample that were acquired with the Akoya PhenocyclerFusion platform. The dataset can be used to test the workflow and establish it on a user’s system or to familiarize oneself with the pipeline. Methods Tissue samples: Tonsil cores were extracted from a larger multi-tumor tissue microarray (TMA), which included a total of 66 unique tissues (51 malignant and semi-malignant tissues, as well as 15 non-malignant tissues). Representative tissue regions were annotated on corresponding hematoxylin and eosin (H&E)-stained sections by a board-certified surgical pathologist (S.Z.). Annotations were used to generate the 66 cores each with cores of 1mm diameter. FFPE tissue blocks were retrieved from the tissue archives of the Institute of Pathology, University Medical Center Mainz, Germany, and the Department of Dermatology, University Medical Center Mainz, Germany. The multi-tumor-TMA block was sectioned at 3µm thickness onto SuperFrost Plus microscopy slides before being processed for CODEX multiplex imaging as previously described. CODEX multiplexed imaging and processing To run the CODEX machine, the slide was taken from the storage buffer and placed in PBS for 10 minutes to equilibrate. After drying the PBS with a tissue, a flow cell was sealed onto the tissue slide. The assembled slide and flow cell were then placed in a PhenoCycler Buffer made from 10X PhenoCycler Buffer & Additive for at least 10 minutes before starting the experiment. A 96-well reporter plate was prepared with each reporter corresponding to the correct barcoded antibody for each cycle, with up to 3 reporters per cycle per well. The fluorescence reporters were mixed with 1X PhenoCycler Buffer, Additive, nuclear-staining reagent, and assay reagent according to the manufacturer's instructions. With the reporter plate and assembled slide and flow cell placed into the CODEX machine, the automated multiplexed imaging experiment was initiated. Each imaging cycle included steps for reporter binding, imaging of three fluorescent channels, and reporter stripping to prepare for the next cycle and set of markers. This was repeated until all markers were imaged. After the experiment, a .qptiff image file containing individual antibody channels and the DAPI channel was obtained. Image stitching, drift compensation, deconvolution, and cycle concatenation are performed within the Akoya PhenoCycler software. The raw imaging data output (tiff, 377.442nm per pixel for 20x CODEX) is first examined with QuPath software (https://qupath.github.io/) for inspection of staining quality. Any markers that produce unexpected patterns or low signal-to-noise ratios should be excluded from the ensuing analysis. The qptiff files must be converted into tiff files for input into SPACEc. Data preprocessing includes image stitching, drift compensation, deconvolution, and cycle concatenation performed using the Akoya Phenocycler software. The raw imaging data (qptiff, 377.442 nm/pixel for 20x CODEX) files from the Akoya PhenoCycler technology were first examined with QuPath software (https://qupath.github.io/) to inspect staining qualities. Markers with untenable patterns or low signal-to-noise ratios were excluded from further analysis. A custom CODEX analysis pipeline was used to process all acquired CODEX data (scripts available upon request). The qptiff files were converted into tiff files for tissue detection (watershed algorithm) and cell segmentation.

Tree Canopy (TC) Assessment metrics for New York City. This dataset consists of TC metrics summarized to several different sets of geographic base layers. The metrics presented in this table are based on 2010 high resolution land cover dataset. The TC Assessment is a top-down approach to analyzing the forest. Its purpose is to integrate high resolution land cover data with other GIS datasets to produce a set of detailed metrics on the forest that allow decision makers to know how much tree canopy currently exists (termed Existing TC) and amount of land where is it biophysically feasible to establish tree canopy on (termed Possible TC). Existing TC is determined by extracting all features classified as tree canopy from a high resolution land cover dataset. Possible TC is determined by identifying land where canopy could possibly exist. Possible TC in a GIS context is determined by overlaying high resolution land cover with cadastral and planimetric datasets to include building polygons and road polygons. Possible TC is queried out from this overlay and consists of all land that was not existing canopy, not water, not a building, and not a road. Possible TC is further divided into two subcategories: Possible-impervious and Possible-vegetation. Possible-impervious consists of all impervious land that, through modification, could support tree canopy. Examples of such features are parking lots, driveways (through overhanging coverage) and playgrounds. Possible-vegetation consists of all land that is low-lying vegetation, primarily grass or shrubs, which could conceivably be converted to support tree canopy. Examples of such features include residential lawns and playing fields. TC metrics do not serve to address the issues of where it is socially desirable or financially feasible to plant trees. Rather, the TC metrics serve as the basis for beginning to form answers to these questions. TC metrics are presented in the attribute table as both absolute area (in map units) and relative area (percentage of land area) per parcel. For example, an Existing TC Area (TC_E_A) value of 13,677 and an Existing TC Percentage (TC_E_P) of 21.8 indicate that for the parcel in question the area of Existing TC is 13,677 (in map units) and 21.8% of that feature is tree canopy. This assessment was completed by the University of Vermont's Spatial Analysis Laboratory with funding from National Urban and Community Forestry Advisory Council (NUCFAC) and the National Science Fundation (NSF) and in cooperation with the USDA Forest Service's Northern Research Station. The TC Assessment protocols were developed by the USDA Forest Service's Northern Research Station and the University of Vermont's Spatial Analysis Laboratory in collaboration with the Maryland Department of Natural Resources. TC assessments have been conducted for numerous communities throughout the U.S. where the results have been instrumental in helping to establishing TC goals.

