Digital neuroanatomy, data visualisation, and modelling
Zusammenfassung der Projektergebnisse
The goal of this project was to develop and improve tools that support the creation, management, and visualization of hierarchical brain atlases. The usability of the tools should be evaluated using a standard atlas of the honeybee brain. All methods should be integrated into the visualization and data analysis framework Amira that was (and is) used by our research partners in neurobiology. First, we developed tools and methods that generalize and improve the steps in the processing pipeline for creation of surface-based atlases. These steps consist of imaging and preprocessing, segmentation, registration, surface reconstruction, and assignment of biological semantics to geometrical objects. Secondly, techniques supporting the usage of hierarchical brain atlases were developed. To improve the segmentation and registration steps, a statistical shape model of the central structures of the honeybee brain was created. Based on this shape model, an automatic segmentation method for coarse structures was developed. It computes spatial displacements and deformations of statistical shape models such that they fit to individual microscopy images. The resulting information can be used also for spatial registration of the image data. Besides this method for deriving registration information, we integrated alternative registration techniques into Amira. To enable the integration of semantic information like, e.g., biological identifiers of anatomical structures or relations between such structures, in collaboration with neurobiologists we developed a first exemplary ontology of the honeybee brain. The ontology includes concepts ranging from coarse anatomical structures such as neuropils down to individual neurons of certain types. It further embodies morphological and functional relationships between structures. The structures contained in the ontology are linked to geometric entities of the standard atlas. Using this hierarchical classification scheme, we implemented methods for query-based browsing and automated creation of visualization. In order to enhance the presentation of neurons within their anatomical context, we also designed and evaluated novel visualization methods for line-like structures in complex surface geometries. Here, knowledge from perception theory was used to improve depth perception and visual differentiation of structures. A quantitative user study substantiated these developments. We also provided tools to our cooperation partners in neurobiology for analyzing atlas structures and substructures by calculating, e.g., distance measures or other important parameters. The atlas creation pipeline was used for the generation of a standard moth brain, a standard desert locust brain, and a fly thoracic ganglion. Furthermore, the synaptic distribution of several beebrain projection neurons within mushroom body parts were evaluated with our tools. The browsing and visualization methods developed in the project improved atlas exploration, data retrieval, and the detection of segmentation and registration errors. They also supported the meaningful representation of atlas data for education, presentation, and communication.
Projektbezogene Publikationen (Auswahl)
- Pipeline for the Creation of Surface-Based Averaged Brain Atlases. In: J. Rossignac and V. Skala, editors, Proc. 15th Int. Conf. in Central Europe on Computer Graphics, Visualization and Computer Vision (WSCG 2007), pages 17–24, Plzen, Czech Republic, January 2007
Anja Kuß, Hans-Christian Hege, Sabine Krofczik, and Jana Börner
- A digital, threedimensional standard brain of the moth, heliothis virescens. In: Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008, 2008
Pal Kvello, Jürgen Rybak, Løfaldli B, Anja Kuß, and Hanna Mustaparta
(Siehe online unter https://doi.org/10.3389/neuro.06.014.2009) - Model-based autosegmentation of the central brain of the honeybee, apis mellifera, using active shape models. In: Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008, 2008
Jochen Singer, Matthias Lienhard, Heiko Seim, Dagmar Kainmüller, Anja Kuß, Hans Lamecker, Stefan Zachow, Randolf Menzel, and Jürgen Rybak
(Siehe online unter https://doi.org/10.3389/conf.neuro.11.2008.01.064) - Ontology-Based Visualization of Hierarchical Neuroanatomical Structures. In: C.P. Botha, G. Kindlmann, W. J Niessen, and B. Preim, editors, Proc. of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008, pages 177–184, Delft, Netherlands, October 2008
Anja Kuß, Steffen Prohaska, Björn Meyer, Jürgen Rybak, and Hans-Christian Hege
- Knowledge Representation for Digital Atlases. In: Conference Abstracts from the Workshop of the Working Group Ontologies in Biomedicine and the Life Science, 2009
Anja Kuß and Hans-Christian Hege
- The HoneyBee Standard Brain (HSB) - a versatile atlas tool for integrating data and data exchange in the neuroscience community. In: Don H. Johnson, editor, BMC Neuroscience 2009, volume 10, 2009
Jürgen Rybak, Anja Kuß, Wolfgang Holler, Robert Brandt, Hans-Christian Hege, Martin Nawrot, and Randolf Menzel
(Siehe online unter https://doi.org/10.1186/1471-2202-10-S1-P1) - Using ontologies for the visualization of hierarchical neuroanatomical structures. In: Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics, 2009
Anja Kuß, Steffen Prohaska, and Jürgen Rybak
(Siehe online unter https://doi.org/10.3389/conf.neuro.11.2009.08.017) - Visual accentuation of spatial relationships between filamentous and voluminous surface structures. In: Eurographics/IEEE Symposium on Visualization 2009, Conference Abstract, 2009
Vincent Jasper Dercksen, Maria Gensel, and Anja Kuß
- Effective Techniques to Visualize Filament-Surface Relationships. Computer Graphics Forum, 3 (29):1003–1012, 2010
Anja Kuß, Björn Meyer, Vincent Jasper Dercksen, Maria Gensel, and Steffen Prohaska
(Siehe online unter https://doi.org/10.1111/j.1467-8659.2009.01703.x) - The Digital Bee Brain: Integrating Neurons into a Common 3D Reference System. Frontiers in Systems Neuroscience, 4, Article 30, 15. pp, July 2010
Jürgen Rybak, Anja Kuß, Hans Lamecker, Stefan Zachow, Hans-Christian Hege, and Randolf Menzel
(Siehe online unter https://doi.org/10.3389/fnsys.2010.00030)
