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3 Days of 3D

Upcoming events

2, 3 and 4 November 2015

What are the possibilities of the latest 3D technology Naturalis has to offer? In 3 days you will get the complete 3D picture. We will show you the best examples from our research, from shark skulls to pitcher plants. Speakers from cooperating universities, suppliers of software and hardware and scientists from Naturalis will share their experiences with you.

Location: LiveScience hall at the museum

Time: 10.30 - 12.30 each day.

Registration: not necessary.

Entrance is free for students, please tell the cashier you are visiting 3 days of 3D. You can walk in anytime you like. Main language is English. 

The full programme

Day 1: 2-11-2015 X-ray scanning


10.30 – 10.45
Introduction 3 days of 3D

10.45 – 11.05 Imaging shark jaws using Medical CT scanning
Pepijn Kaminga  – Naturalis Biodiversity Center

Jaws are essential in capturing and processing prey and should therefore be optimized by natural selection for this role. Consequently, jaw morphology is thought to reflect feeding habits, and is frequently used in ecomorphological and paleontological studies to explore the evolution of trophic diversity. However, it may not be a good predictor of feeding habits and the associations are often functionally inferred. To test the association between jaw diversity, diet and phylogeny, I studied jaw shape disparity together with detailed data on diet based on a literature survey in a phylogenetic context. I created three-dimensional (3D) reconstructions from computed tomography scans of 148 left lower jaws from 89 extant shark species. In this presentation I’ll elaborate on CT scanning and how a large part of the sharks from the Naturalis’ spirit collection is used for this purpose.

11.05 – 11.25 3D-imaging of flowers and pitchers
Barbara Gravendeel, Anita Dirks & Rachel Schwallier  – Naturalis Biodiversity Center & Institute of Biology, Leiden University

Background: Over the past 100 million years, orchid flowers became highly adapted to their pollinators and pitcher plants growing on nutrient poor soils evolved special leaf tip traps to obtain extra nutrients.

Goal: Obtain more insight in the evolutionary origin of the morphological adaptations of these plant groups.

Methods: Analysis of 3D scans made by Xradia tomography and the Sense handscanner.

Results: Vascular bundles visualized in 3D scans of orchid flowers support the hypothesis that stelidia evolved from stamens to ensure reproductive isolation. Leaf tip traps of pitcher plants evolved into shapes especially adapted to either catching insects or plant debris but not both.

11.25 – 11.45 Vision impossible? Shedding synchrotron light into deep-time evolution of the vertebrate skeleton
Martin Rücklin  – Naturalis Biodiversity Center

To visualize minute structures and minimal contrasts inside of fossils traditional CT or microCT technology reaches a limit. In order to overcome this problem the use of synchrotron tomography allows high energy, brilliance and enhanced contrasts inside of fossils. Using this method cell spaces and lines of arrested growth demonstrating growth inside of the skeleton are possible. In the talk I will demonstrate the possibility to reconstruct the development of the vertebrate skeleton in the first jawed vertebrates and future possibilities using developmental palaeobiology.

11.45 – 12.20 MicroCT scanning at Naturalis
Rob Langelaan and Bertie Joan van Heuven – Naturalis Biodiversity Center

X-ray scanning facilities at Naturalis, an introduction to our SkyScan and brand new Zeiss Xradia versa. In a live stream from the X-ray lab we will show how to set-up a scan, explain the possibilities of the new machine, which is one of the best lab-based MicroCT scanners available today and what we plan to do with it in the future.

Day 2: 3-11-2015 3D visualization

10.30 – 10.50 Photogrammetry, a poor man's guide to 3D digitization
Edwin van Spronsen – Naturalis Biodiversity Center

Photogrammetry is a technique for turning photographs into 3D objects. All it requires is a digital camera and a computer to do the calculations. Typically, 10-100 photographs are needed. An additional bonus of photogrammetry - as compared to other 3D digitization techniques - is the fact that the original images will also provide a photorealistic texture of the object. It is a cheap, accurate and robust technique that produces highly realistic models for 3D printing, gaming and display on the web. Several collection objects from the museum have been digitized this way. Examples will be shown and do's and don’ts will be discussed.

