Picturing Research at Biosphere 2

What will happen to rainforests as global temperatures rise with climate change? Biosphere 2 has the hottest rainforest on the planet—there’s a huge temperature change from the shaded forest floor to the top of the tree canopy under the Arizona sun. That makes it the ideal place for postdoctoral researcher Justin Bestily to study resilience in plant life.

The trick is to translate Justin’s data, the graphs and charts of the scientific instruments into information that the public can grasp. 

Justin is looking at water use in plants using sap flow sensors on trees. What the sensors actually measure is the water flow as it passes on its way from the soil, to the roots, through the trunk, to the leaves. Because of the relationship between water use and carbon dioxide in trees, this can give indications of tree health and growth rates. 

The Wonder Studio is Biosphere 2’s initiative, funded by a Provost Investment Fund grant,  to increase the interdisciplinary work and make their science more accessible to the community. Recently team lead Aaron Bugaj guided MrBeast on a tour. Science visualizations are used for visitors to the site to understand the research happening there, and might be used in stories in the media. 

UITS Research Technologies’ Devin Bayly often assists Aaron and the Biosphere 2 researchers with specialized software in his role as a data visualization consultant. Devin started meeting with Justin's team every Friday to work on two visualizations representing his work the rainforest—one a 3D representation of the cacao tree on site in the rainforest and one a cinematic visualization demonstrating the water flow through the tree based on the data. 

To recreate the 3D model of the tree in the rainforest, Aaron, Devin and Justin took 160 4K photos of the tree from all angles, encompassing the 20 ft.–tall tree. Devin leveraged the open source program NerfStudio to convert the collection of photos into a photorealistic 3D version of the space called a gaussian splat. This 3D model can be viewed from new perspectives not captured in the original image collection. Using this technique avoids the complex time consuming task of building 3D models like this cacao tree from scratch.  Some of this work took place in the UITS Data Center, and some on the Indiana University JetStream 2.

The movie of the water flow through the tree started from the data from the sensor. It initially looks like a standard pulse graph, similar to an electrocardiogram. Devin used Python and Blender to combine the sap flow sensor's point-in-time data with the 3D model to visualize how the flow might look throughout the tree. He explains, “We had the sensor data, we had photos of the plant, but when it comes to visualizing these things, sometimes traditional charts and time series charts don't preserve the context of the actual subject. What is the organism that this data belongs to? Bringing those together is the realm of cinematic visualization.” 

These outputs completed the first phase of Devin’s projects with Justin, with more to come. Devin is also hoping to build on the work of creating this model to apply to research done on other trees. He sees it as a prototype to help future tree health researchers get up and running faster at visualizing their data. This project also gave him templates for future projects. For example, this was the first project where he animated output from NerfStudio with Blender to create a video clip of the 3D re-creation. 

Visualization Consulting is often used to create images or movies used in examining research data or in scientific publications. But communication to the broader public is an important step in both educating the public and in promoting the important work that University of Arizona researchers are doing to understand our world.