Project duration: 01.7.2016 – 30.09.2020
Synchrotron X-ray microtomography offers unique opportunities for the morphological analysis of animals. Internal structures become observable even in opaque organisms in a non-invasive, three-dimensional way, and with a sub-micron resolution. The method thus allows for the investigation of objects from a wide field of biological research. Biomechanics, for example, is dealing with the complex dynamics of muscle-skeleton interactions, neurobiology with the topology of sensory centres in the brain, and developmental biology with differential comparisons of developmental stages. So far, the enormous potential of collaborative work on the same specimens is mostly untapped. By using a new collaborative approach, this project aims to create new possibilities, that allow for a more efficient use of the valuable beam time at tomographic synchrotron beamlines through the coordination of research on different organ systems and a regulation of the data usage by a common data policy.
The (associated) biological partners of the joint research project NOVA cover different scientific aspects of morphology and thus serve as a model community for the cooperative, integrative approach. As exemplification for the biological objects, complementary aspects of insect head morphology will be investigated. On this basis, a tomography catalogue (and most notably a freely accessible one) can be created in cooperation with the operators of the tomography instrumentation at PETRA III. Additionally, datasets already obtained at the ANKA in the framework of ASTOR will be added. In a later stage of the project additional scientific communities ought to be enlisted to participate in this open and cooperative way of data usage.
The demand for cross-community chains of analyses necessitates several technological developments within the framework of this project. Within the ASTOR project the close cooperation of biologists and image processing experts has already successfully demonstrated considerable progress in semi-automatic segmentation and classification of internal structures. Further enhancement of the semi-automatic segmentation is essential for an efficient use of synchrotron beam time and will be – based on already accomplished preliminary studies – developed and refined in this project. Significant enhancements are planned at the PETRA III instrumentation (phase contrast), the reconstruction algorithms (based on intensity as well as absorption), and the tools for subsequent analyses of the data. In principle, improvements made on key technologies within this project will be equally beneficial for all users of tomography instrumentations. The intended cooperative analysis infrastructure makes tomographic data available to a broad scientific audience, allows embedding tomographic methods in teaching, and even provides a platform for ‘citizen science’ projects.
Main goals of NOVA are:
- the development of collaborative analysis tools
- the complete analysis of tomographic datasets by complementary groups
- Low-latency Big Data Visualisation - Tan Jerome, Nicholas PhD thesis, Faculty of Electrical Engineering and Information Technology, Karlsruhe Institute of Technology, 2019. Abstract Exploring large and complex data sets is a crucial factor in a digital library framework. To find a specific data set within a large repository, visualisation can help to validate the content apart from the textual description. However, ...
- Parasitoid biology preserved in mineralized fossils - van de Kamp T. et al., in Nature Communications, 9 (2018), 3325.
- The NOVA project: Maximizing beam time efficiency through synergistic analyses of SRμCT data - Schmelzle S. et al., in Proceedings of SPIE - The International Society for Optical Engineering, 10391 (2017), 103910P.
Consortium für integrative Morphologie:
- M. Heethoff
Technische Universität Darmstadt (TUD, Sprecher)
- V. Heuveline
Universität Heidelberg (UHD)
- J. Becker
Karlsruher Institut für Technologie (KIT)
Associated partners (infrastructure):
- F. Beckmann, J.U. Hammel
Helmholtz-Zentrum Geesthacht, Zentrum für Materialforschung und Küstenforschung (HZG)
- A. Kopmann
Karlsruher Institut für Technologie, Institut für Prozessdatenverarbeitung und Elektronik (IPE)
- W. Mexner
Karlsruher Institut für Technologie, Synchrotronstrahlungsquelle (ANKA)
Associated partners (Morphology):
- O. Betz
Universität Tübingen (OB)
- R. G. Beutel, B. Wipfler
Universität Jena (RB, BW)
- A. Blanke
University of Hull (AB)
- S. Harzsch
Universität Greifswald (SH)
- T. van de Kamp
Karlsruher Institut für Technologie (TK)
ContactTechnical University Darmstadt
64287 Darmstadt Michael Heethoff
P: +49 721 6151 1675417
The project is funded within the BMBF programme “Research on condensed matter 2016-2019”.