10.50 – 11.10 Visualizing shark jaws
Pepijn Kamminga (Mimics) – Naturalis Biodiversity Center

For his PhD research on the ecomorphology of the lower jaw in extant sharks, Pepijn Kamminga CT scanned a large part of the Naturalis’ shark spirit collection. The raw data produced from this method needs to be processed in order to be useable for quantitative analysis. In this presentation Pepijn focusses on the process of visualisation of shark jaws in 3D using the software package MIMICS.

11.10 – 11.30 Visualizing the nothing: A reconstruction of the fossil fish brain
Sophie van der Hart – Naturalis Biodiversity Center & Institute of Biology, Leiden University

Fossils can provide important information about brain architecture by examining the openings and canals left in the brain. Traditionally, Xrays are used to visualize mineralised tissues like the skeleton. However, soft-tissue structures are usually poorly preserved or entirely missing in vertebrate fossils. This makes it extremely difficult to separate and follow the course of each individual nerve or fibre through the brain. Using three dimensional software for model reconstruction, a 3D model of the internal structure of the braincase can be achieved. Sophie will show that this virtual approach gives a reliable data base for studies in comparative anatomy and enables us to learn more about the evolution of the vertebrate brain.

11.30 – 12.00 Amira|Avizo: software solutions for 3D visualization and analysis
FEI: Amira/Avizo

Amira and Avizo are comprehensive, integrated software solutions for spatial data visualization, image processing, analysis and quantification dedicated respectively to life and materials sciences. The broad range of functionalities, exposed through an intuitive visual programming interface, enable the processing of extremely diverse kinds of images and data from any type of imaging device. This presentation will propose an overview of the software functionalities, highlighting the main features of the software with illustrations in paleontology, biology and materials science domains. FEI will in particular highlight a recently added feature dedicated to the robust detection and centerline tracing of fibers.

12.00 – 12.30 Blending in! Visualisation, animation and analysis of palaeontological data with Blender
Stephan Lautenschlager – University of Bristol

In the last decade, computer-aided visualisation and digital analysis techniques have revolutionised palaeontological research and transformed the way fossils can be studied. Computational methods, such as various forms of computed tomography (CT), finite element analysis (FEA) or multibody dynamics analysis (MDA), now provide a wealth of digital data with a potential to be used for research publications, conference contributions and public outreach activities. The freely available digital visualisation and modelling software Blender offers a powerful tool to visualise three-dimensional models and analytical data and to create animations. However, Blender holds further potential to perform different analyses by using the in-built Python interpreter. Two examples will be presented of how Blender can be used to analyse muscle function in theropod dinosaurs, such as Tyrannosaurus rex, and to study the locomotion of ichthyosaurs, a group of fossil marine reptiles. 

Day 3: 4-11-2015 Geometric Morphometrics (Microscribe and laser scanning)

3D Trex

10.30 – 11.00 Measuring shape in biology – a short guide to Geometric Morphometrics
Thibaut De Meulemeester – Naturalis Biodiversity Center

The basics of GMM will be introduced and explained with some examples using 2D and 3D morphometrics.


11.00 – 11.20 Tracking and printing dinosaurs: 3D scanning and 3D printing in the upcoming dinosaur exhibits in Naturalis
Anne Schulp – Naturalis Biodiversity Center

Next year, Naturalis will present a new Tyrannosaurus rex specimen, and in 2018, the new dinosaur gallery in the new museum will open. The developments in 3D imaging and 3D printing techniques have many applications in paleontology; not only in research but also in outreach and museology. The upcoming "Welcome T. rex"-exhibition at Naturalis will feature (the results of) 3D Laser scanning, 3D photogrammetry, CT-scanning and 3D printing. This short presentation will provide an overview of the ongoing 3D projects on and around the Naturalis T. rex.

11.20 – 11.50
Hans Cornelisse – M&H reverse

Examples and possibilities using laser and light scanners.

11.50 – 12.20 "Why do different birds have different beaks? Linking shape with biomechanics"
Jen Bright – University of Sheffield

During evolution we see how animals change in shape to become better adapted to their environments, but what is not always clear is why a certain shape is better than another. Finite Element Analysis (FEA) is a method borrowed from engineering that can be used to see how complex shapes (like skulls and other bones) respond to forces that an animal encounters every day, like biting on food, running, or fighting. By using FEA together with shape analysis like geometric morphometrics, we can investigate how the relationship between shape and function works. Jen will show these ideas using examples from modern birds, and also show how everyone who is interested can help us build the biggest shape database of bird beaks ever collected!