eReefs visualisation suite - pre rendered animations and maps (AIMS, Source: CSIRO)

This record describes the visualisations made available through the AIMS eReefs visualisation platform (https://ereefs.aims.gov.au/). It is a collection of 88,000 pre-rendered animations and static maps of selected combinations of model variables from the eReefs hydrodynamic and biogeochemical models. Each visualisation product shows multiple related variables together to assist in understanding the dynamics that drive the marine environmental conditions on the Great Barrier Reef and Coral Sea. Visualisations are provided from fine temporal scales through to long term averages. Each visualisation product provides quick access to the full time series for the underlying model outputs. Background and rationale: The eReefs models capture the dynamics of the waters of the Great Barrier Reef (GBR), including physical parameters such as temperature, salinity, currents and tides, along with many biogeochemical parameters that characterise the transport of sediment and nutrients. These parameters are highly interconnected - for example, wind drives currents, which move water masses that in turn influence nutrient dynamics. Viewing individual variables at individual time steps makes it very hard to understand these dynamics. To enable users to better understand the ocean dynamics represented by eReefs we have developed a large catalogue of pre-rendered visualisation products. Each visualisation product clusters a group of related model variables to showcase and highlight a set of dynamics. Each visualisation product is accompanied by an explanatory page that describes the relationships between the variables and what they show. Each visualisation product is provided with a range of temporal aggregations (hourly, daily, monthly, annual, and the full time series average, referred to as 'overall') and spatial zoom levels. Hourly and daily visualisations are presented as animations using pre-rendered MP4 videos. Monthly, annual and overall visualisations are provided as static pre-rendered map images. Each visualisation set is made available using a fixed set of bounding boxes at different zoom levels. Zoom levels are organised into four tiers, starting with a top level showing the whole GBR (approximately 3000 km) and the lowest level showing sections of the coast (approximately 300 km). The placement of the zoom level regions was chosen to follow the coastline and to focus on locations that stakeholders are most likely to use directly. The finest zoom level does not cover the full coastline, but provides coverage of key locations. A collection of 21 zoom levels was chosen to allow users to get a clear view of the data, while minimising the total number of zoom locations. Typically GBR4 products provide visualisations for the top three zoom levels, while GBR1 products provide all four zoom levels so that the finer model detail is easily visible. How were the visualisations made? All visualisation products are rendered using a custom Java tool ('ncanimate') (https://github.com/open-AIMS/ereefs-ncanimate2). This software was developed to allow configurable visualisation of eReefs data and to fit into a near real time production environment. Java was used for its rendering speed. Each product is configured as a set of map panels that display a set of base reference layers (such as land, cities, reef boundaries) (Lawrey, 2023) with data layers. Colour-vision-deficiency compatible colour ramps were used in each visualisation (https://github.com/eatlas/GBR_AIMS_eReefs-basemap/tree/main/colour-ramps). Most of the colour ramps represent a rainbow from blue to red, excluding green. The scale (minimum and maximum displayed values) and the transition point between blue and red in the colour ramp were tailored for each visualisation variable. The value range was chosen to allow broad-scale patterns to be visible. The threshold values were chosen to align with ecologically relevant transition points where these could be established. For example, for temperature the transition from cool colours (blue) to warm colours (red) was chosen to align with the temperature where coral reefs, on average, start to experience thermal stress. Each visualisation product draws from one or more input NetCDF data sources stored on S3. Each output visualisation is saved to S3. ncanimate performs a cross-check between the set of visualisations already rendered and the set of products that could be generated from the input data. It renders any missing visualisations. This processing was designed to run in near real time and to be robust to modifications to the input data files. Changes to the input source data invalidate any previously generated