Science Spotlight: Lund University Department of Biology

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The 3D Laboratory at the Department of Biology is one of the infrastructures at Lund University in Sweden, one of northern Europe’s oldest universities. We focus on visualization and quantification of 3D complex phenotypes of both living and extinct (fossils) organisms.

Fossilised shark tooth 3D scanned at the 3D Laboratory, Department of Biology, Lund University.

My background is in ecology and marine science but since my master’s studies, I have worked to integrate new technologies in novel research tools. I have long experience using computer vision and 3D image analysis and, as part-time manager of the 3D Lab, I am helping my colleagues to introduce the use of 3D technologies in their research, teaching, and outreach events.

3D at the Department of Biology

In 2017, it was decided to create a new 3D infrastructure at the Department of Biology at Lund University by using state-of-the-art 3D scanning technologies. It was clear that we have access to a tremendous amount of technology and large infrastructure to get the genetic information of any organism (the genotype). On the other end, however, accurate and high-throughput quantification of organismal size and shape (the phenotype) is still lacking. Furthermore, our Department also hosts the Lund University Biological Museum, which stores an astonishing collection of 12 million specimens collected in the course of the last three centuries. Our 3D Lab provides the Biological Museum a modern platform to create a virtual display of their most important and recognized items.

Our target applications are research, education, and divulgation. The acquisition of 3D organism models will help researchers to increase their understanding of key ecological and evolutionary processes. For example, how size and shape are influenced by climatic regimes or if size evolves faster than shape over macroevolutionary time scales. In animal biomechanics, quantification of shape and size is of fundamental interest in observational and experimental studies of the aerodynamics of flight (birds, bats, insects) and in the hydrodynamics of swimming (fish). The wing of the common swift (Apus apus) below was 3D scanned in our lab and printed to be used in the wind tunnel available at our department to test aerodynamic theories.

3D printed wing of the common swift (Apus apus) used to test aerodynamics theories in the wind tunnel at the Department of Biology, Lund University. Project and photos by Per Henningsson.

3D scanning and 3D printing have already been proven to be excellent tools in education. My favorite example is the project by Atticus Pinzon‐Rodriguez. He was facing the problem of not being able to use wax models of echinoderm larvae (starfish, sea urchins, etc.) for teaching the zoology course. The wax models in the Biological Museum were handmade almost 100 years ago, which makes them unique but not ideal for constant manipulation by the students. He 3D scanned and 3D printed some of the specimens that are currently in use as teaching material.

All the echinoderm larvae models are also visible in our 3D collection on Sketchfab:

Sometimes we receive questions from outside academia, and we try to meet the curiosity of the public, especially of the youngest ones. For example, children are often fascinated by the variety of eggs they can see at the museum. For this reason, we assembled a virtual collection spanning the entire size range of bird eggs in the Biological Museum collection.

Collection of birds’ eggs at the Biological Museum, Lund University. Tip: check the date hand-written on the stork egg.

Since you cannot touch museum specimens or virtual objects, we also 3D printed a selection of the eggs and arranged them in a “matryoshka” style to show how many different egg shapes and sizes exist in nature.

Tools

We deal with different technologies and, in particular with tools that are not already available at the university (CT and MRI scanners, for example). Currently, we work with photogrammetry and structured-light scanners, both stationary industrial-standard (GOM) and handheld portable scanners (Artec 3D). We find the structured-light scanners available on the market to be excellent for most applications and easy to use. For more challenging tasks (small and complex phenotypes with lots of color information), we developed our custom photogrammetry platform, including a custom 3-axis focus stacking system entirely dedicated to 3D scanning pinned entomological specimens.

Custom 3-axis focus stacking platform for scanning pinned entomological specimens. A motorized 2-axis turntable rotates the specimen while a motorized macro rail moves the camera to capture depth-extended pictures to be used for photogrammetry.

The 3D Lab never rests. And while we are struggling to scan our smaller specimens, we are already working on how to scan our bigger ones. Our future plan is to unlock the access also of the macrofauna specimens available at the Biological Museum with a special focus on the extinct species as the great auk below.

Scan of a fiberglass model of the original taxidermy mount specimen great auk (Pinguinus impennis) from the Biological Museum at Lund University (catalog number: L835/3026 – Year 1835).

Sketchfab

Sketchfab has been an incredible opportunity for us to show examples of what we can do and to share our models with colleagues in our department and all over the world. Since our goal is to facilitate the use of 3D technology in research, teaching, and communication, we often meet people using 3D technology for the first time who do not know how to handle 3D models on their computer. Sketchfab makes it so easy and helps inspire scientists on how to use 3D technology in their projects.

Looking ahead

New tools for fast and accurate measurements of 3D phenotypes will have a huge impact on research and teaching in biology. We now have access to new, previously inaccessible data on our model organisms as well as new exciting opportunities for teaching. The COVID-19 pandemic forced almost all universities to move their courses online and researchers and lecturers were no longer able to access laboratories and teaching material. This has probably been the ultimate wake-up call for research institutions to invest in the digitization of museum specimens and to make virtual display collections a reality.

About the author

Giuseppe Bianco

Lab manager



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