Scientific Visualization

2026-06-08

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Ecological data has shape — in space, in time, in three dimensions. Movement is not a line on a map; it is a volume carved out of the air or the landscape. Terrain is not a colored grid; it is structure that determines where water flows, where animals can go, where fire will spread. A drone survey is not a mosaic; it is a textured surface you can move through.

Three-dimensional visualization makes that structure visible. These are examples from across the research program, built with R, Python, ParaView, and WebODM.

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Animal Movement in 3D Space

Movement kernel density estimation (MKDE) extended to three dimensions captures how animals actually use space — including altitude, thermals, and vertical habitat structure. Each probability surface represents where an individual spent its time, at what elevation, over what period.

3D MKDE for a California condor breeding pair over the Baja California landscape. Green and blue surfaces show the 95% and 50% utilization volumes for each bird. Computed with the mkde R package; visualized in ParaView. (Figure: Jeff A. Tracey)

3D MKDE probability surfaces with GPS locations shown as spheres, built from a minimal two-step movement path to illustrate how the density volume is constructed. (Figure: Jeff A. Tracey)

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Landscape Structure

Terrain rendered in three dimensions reveals drainage patterns, ridge lines, and topographic complexity that flat maps obscure. These visualizations combine digital elevation models with land cover data to show the landscape as animals and ecologists experience it.

3D digital elevation model with elevation color ramp. Low elevation in blue-purple; high elevation in red-orange. Built in R; visualized in ParaView. (Figure: Jeff A. Tracey)

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Drone-Derived Surface Models

Structure-from-motion photogrammetry from UAV imagery produces textured 3D surface models at centimeter resolution — enough to resolve individual shrubs, trails, and terrain features. This is the landscape at the scale an animal actually navigates.

Textured 3D surface model of Rancho Mission Canyon Open Space, San Diego. Built from Mavic 3M multispectral imagery processed in WebODM. The chaparral-covered hillside with trail is clearly resolved. (Model and figure: Jeff A. Tracey 2026)

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Coastal Bathymetry and Sea Level

Combining coastal terrain with seafloor bathymetry in a single 3D model reveals the underwater landscape adjacent to the shore — and what happens to it as sea levels rise. These visualizations were built from NOAA and USGS digital elevation data using Python and ParaView.

3D bathymetric visualization of the Southern California coast. The submarine canyon cutting through the continental shelf is La Jolla Canyon. (Figure: Jeff A. Tracey)

Sea level rise scenario for the San Diego coast and Mission Bay. Red markers indicate corners of Marine Protected Area (MPA) boundaries. The inland flooding of Mission Bay and surrounding lowlands is clearly visible. (Figure: Jeff A. Tracey)