Visualizing Island Biodiversity in 3D: A Geotour of Crete using iNaturalist Data

General
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The Geotour Interactive 3D Map for Crete has recently been updated to include a Biodiversity Explorer Module. By connecting directly with the iNaturalist database, the platform is designed to serve as a live tool for environmental monitoring and education, helping users visualize the relationship between terrain, human activity, and nature across the island.

Below is an overview of the implementation and how the data is visualized in a 3D environment.

Features and User Experience

The Biodiversity Explorer acts as a specialized “Mode” within the CesiumJS map. When active, the interface shifts focus to biological data analysis.

  • Category Filters: Users can narrow the view by selecting specific iconic taxa (Plants, Insects, Birds, Mammals, Reptiles, Amphibians, and Fungi).

  • Point Overlays: The 3D terrain utilizes a tiled overlay to indicate observation locations. These are color-coded by group (e.g., green for plants, blue for mammals) to display distribution patterns.

  • The Biodiversity Inspector: A dedicated panel displays live counters for Total Observations and Unique Species currently visible within the camera’s view.

Exploration by Observation Count

A “Discovery Slider” has been implemented to assist with species sorting:

  • High Observation Count: Sliding to the left displays species with the most recorded observations.

  • Low Observation Count: Sliding to the right filters for species with minimal recorded sightings. The species list updates automatically (with a 500ms debounce) as the slider is adjusted.

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Technical Implementation

The system is managed by an internal BiodiversityManager.js that handles the CesiumJS visuals and data requests.

1. Smart Data Loading (Dynamic Bounding Box) To maintain performance, data is requested only for the visible area. The system tracks camera movement via camera.moveEnd and calculates a bounding box to fetch information specific to the current view. Safety checks are in place to prevent API calls if the camera is outside valid coordinates.

2. Visuals and Pinning To reduce visual clutter on the 3D map, specific data points are highlighted using “Visual Halos.” When a species is selected from the list, up to 50 precise locations are fetched and marked with a Cesium billboard clamped to the ground (featuring a 40-meter radius yellow halo).

3. Data Sources (iNaturalist API v1) The module communicates with three specific endpoints for the Region of Crete:

  • Points Tiles Map (GET /v1/points/{z}/{x}/{y}.png): Renders the grid of color-coded points.

  • Species Statistics (GET /v1/observations/species_counts): Populates the side panel with species names and counts for the current view.

  • Observation Points (GET /v1/observations): Fetches precise coordinates for the “Halo” markers when a species is selected.

Interaction Users can select a species row to visualize specific locations on the map. A direct link is provided to the official iNaturalist taxon page for further scientific details. Exiting the mode clears all imagery layers and entity collections, returning the map to its standard state.

Link to the tool: https://www.geotour.gr/vt/3dmap/

Feedback on this visualization approach is welcome.

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