visualisations, triggering the visualisations to be regenerated. This guarantees that the visualisations are always up to date with the input data. What do the visualisations show? In all cases except for hydrodynamic hourly animations, the data behind the visualisation is produced from regridded, aggregate eReefs data products (Lawrey et al., 2025: https://doi.org/10.26274/Y74K-T032). These datasets are derived from the eReefs model data 'simple' files provided from the NCI THREDDS data service. The original curvilinear grid data is interpolated onto a rectangular grid and the values averaged over the selected time aggregation period. See Lawrey et al., 2025, for technical details. This averaging removes high frequency signals from the data resulting in the loss of tides and daily temperature fluctuations. These changes may or may not be suitable for the analysis being performed. The effect of averaging on ocean currents In the temp-wind-salt-current and current-multi-depth products the eastward and northward components of the current vector (u, v) were averaged separately. This removes in most of the tidal signal. Tides typically drive currents back and forth with very little net flow. Daily averaging cancels out most of this tidal signal. For monthly averages there is no significant tidal signal remaining, and the visualisations show net flow only. Where understanding the current magnitude is important the 'GBR1 - Current magnitude average' visualisation product shows the average strength of the current. No explicit process was used to remove tidal-period signals. This happens as a by-product of temporal averaging. The daily averages still contain some tidal effects, however, for monthly and longer periods the tidal effects are almost completely absent. This makes the monthly average current visualisations well suited for studying the net current flows without the distraction of tides. Visualisation depth choices: The eReefs models provide 47 depth layers for the GBR4 models and 44 depth layers for the GBR1 model. It is impractical to pre-render visualisations for all these depths due to the processing and storage costs, so we focus on depth levels that are likely to be most useful for the intended purpose of each visualisation product. Most visualisations focus on near-surface waters because these align closely with remote sensing products and shallow water reef monitoring. We avoid the topmost layers (height of 1.5 m to -0.5 m) as the tides pass through these layers. Where these layers are 'dry' due to low tide, the model output presents data from lower depths to ensure that surface conditions are shown rather than null values. This process can lead to slight imperfections, so we avoid it by focusing visualisations only on depth levels that remain below the surface. The GBR1 and GBR4 models have a different number of depth layers, resulting in slightly different depth levels being available. For products where we wish to show different depths we try to align GBR1 and GBR4 depth choices as closely as possible. Product descriptions: The following is a short overview of each visualisation product category. These summaries combine similar products for multiple eReefs models. Temperature, wind, salinity and current (Product: temp-wind-salt-current) This product aims to capture the key hydrodynamic processes in one visualisation. Wind is a key causal input driver for the eReefs hydrodynamic models. This visualisation product allows the movement of cyclones to be viewed alongside their effects on the waters, including shifting the direction and strength of the ocean currents and the cooling of the water temperature by mixing and shading. The salinity variable shows the extent and movement of flood plumes, which are largely driven by the currents and wind. Temperature at multiple depths (Product: temp-multi-depth, GBR1 2.35m, 18m and 49m depths, GBR4 1.5m, 18m and 49m): This product aims to show the temperature at depth. During marine heatwaves, the depth of the hot water varies depending on the level of mixing. Low wind conditions can lead to thermal stratification and higher surface temperatures. High wind mixes the heat to greater depths. This product is useful for studying the depth to which coral reefs might be affected by marine heat waves. Current at multiple depths (Product: current-multi-depth, GBR1 2.35m, 18m and 103m depths, GBR4 1.5m, 18m and 103m): This product aims to help explain whether surface waters are moving in the same direction as deeper currents. Salinity at 2.35m, 5.35m and 18m depth (Product: salt-multi-depth) Freshwater from flood plumes tends to float on the surface. How deep the freshwater extends depends on the amount of freshwater coming from the rivers and the amount of