Science Spotlight: Digital Atlas of Ancient Life

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The Paleontological Research Institution (PRI) was founded in Ithaca, New York in 1932 and as its mission “serves society by increasing and disseminating knowledge about the history of life on Earth.” The organization has one of the ten largest fossil invertebrate collections in the United States and has been a publisher of scholarly works in paleontology since its founding. In addition to having long roots in the science of paleontology, the mission of PRI has broadened in recent years to expand earth science literacy at local and national scales. While PRI is affiliated with nearby Cornell University, it is an independent, nonprofit institution.

Like many natural history museums, PRI has been heavily involved in recent years in digitizing its specimen collections. While we have over three million fossils in our collection, data associated with the vast majority of these specimens–such as the scientific name of a fossil, the geographic place where it was found, and its position in the geological column–have never been entered into a computer database. So, we have now begun to transcribe these data from paper labels (some well over a hundred years old!) onto an internal database; after vetting for quality control, these data are then freely shared with scientists around the world via the Integrated Digitized Biocollections (iDigBio) platform. Paleontologists are hopeful that new insights will be discovered about the history of life on Earth as many museums digitize their specimen collections and pool their combined data, perhaps leading to a “big data” revolution in paleobiology.

Five-million year old mollusk fossils from PRI’s type and figured specimen collection.

PRI is currently a partner in a National Science Foundation-supported initiative to digitize fossil collections from the Western Interior Seaway (WIS). The WIS was a shallow body of seawater that extended from the modern Gulf of Mexico to the Arctic Circle during the end of the age of dinosaurs, dividing North America in two. At this time during the Late Cretaceous period (100 to 66 million years ago)–when familiar dinosaurs like Tyrannosaurus and Triceratops lived in places like modern-day South Dakota, abundant sea life thrived in the WIS. Large oysters lived on the seafloor, schools of ammonites (shelled relatives of modern squids and octopuses) swam through the water, giant fish and marine reptiles pursued their prey, and flying reptiles like Pteranodon soared in the air above the water. These animals left behind a remarkable fossil record in formerly submerged places like western Kansas. These fossils are on display at museums around the world and also stored “behind the scenes” in museum collections. Digitizing this fossil record will allow paleontologists to better reconstruct ancient ecosystems during the Late Cretaceous and also investigate how these organisms and their interactions and geographic distributions changed over time.

Examples of ancient animals from the Western Interior Seaway. Left: Xiphactinus, a giant Cretaceous fish (on display at the University of Kansas Natural History Museum). Right, the ammonite Hoploscaphites (a specimen from the collections of the Yale Peabody Museum).

Why 3D?

In addition to digitizing records of WIS fossils, partner institutions are also creating new resources to help avocational paleontologists, students, their teachers, and the broader public learn more about paleontology and the history of life. As part of this work, the Paleontological Research Institution is developing two new online resources that are part of the broader Digital Atlas of Ancient Life project. One is the Cretaceous Atlas of Ancient Life, an online field guide to fossils from the WIS (digital field guides to fossils from other regions have also been developed). The other is an open access paleontology textbook called the Digital Encyclopedia of Ancient Life (DEAL), which is under active development. We have planned over 20 chapters for the textbook, ranging from coverage of important concepts in paleontology (e.g., fossil preservation, geological time, and phylogenetic systematics) to summaries of individual groups of ancient organisms (e.g., chapters about snails and cephalopods are online now).

Besides being open and free, the online platform of DEAL allows it to incorporate media that are impossible to include in traditional printed textbooks (e.g. videos and links to other online material). This is where 3D models come in. In an ideal world, students study and learn about fossils from hand samples in a laboratory setting. This is not, of course, always possible. Some colleges and universities do not have any fossil collections, or their collections are very limited (either in taxonomic coverage or in quality of preservation). Even if a student has access to fossils during a designated class time, they cannot continue their studies of those specimens outside of class (e.g., when they are preparing for an exam). Because of this, we have set out to create 3D models of representatives of most major groups of animal fossils using specimens from the research and teaching collections of the PRI. To date, we have added 239 models of PRI fossils and museum exhibits (as well as some modern specimens) to our Sketchfab page and have applied Creative Commons licensing to all of these, allowing them to be freely downloaded. We are now in the process of using Sketchfab to add annotations to some of our models, which greatly enhances their educational value. For example, the model below shows a three million year old snail shell from Florida; some of the most important features of its shell morphology have been labeled using annotations.

Our models are also being developed into Virtual Teaching Collections. We like to think of these as virtual “drawers” of fossils, akin to what an instructor might put out on a table during a paleontology lab. These are being arranged by topic on our Virtual Teaching Collections page. For example, the Fossil Preservation VTC highlights how fossils vary in their style of preservation. The top model below shows a fossil snail that preserves the original calcite that the living animal used to make its shell. The bottom model shows the internal and external molds of a fossil snail: the original shell is long gone (perhaps dissolved away by groundwater) and all that remains is the hardened sediment that surrounded the specimen and filled its shell.