The vector grid system provides a spatial and statistical infrastructure that allows the integration of environmental and socio-economic data. Its exploitation allows the crossing of different spatial data within the same grid units. Project results obtained using this grid system can be more easily linked. This grid system forms the geographic and statistical infrastructure of the Southern Quebec Land Accounts of the Institute of Statistics of Quebec (ISQ). It forms the geospatial and statistical context for the development of ecosystem accounting in Quebec. **In order to improve the vector grid system and the Land Accounts of Southern Quebec and to better anticipate the future needs of users, we would like to be informed of their use (field of application, objectives of use, territory, association with other products, etc.). You can write to us at maxime.keith@stat.gouv.qc.ca **. This grid system allows the spatial integration of various data relating, for example, to human populations, the economy or the characteristics of land. The ISQ wishes to encourage the use of this system in projects that require the integration of several data sources, the analysis of this data at different spatial scales and the monitoring of this data over time. The fixed geographic references of the grids simplify the compilation of statistics according to different territorial divisions and facilitate the monitoring of changes over time. In particular, the grid system promotes the consistency of data at the provincial level. The spatial intersection of the grid and the spatial data layer to be integrated makes it possible to transfer the information underlying the layer within each cell of the grid. In the case of the Southern Quebec Land Accounts, the spatial intersection of the grid and each of the three land cover layers (1990s, 2000s and 2010s) made it possible to report the dominant coverage within each grid cell. The set of matrix files of Southern Quebec Land Accounts is the result of this intersection. **Characteristics: ** The product includes two vector grids: one formed of cells of 1 km² (or 1,000 m on a side), which covers all of Quebec, and another of 2,500 m² cells (or 50 m on a side, or a quarter of a hectare), which fits perfectly into the first and covers Quebec territory located south of the 52nd parallel. Note that the nomenclature of this system, designed according to a Cartesian plan, was developed so that it was possible to integrate cells with finer resolutions (up to 5 meters on a side). In its 2024 update, the 50 m grid system is divided into 331 parts with a side of 50 km in order to limit the number of cells per part of the grid to millions and thus facilitate geospatial processing. This grid includes a total of approximately 350 million cells or 875,000 km2. It is backwards compatible with the 50m grid broadcast by the ISQ in 2018 (spatial structure and unique identifiers are identical, only the fragmentation is different). **Attribute information for 50 m cells: ** * ID_m50: unique code of the cell; * CO_MUN_2022: geographic code of the municipality of January 2022; * CERQ_NV2: code of the natural region of the ecological reference framework of Quebec; * CL_COUV_T50: unique code of the cell; * CL_COUV_T00, CL_COUV_T01: codes for coverage classes Terrestrial maps from the years 1990, 2000 and 2010. Note: the 2000s are covered by two land cover maps: CL_COUV_T01A and CL_COUV_T01b. The first inventories land cover prior to reassessment using the 2010s map, while the second shows land cover after this reassessment process. **Complementary entity classes: ** * Index_grille50m: index of the parts of the grid; * Decoupage_mun_01_2022: division of municipalities; * Decoupage_MRC_01_2022: division of geographical MRCs; * Decoupage_RA_01_2022: division of administrative regions. Source: System on administrative divisions [SDA] of the Ministry of Natural Resources and Forests [MRNF], January 2022, allows statistical compilations to be carried out according to administrative divisions hierarchically superior to municipalities. * Decoupage_CERQ_NV2_2018: division of level 2 of the CERQ, natural regions. Source: Ministry of the Environment, the Fight against Climate Change, Wildlife and Parks [MELCCFP]. Geospatial processes delivered with the grid (only with the FGDB data set) : * ArcGIS ModelBuilder allowing the spatial intersection and the selection of the dominant value of the geographic layer to populate the grid; * ModelBuilder allowing the statistical compilation of results according to various divisions. Additional information on the grid in the report Southern Quebec Land Accounts published in October 2018 (p. 46). View the results of the Southern Quebec Land Accounts on the interactive map of the Institut de la Statistique du Québec.**This third party metadata element was translated using an automated translation tool (Amazon Translate).**

