Tuesday 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. Agisoft software (free for 30 days). Typically, 10-100 photographs are needed from different angles. 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. So it is important to have the object totally in focus; use a stacking program (e.g., Helicon Stacking) to ensure this. Presentation can be made with ThreeJS, Adobe Acrobat, or dedicated viewers (Meshlab).
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. It is a relatively user-friendly program, which I also used myself, that allows segmentation of particular organs. Landmarking was done using Landmark Editor and MorphoJ (tomorrow more).
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
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. The initial learning curve is, however, very steep.
Some of the visualization programs are freeware, others (Avizo, Mimics) are very costly. Also there is much difference in ‘intuitively’ of the software packages. And although the end result is always eye-catching, the time investment can be cumbersome.