One of our favorite models in the Fossil Preservation VTC is the fossil camel skull shown below. It is a remarkable specimen because it shows an “endocast” of the camel’s brain: sediment filled the brain case after the animal died and decomposed, filling the space once occupied by the brain and forming a natural model of it. This specimen is on display in PRI’s public exhibit space, the Museum of the Earth. We are happy that the 3D model provides a way for visitors to interact virtually with this fossil, which is housed behind glass and cannot be touched.

Of course, another benefit of 3D models is that they can be 3D printed. This can potentially make it feasible for paleontology instructors to download models of types of organisms that might be missing from their collections and print plastic representatives instead. A 3D model of a modern crab and a scaled-down 3D print of the same specimen are shown below.

A 3D print of the crab model shown above.

Workflow and Equipment

We used photogrammetry to create our 3D models. Based on the experiences of others (see below), we developed a relatively simple equipment setup. We used a Canon 80D DSLR camera mounted on a short table-top tripod to take our pictures. The specimens were rotated on an inexpensive lazy susan-like platform. We used three inexpensive LED desk lamps to illuminate the specimens. Agisoft PhotoScan Standard Edition software was used to create the models themselves. Once we had developed a workflow that worked for us, we developed a detailed photogrammetry guide that we have shared online.

Our photogrammetry setup at PRI.

While creating 3D models worked well for most specimens, some proved tricky. The most challenging were specimens that were “self-similar” when rotated. For example, some snail shells look more-or-less the same as they are rotated about their coiling axis, which created problems during model building. Specimens that have surfaces that are very smooth also sometimes proved difficult to model. Every fossil is different. Even members of the same species often show different styles of preservation, especially when found at different locations. Because of this, a bit of trial and error–especially with the Agisoft software–was necessary for development of many of the models that we have posted on Sketchfab.

At the beginning of our project in June 2018, we did not really know anything about photogrammetry. Just one week after beginning, however, we had produced our first model. Before jumping into photogrammetry and 3D modeling, it is useful to read online about other people’s experiences both with specimen photography and the modeling software itself. There are many excellent blog articles that can help with this and we especially found the multi-part photogrammetry guide on the dinosaurpalaeo blog to be very helpful with getting started. We also greatly benefitted from correspondence with two other Sketchfab users (Paleogirl and paleoteach) who have contributed a large number of 3D models of fossils to Sketchfab.

As might be expected, we found that practice and experience ultimately leads to better models. This is especially true for determining how to take the “right” combination of overlapping photos, which facilitates model building in Agisoft PhotoScan (this has greater benefit than perfectly understanding all of the varied options in the Agisoft program). The majority of the fine details of the final model will be determined by the ability of the photographer to correctly illuminate and capture all of the angles of the specimen. Novice 3D model builders should also be aware that not every model will be perfect, especially the first few. There will be models that are a breeze to create and there will be models that will not work entirely. Don’t give up on specimens that don’t produce perfect models right away. Adding a new angle to the set of photos (i.e., creating overlap where it might have been missing) or trying different settings in Agisoft can often be the “missing piece” that fixes a formerly troublesome model.


The ability to create online 3D digital models of museum specimens has numerous benefits. The greatest of these is to be able to share natural history specimens or cultural artifacts with people who are not able to visit a given museum in person. 3D digitization also allows museums to share specimens with the public that are locked away “behind the scenes” in collections, perhaps because they are too scientifically important or fragile to put on display, or–perhaps more commonly–because there is simply not enough public exhibit space to share all of the treasures held by a museum. The PRI specimen shown below is the type specimen of the fossil cephalopod Agoniatites intermedius. Because it is the name-bearing voucher specimen for this species, the physical specimen is not allowed on public display, but the model allows it to nevertheless be shared with the world.

Interactive 3D models may sometimes also encourage viewers to make a more personal connection to a particular specimen than when it is sitting statically behind glass in a museum display. Viewers may turn these digital models about, zoom in on tiny features, and read annotations of key features; none of these actions are possible in traditional museum settings. Thus, the educational value of creating 3D models of museum specimens–and our ability to share them on platforms like Sketchfab and websites like the Digital Encyclopedia of Ancient Life–is that there are innumerable ways to give a particular specimen connection and context to the natural or cultural history that surrounds it, all while protecting the physical object itself. Physical objects–be they fossils bones or an ancient pieces of jewelry–provide heartfelt, tangible connections to the past. 3D models, however, have the potential to greatly increase understanding, appreciation, and awareness of these same objects.

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About the author

Jonathan Hendricks and Emily Hauf

Jonathan Hendricks is Director of Publications at the Paleontological Research Institution in Ithaca, New York. Emily Hauf is an undergraduate geology student at the State University of New York-Geneseo.

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