mixing from waves and wind. Inshore reefs and seagrass meadows can be affected by freshwater from flood plumes. Coral can bleach from freshwater stress. This visualisation is intended to help determine the depth to which flood waters might affect inshore reefs. This visualisation is only available for the GBR1 model. We considered the 4 km grid (GBR4) to be too low in resolution to show the close-in flood plumes. Fresh water exposure at 2.35m (Product: fresh-water-exposure) This product aims to estimate the level of freshwater exposure for inshore coral reefs. This is based on accumulating salinity levels below a given threshold over time. This calculation is similar in concept to the mathematics of Degree Heating Weeks, but is a measure of PSU-days relative to a PSU threshold value. More details for these calculations is provided in the article on the product page. Current magnitude average at 2.35m (Product: current-magnitude-average) This product shows the average strength of the surface currents. This product was developed to help understand where strong currents occur, regardless of the direction. This can be used to help with survey planning to avoid areas with high average currents that may be too dangerous to work in. The monthly and annual products are most useful because they provide an indication of typical conditions. The annual average visualisation ('Yearly' time step tab) shows that the currents are strongest on the outer edge of the GBR shelf due to the East Australian Current, and in the southern GBR and Torres Strait where tidal currents are strong. Temperature range at surface (Product: temp-range, GBR1: 2.35m, GBR4: 1.5m) This product was developed to assist in finding reefs that are naturally exposed to high temperature ranges, as these might contain corals that are more resilient. The daily time-step visualisation shows the daily minimum, maximum and daily temperature range. The monthly visualiastions show the monthly minimum, the mean of the daily minima, the monthly maximum, the mean of the daily maxima and the mean daily temperature for the month. Flood plume extents for major rivers on GBR based on modelled river tracers (Product: river-tracer) This product visualises the flood plumes produced by the 15 largest rivers on the Queensland eastern coastline. The flood water is attributed to the source river using a tracer within the eReefs hydrodynamic model. This allows the contribution of each river to be determined, helping to understand marine foot print of each catchment. The visualisations present the salinity as an indicator of the total amount of freshwater in the system. Three map panels are then used to present the plumes from five catchments. The rivers shown in each panel were chosen to minimise the typical amount of overlap between the flood plumes. Colours for each river were chosen to work for colour vision deficiency and to allow robust reading of the percentage of river water in the sea water, even when two river plumes overlap. The concentration levels (percent river water in seawater) to show in the visualisation were chosen to be ecologically relevant. The lowest threshold displayed was calibrated to closely align with the visible edge of a flood plume in Sentinel-2 imagery. This threshold represents where there is typically a reduction in light available to benthic organisms. It should be noted that the river tracer only tracks the water and does not indicate the amount of suspended sediment or nutrients. Comparing eReefs (GBR4 [v2.0,v4.0] temperature, current) to IMOS satellite temperature and ocean current These products compare the surface temperatures and currents against the satellite-derived sea surface temperature (IMOS - SRS - SST - L3S) and IMOS - OceanCurrent. These are intended to help identify the strengths and weakness of the eReefs modelling. The comparison data were sourced from Australia’s Integrated Marine Observing System (IMOS) – IMOS is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS). Water chemistry Total alkalinity, PH and aragonite saturation state (GBR4 BGC v3.1 baseline) (Product: alk_ph_omega-ar) This shows the key BGC variables that capture the carbonate chemistry. These are useful for understanding areas that might be more affected by ocean acidification. The eReefs models are not intended to show trends in ocean acidification. They can however show spatial differences, indicating that inshore areas from Broad Sound through to Hinchinbrook and from Cooktown to the tip of Cape York have a lower PH than more offshore waters. They also show that PH is typically lower in summer months. Dissolved inorganic nitrogen, nitrate & ammonia (Product: din_no3_nh4), Dissolved oxygen & oxygen saturation percentage (Product: