Dogu Baran Aydogan

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We propose a new technique to clean outlier tracks from fiber bundles reconstructed by tractography. Previous techniques were mainly based on computing pair-wise distances and clustering methods to identify unwanted tracks, which relied heavy upon user inputs for parameter tuning. In this work, we propose the use of topological information in track density(More)
While tractography is widely used in brain imaging research, its quantitative validation is highly difficult. Many fiber systems, however, have well-known topographic organization which can even be quantitatively mapped such as the retinotopy of visual pathway. Motivated by this previously untapped anatomical knowledge, we develop a novel tractography(More)
Millions of people worldwide suffer from fragility fractures, which cause significant morbidity, financial costs and even mortality. The gold standard to quantify structural properties of trabecular bone is based on the morphometric parameters obtained from microCT images of clinical bone biopsy specimens. The currently used image processing approaches are(More)
We propose a novel feature for binary images that provides connectivity information by taking into account the proximity of connected components and cavities. We start by applying the Euclidean distance transform and then we compute the contour tree. Finally, we assign the normalized algebraic connectivity of a contour tree derivative as a feature for(More)
The additive manufacturing technique of direct laser writing by two-photon polymerization (2PP-DLW) enables the fabrication of three-dimensional microstructures with superior accuracy and flexibility. When combined with biomimetic hydrogel materials, 2PP-DLW can be used to recreate the microarchitectures of the extracellular matrix. However, there are(More)
Microscaffolds play a crucial role in cell culturing. They can be designed and produced in different ways depending on the applications and materials used. The cell medium (fluid) transports the cells into the microscaffold and is an effective factor for cell growth and stimulation. The architecture of microscaffolds influences fluid flow characteristics(More)
Quantifying the connectivity of material microstructures is important for a wide range of applications from filters to biomaterials. Currently, the most used measure of connectivity is the Euler number, which is a topological invariant. Topology alone, however, is not sufficient for most practical purposes. In this study, we use our recently introduced(More)