Australia's Land Borders is a product within the Foundation Spatial Data Framework (FSDF) suite of datasets. It is endorsed by the ANZLIC - the Spatial Information Council and the Intergovernmental Committee on Surveying and Mapping (ICSM) as a nationally consistent and topologically correct representation of the land borders published by the Australian states and territories.

The purpose of this product is to provide: (i) a building block which enables development of other national datasets; (ii) integration with other geospatial frameworks in support of data analysis; and (iii) visualisation of these borders as cartographic depiction on a map. Although this dataset depicts land borders, it is not nor does it suggests to be a legal definition of these borders. Therefore it cannot and must not be used for those use-cases pertaining to legal context.

This product is constructed by Geoscience Australia (GA), on behalf of the ICSM, from authoritative open data published by the land mapping agencies in their respective Australian state and territory jurisdictions. Construction of a nationally consistent dataset required harmonisation and mediation of data issues at abutting land borders. In order to make informed and consistent determinations, other datasets were used as visual aid in determining which elements of published jurisdictional data to promote into the national product. These datasets include, but are not restricted to: (i) PSMA Australia's commercial products such as the cadastral (property) boundaries (CadLite) and Geocoded National Address File (GNAF); (ii) Esri's World Imagery and Imagery with Labels base maps; and (iii) Geoscience Australia's GEODATA TOPO 250K Series 3. Where practical, Land Borders do not cross cadastral boundaries and are logically consistent with addressing data in GNAF.

It is important to reaffirm that although third-party commercial datasets are used for validation, which is within remit of the licence agreement between PSMA and GA, no commercially licenced data has been promoted into the product. Australian Land Borders are constructed exclusively from published open data originating from state, territory and federal agencies.

This foundation dataset consists of edges (polylines) representing mediated segments of state and/or territory borders, connected at the nodes and terminated at the coastline defined as the Mean High Water Mark (MHWM) tidal boundary. These polylines are attributed to convey information about provenance of the source. It is envisaged that land borders will be topologically interoperable with the future national coastline dataset/s, currently being built through the ICSM coastline capture collaboration program. Topological interoperability will enable closure of land mass polygon, permitting spatial analysis operations such as vector overly, intersect, or raster map algebra. In addition to polylines, the product incorporates a number of well-known survey-monumented corners which have historical and cultural significance associated with the place name.

This foundation dataset is constructed from the best-available data, as published by relevant custodian in state and territory jurisdiction. It should be noted that some custodians - in particular the Northern Territory and New South Wales - have opted out or to rely on data from abutting jurisdiction as an agreed portrayal of their border. Accuracy and precision of land borders as depicted by spatial objects (features) may vary according to custodian specifications, although there is topological coherence across all the objects within this integrated product. The guaranteed minimum nominal scale for all use-cases, applying to complete spatial coverage of this product, is 1:25 000. In some areas the accuracy is much better and maybe approaching cadastre survey specification, however, this is an artefact of data assembly from disparate sources, rather than the product design. As the principle, no data was generalised or spatially degraded in the process of constructing this product.

Some use-cases for this product are: general digital and web map-making applications; a reference dataset to use for cartographic generalisation for a smaller-scale map applications; constraining geometric objects for revision and updates to the Mesh Blocks, the building blocks for the larger regions of the Australian Statistical Geography Standard (ASGS) framework; rapid resolution of cross-border data issues to enable construction and visual display of a common operating picture, etc.