oxygen_oxy-sat), Dissolved Inorganic (Carbon, Nitrogen & Phosphorus) (Product: din_dip_dic), Dissolved Organic (Carbon, Nitrogen & Phosphorus) (Product: dor-c_dor-n_dor-p), Particulate inorganic phosphorus & particulate inorganic (Product: pip_pip-sed) These products focus on presenting water chemistry processes. These are based on the GBR_H2p0_B3p1_Cq3b_Dhnd model, which corresponds to the baseline scenario of v3.1 of the BGC model that is driven by the v2.0 hydrodynamic model. The baseline corresponds to weather and river flows from 2011 to 2019, but nutrients and sediment loads modelled by the input SOURCE catchment model based on land practices from 2019 - that is, the land practice changes are not time varying over the model run period. Coral symbiont (nitrogen & chlorophyll) & coral host nitrogen (GBR4 BGC v3.1 baseline) (Product: cs-n_cs-chl_ch-n) These visualisations show model results of the uptake of nitrogen by corals, showing how much is contained in the coral tissue (coral host nitrogen) and how much is contained in the symbiotic zooxanthellae algae that grow inside the coral (coral symbiont). These visualisations show some of the internal dynamics of the coral modelling performed within the BGC model. Nitrogen (macroalgae, seagrass zostera, seagrass halophila & deep seagrass) (GBR4 BGC baseline) (Product: ma-n_sg-n_sgh-n_sgd-n) These visualisations show the amount of modelled seagrass and macroalgae represented as the amount of nitrogen contained in their biomass in each modelled pixel. Seagrass and macroalgae play a key role in the nitrogen cycle of inshore areas. When they grow they take up nitrogen, phosphorus and carbon from the water into their leaf and root structures. When they die they break down and release these nutrient stores back into the water column. These visualisations are not intended to be an accurate prediction of the state of seagrass as they are largely unvalidated. They are intended to ensure the model reasonably recycles nutrients appropriately. GBR4 BGC Scenario Comparison - Dissolved inorganic nitrogen (DIN) (Product: din), GBR4 BGC Scenario Comparison - Total Chlorophyll (Product: chl-a-sum), GBR4 BGC Scenario Comparison - Secchi depth (Product: secchi), GBR4 BGC Scenario Comparison - Total suspended solids (Product: efi), GBR4 BGC Scenario Comparison - Light intensity above seagrass (Product: epipar-sg) This series of visualisations show the difference between the baseline BGC simulation, that represents current conditions, and two hypothetical scenarios. The pre-industrial scenario is intended to be an estimate of the nutrients and sediments from rivers under pre-industrial land conditions, using modern weather so that it can be compared to the baseline. This is based on SOURCE catchment modelling under the Reef 2050 Water Quality Improvement Plan. Comparing the baseline to the pre-industrial conditions provides an indication of the anthropogenic changes to water conditions and the spatial footprint of change. Confidence in the pre-industrial land modelling is low. The 'WQIP-Targets' panel shows the effects of the planned Water Quality Improvement Plan targets if they are achieved. These visualisations show the baseline scenario parameter, along with the pre-industrial minus the baseline senario, the WQIP targets scenario minus the baseline scenario and the percentage of river water in seawater. The river water percentage is provided as a reference for the extent of flood plumes. How are the visualisations organised? There are over 88,000 combinations of visualisations (product combinations x temporal aggregation periods x time steps x depths x zoom levels) available. These are organised into product pages with a user interface that allows the user to select between combinations of the temporal parameters (aggregation and time step) and zoom locations. Each product page shows all combinations of visualisation for the same set of input variables for a given model. All visualisation products are stored in an AWS S3 bucket. The user interface on the product page queries the backend database for details of all the visualisation combinations available (times, depths, zoom levels) for a given visualisation product, allowing it to determine the URLs on S3. The visualisation products are made available via a website (https://ereefs.aims.gov.au/) that was created using Quarto to generate static HTML pages hosted on GitHub pages. This website contains additional article content written about each visualisation product. The source code for this website is available on GitHub (https://github.com/open-AIMS/ereefs-visualisation-portal-static-website). What are the URLs of the visualisations? Each combination of product, depth, temporal aggregation, time step and