Project duration: 01.11.2013 – 30.06.2016
Advanced high-quality semi-automatic segmentation with unrivaled precision
Segmentation of only a few labeled slice reduces the segmentation effort by factors
Comparison of manual and semi-automatic segmentation
X-ray tomogram with fine internal structures
The interdisciplinary ASTOR collaboration
The interdisciplinary ASTOR collaboration
Interactive 3D visualization of tomographic data in the web
Analysis workflow for biological studies with X-ray tomography
Idea
X-rays and tomography provide the opportunity to visualize internal structures of optically dense materials in 3D. The invention of synchrotron-X-ray-microtomography was the onset of a new era of morphological research on microscopically small animals (e.g. micro-arthropods). Analyzing such 3D-data is time consuming and technically challenging. Especially the automation of classification processes needs close cooperation of biologists and image processing experts. Using the most speciose animal group on earth (arthropods) as a model system, the network for functional morphology and systematics aims to establish and standardize measuring parameters to meet the needs of a broad range of biological research. This will be achieved by optimizing data acquisition and processing, semi-automation of data analysis (reconstruction and segmentation/classification) and the creation of an online-portal providing easy access, 3D-visualization and semi-automatic analyses of the data using cloud technologies.
Key technologies developed in ASTOR are:
- Automatized data transfer workflows for X-ray tomography
- Virtual analysis environment with remote access to graphically demanding applications
- Semi-automatic segmentation of tomograms
- Interactive 3D-web visualization of volumes
Results
- Parasitoid biology preserved in mineralized fossils - van de Kamp T. et al., in Nature Communications, 9 (2018), 3325.
- ASTOR – Arthropod Structure revealed by ultra-fast Tomography and Online Reconstruction - M. Heethoff, V. Heuveline, H. Hartenstein, W. Mexner, T. van de Kamp, A. Kopmann, Final report, BMBF Programme: "Erforschung kondensierter Materie", 2016 (in German)
- Scalable visualization of large tomographic 3D volumes on the web - F. Schultze, Master thesis, Faculty of Computer Science, Karlsruhe Institute of Technology, 2015
Partners
Network for functional morphology and systematics:
- M. Heethoff
Technical University of Darmstadt (TUD) - V. Heuveline
University of Heidelberg (UHD) - H. Hartenstein
Steinbuch Computing Center, KIT Karlsruhe (KA) - W. Mexner
ANKA Synchrotron Radiation Source, KIT Karlsruhe (ANKA) - T. van de Kamp
Institut für Photos Science and Synchron Radiation, KIT Karlsruhe (IPS) - A. Kopmann
Institut for Data Processing and Electronics, KIT Karlsruhe (IPE)
Contact
Technical University DarmstadtSchnittspahnstraße 3
64287 Darmstadt Michael Heethoff
Project Manager
heethoff@bio.tu-darmstadt.de
P: +49 6151 1675417
Funding
The project is funded within the BMBF programme “Research on condensed matter 2013-2016”.