This foundation dataset will be maintained at irregular intervals, for example if a state or territory jurisdiction decides to publish or republish their land borders. If there is a new version of this dataset, past version will be archived and information about the changes will be made available in the change log.

This dataset contains the data processed to demonstrate the multi-source spatial data integration methodology proposed in the paper "Multisource spatial data integration for use cases applications".

It contains:

- the building footprint extracted from the IFC model of a newly designed building in WKT format, by using the GeoBIM_Tool (https://github.com/twut/GEOBIM_Tool);

- the extrusion of the footprint until the measured height measured with the same GeoBIM_Tool;

- a portion of the Rotterdam 3D city model generated with 3dfier and available at https://3d.bk.tudelft.nl/opendata/3dfier/, converted in CityJSON with the citygml-tools (https://www.cityjson.org/tutorials/conversion/), developed to convert data between CityGML and CityJSON.

A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of Stipa grandis in grazed and ungrazed S. grandis communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of S. grandis by using the pair correlation function g(r) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of S. grandis were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.

Methods 1. Data collection using digital photographs and GIS

A flat 5 m x 5 m sampling block was chosen in a study grassland community and divided with bamboo chopsticks into 100 sub-blocks of 50 cm x 50 cm (Fig. 1). A digital camera was then mounted to a telescoping stake and positioned in the center of each sub-block to photograph vegetation within a 0.25 m2 area. Pictures were taken 1.75 m above the ground at an approximate downward angle of 90° (Fig. 2). Automatic camera settings were used for focus, lighting and shutter speed. After photographing the plot as a whole, photographs were taken of each individual plant in each sub-block. In order to identify each individual plant from the digital images, each plant was uniquely marked before the pictures were taken (Fig. 2 B).

Digital images were imported into a computer as JPEG files, and the position of each plant in the pictures was determined using GIS. This involved four steps: 1) A reference frame (Fig. 3) was established using R2V software to designate control points, or the four vertexes of each sub-block (Appendix S1), so that all plants in each sub-block were within the same reference frame. The parallax and optical distortion in the raster images was then geometrically corrected based on these selected control points; 2) Maps, or layers in GIS terminology, were set up for each species as PROJECT files (Appendix S2), and all individuals in each sub-block were digitized using R2V software (Appendix S3). For accuracy, the digitization of plant individual locations was performed manually; 3) Each plant species layer was exported from a PROJECT file to a SHAPE file in R2V software (Appendix S4); 4) Finally each species layer was opened in Arc GIS software in the SHAPE file format, and attribute data from each species layer was exported into Arc GIS to obtain the precise coordinates for each species. This last phase involved four steps of its own, from adding the data (Appendix S5), to opening the attribute table (Appendix S6), to adding new x and y coordinate fields (Appendix S7) and to obtaining the x and y coordinates and filling in the new fields (Appendix S8).

1. Data reliability assessment

To determine the accuracy of our new method, we measured the individual locations of Leymus chinensis, a perennial rhizome grass, in representative community blocks 5 m x 5 m in size in typical steppe habitat in the Inner Mongolia Autonomous Region of China in July 2010 (Fig. 4 A). As our standard for comparison, we used a ruler to measure the individual coordinates of L. chinensis. We tested for significant differences between (1) the coordinates of L. chinensis, as measured with our new method and with the ruler, and (2) the pair correlation function g of L. chinensis, as measured with our new method and with the ruler (see section 3.2 Data Analysis). If (1) the coordinates of L. chinensis, as measured with our new method and with the ruler, and (2) the pair correlation function g of L. chinensis, as measured with our new method and with the ruler, did not differ significantly, then we could conclude that our new method of measuring the coordinates of L. chinensis was reliable.

We compared the results using a t-test (Table 1). We found no significant differences in either (1) the coordinates of L. chinensis or (2) the pair correlation function g of L. chinensis. Further, we compared the pattern characteristics of L. chinensis when measured by our new method against the ruler measurements using a null model. We found that the two pattern characteristics of L. chinensis did not differ significantly based on the homogenous Poisson process or complete spatial randomness (Fig. 4 B). Thus, we concluded that the data obtained using our new method was reliable enough to perform point pattern analysis with a null model in grassland communities.