zoom level are URL addressable, allowing precise sharing of specific visualisations. This uses the following URL pattern: https://ereefs.aims.gov.au/{model}/{product}/#frame={time_aggregation};region={named_zoom_location};elevation={depth};year={YYYY};month={month_number}. Each parameter has a default value appropriate for that product, in which case the parameter can be dropped if it is unknown. model: gbr1, gbr4_v2, gbr4_v4, gbr4/bgc/baseline, gbr4/bgc/scenarios product: - gbr1: temp-wind-salt-current, temp-multi-depth, current-multi-depth, salt-multi-depth, fresh-water-exposure, current-magnitude-average, temp-range, river-tracers. - gbr4_v2, gbr4_v4: temp-wind-salt-current, temp-multi-depth, current-multi-depth, temp-range, imos-vs-ereefs - gbr4/bgc/baseline: alk_ph_omega-ar, din_no3_nh4, oxygen_oxy-sat, din_dip_dic, dor-c_dor-n_dor-p, pip_pip-sed, chl-a-sum_din_efi, efi_dust_mud-carbonate_mud-mineral, secchi_kd-490_epipar-sg, true-colour, cs-n_cs-chl_ch-n, ma-n_sg-n_sgh-n_sgd-n - gbr4/bgc/scenarios: din, chl-a-sum, secchi, efi, epipar-sg frame: - gbr1, gbr4_v2, gbr4_v4: Hourly, Daily, Monthly, Yearly, Overall - gbr4/bgc/scenarios, gbr4/bgc/baseline: Daily, Monthly - region: - zoom level 1: queensland-1 - zoom level 2: north-2, central-2, south-2 - zoom level 3: torres-strait-3, princess-charolett-bay-3, lizard-island-3, cairns-3, townsville-3, whitsundays-3, broad-sound-3, fitzroy-3, hervey-bay-3, brisbane-3 - zoom level 4: lizard-island-4 (Cape Melville to 30 km south Cooktown), cairns-4 (60 km north Daintree to Innisfail), townsville-4 (30 km south Ingham to Burdekin river mouth), whitsundays-4 (Just south Bowen to Mackay), keppels-4 (50 km south Gladstone to 80km north Yepoon), heron-4 (Capricorn bunker group of reefs), moreton-bay-4 (Gold coast to just north of Sunshine Coast) depth: The following is the list of products that support the depth URL parameter. - temp-wind-salt-current GBR4: -1.5m, -8.8m, GBR1: -2.4m, -9.0m Product list and number of visualisation combinations: Each product page collates together all the variations of each visualisation across time, depth, and zoom levels dimensions. This is a list of all the product pages and the number of visualisation combinations accessible. GBR1 visualisations: - Temperature, wind, salinity and current (10163 combinations) - Temperature at 2.35m, 18m and 49m depth (5081 combinations) - Current at 2.35m, 18m and 103m depth (5081 combinations) - Salinity at 2.35m, 5.35m and 18m depth (4619 combinations) - Fresh water exposure at 2.35m (1427 combinations) - Current magnitude average at 2.35m (2771 combinations) - Temperature range at 2.35m (2540 combinations) - Flood plume extents for major rivers on GBR based on modelled river tracers (153 combinations) GBR4 Hydro v4 visualisations: - Temperature, wind, salinity and current (8987 combinations) - Temperature at 1.5m, 18m and 49m depth (4493 combinations) - Current at 1.5m, 18m and 103m depth (4493 combinations) - Temperature range at 1.5m (2239 combinations) - Comparing eReefs (GBR4 temperature, current) to IMOS satellite temperature and ocean current (12 combinations) GBR4 Hydro v2 visualisations - Temperature, wind, salinity and current (9883 combinations) - Temperature at 1.5m, 18m and 49m depth (4941 combinations) - Current at 1.5m, 18m and 103m depth (4941 combinations) - Temperature range at 1.5m (2463 combinations) - Comparing eReefs (GBR4 temperature, current) to IMOS satellite temperature and ocean current (14 combinations) BioGeoChemical Model (4 km) Water chemistry - Total alkalinity, PH & Aragonite saturation state (483 combinations) - Dissolved inorganic nitrogen, nitrate & ammonia (483 combinations) - Dissolved oxygen & oxygen saturation percentage (483 combinations) - Dissolved Inorganic (Carbon, Nitrogen & Phosphorus) (483 combinations) - Dissolved Organic (Carbon, Nitrogen & Phosphorus) (483 combinations) - Particulate inorganic phosphorus & particulate inorganic (483 combinations) Water quality measures - Total chlorophyll, dissolved inorganic nitrogen & total suspended solids (483 combinations) - Total Suspended Solids, dust, mud carbonate & mud mineral (483 combinations) - Secchi depth, vertical attenuation at 490nm & light intensity above seagrass (967 combinations) - Simulated true colour (39 combinations) Macroalgae, seagrass and coral - Coral symbiont (nitrogen & chlorophyll) & coral host nitrogen (483 combinations) - Nitrogen (macroalgae, seagrass zostera, seagrass halophila & deep seagrass) (483 combinations) Catchment scenarios comparison - Disolved inorganic nitrogen (1553 combinations) - Total Chlorophyll (1553 combinations) - Secchi depth (1553 combinations) - Total suspended solids (1553 combinations) - Light intensity above seagrass (1553 combinations)