• Earth Science

Trezona Fossil Reconstruction

Situ Studio collaborated with Professor Adam Maloof of Princeton University's Department of Geosciences in a body of research suggesting that fossils unearthed in South Australia could be the oldest animal bodies ever discovered. Estimated at 640 million years old, these fossils would predate the earliest evidence of animal body forms in the current fossil record by at least 70 million years. Situ worked with Maloof to develop a system to both process and digitally reconstruct these fossils for morphogenetic analysis.


  • Professor Adam Maloof
    Dept. of Geosciences, Princeton University

Visualization procedure employed in the Trezona Fossil reconstruction project.

The video above depicts the digital imaging of the earliest animal fossil on earth - older than any other animal fossil by at least 70 million years, and most importantly, older than the Marinoan (second) ice age. For over a century, researchers have been struggling to overcome how to reveal such hidden structures, often embedded in a solid rock matrix. As such, with this paradigm shift in the understanding of early life, identified by Professor Adam Maloof of Princeton University’s Geosciences Department, also comes an extreme enhancement in fossil reconstruction technique, seen above, designed and engineered by Situ.   


In 2010, Professor Maloof was puzzled over oddly recurrent structures visible in cross sections taken from samples of the 640 million year old Trezona Formation in South Australia, an ancient stromatolite reef. Because these calcified structures were similar in density and solubility to their surrounding rock matrix, limestone, it was impossible for Maloof to use a modern X-ray based CT (computed tomography) scanning method, which relies on a density gradient, to reveal the enclosed structure. This predicament left the lab to interpret only two dimensional sections of what they suspected to be early fossils, seen below, in recurring wishbone, circle and anvil shapes.


Left: Anvil, wishbone and circular shapes found in fossils. Right: Fossil shown at human scale. Courtesy of Adam Maloof.

In order to produce a sequential view of these cross sections (serial sections) Maloof embarked on the labor intensive process of grinding away precisely 50.8 µm of sample at a time and subsequently desktop scanning the newly revealed layer. The lab spent two and a half weeks producing 500 sections of the fossil and surrounding matrix, amounting to less than one vertical inch of material, before collaborating with Situ in an attempt to visualize the three dimensional form infixed in rock, imaged below.


High resolution scan of Trezona Fossil cross section


Drawing on the toolkit of a design practice, Situ applied a host of design based software implicating a computer protocol to visually consolidate Maloof’s two dimensional data into a three dimensional form, creating a more efficient and less subjective approach to fossil reconstruction. The following is a summary of the workflow that was used to translate the sequential layers into a digital model.



Visualization Procedure (mouseover or click to view images)


1. Matlab script cross-correlates and precisely orients each section to create an aligned image stack


2. Adobe Photoshop applies a batch crop to zero-in on fossil of interest, while color correcting to homogenize color contrast between images *


3. Adobe Illustrator auto traces each image based off threshold red-green-blue values to generate vector outlines of fossil shapes *


4. Rhino realigns the vectors with respect to the z axis employing a low-pass filter algorithm *


5. The resulting 3D point cloud is converted to a triangulated mesh that can be analyzed for surface area, volume and porosity *


6. Blender creates a smooth 3D surface model, using the point cloud as scaffolding.

* run using Visual Basic script

To the excitement of Dr. Maloof and Situ, the morphology of the reconstructions indicate that the Trezona Formation fossils are of the earliest animals, or metazoans, on earth, predating all other known species by at least 70 million years. The fossils’ asymmetric topology riddled with entering and exiting interconnected tubular passages suggests the ancient form is a sponge-grade organism, and the only known animal to predate the Marinoan ice age - a paradigm shifting discovery predicted though never confirmed by evolutionary theory. Aiding this discovery, Situ’s method of digital reconstruction served to provide not only a 3D model of the embedded fossil, elucidating its animal morphology, but also quantitative information about the porosity, permeability, and other feature-related characteristics, unattainable using comparable techniques. See the Ted Talk below for a comprehensive overview of the project. Click on the image to the right to read the research article published in Nature Geoscience.



Left: TED talk on the Trezona Project. Right: Nature cover (link) featuring the Trezona Fossil reconstruction.


The laborious technique of producing serial sections by grinding away sequential layers of geological samples is not a new one, having tormented researchers for over a century. The two and a half weeks it took the Maloof lab to grind less than one inch of sample is simply too time-consuming for any laboratory to pursue on a regular basis, and must be reconsidered in order to continue such valuable research. Geologists and Paleontologists alike have been painstakingly pulverizing samples at least since 1904, when Professor W.J. Sollas of Oxford University published both plans for a grinding apparatus, shown below, and a method for manual fossil reconstruction, employing the use of thin wax layers, traced from section outlines then pressed together to create a three dimensional form. Illustrating this technique’s laborious nature, paleozoologist Erik Jarvik spent 25 years employing Sollas’ grinding and wax reconstruction methods in a detailed model, shown below, of the cranial bones found in Eusthenopteron foordi, an evolutionarily significant fish.




Top: early serial sectioning instruments. Bottom: wax reconstruction of Eusthenopteron cranial bones


Like Trezona, many other specimens are embedded in calcite, a material too similar in density to the fossil itself for X-ray or Synchrotron technologies to be effective. One such example is the metazoan fossil Namacalathus for which Situ created a 3D printed model for Cal Tech Professor John Grotzinger.  


3D printed model of Namacalathus (left) and digital model (right).


In order to modernize the process of serial sectioning without relying on a well defined density gradient, Situ continues to collaborate with Professor Maloof, and has received a grant from the National Science Foundation (NSF), to automate the procedure of physically attaining the ever important serial sections. Leveraging a professional knowledge of Computer Numerically Controlled (CNC) fabrication technology, Situ has automated the prohibitively time consuming process of producing and recording serial sections from geological samples. See the GIRI project page for more information on the machine.