@article{SchmittTitschackBaum, author = {Schmitt, Kira and Titschack, J{\"u}rgen and Baum, Daniel}, title = {Polyp-Cavity Segmentation of Cold-Water Corals guided by Ambient Occlusion and Ambient Curvature}, series = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, journal = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, doi = {10.2312/vcbm.20221189}, abstract = {The segmentation of cavities in three-dimensional images of arbitrary objects is a difficult problem since the cavities are usually connected to the outside of the object without any difference in image intensity. Hence, the information whether a voxel belongs to a cavity or the outside needs to be derived from the ambient space. If a voxel is enclosed by object material, it is very likely that this voxel belongs to a cavity. However, there are dense structures where a voxel might still belong to the outside even though it is surrounded to a large degree by the object. This is, for example, the case for coral colonies. Therefore, additional information needs to be considered to distinguish between those cases. In this paper, we introduce the notion of ambient curvature, present an efficient way to compute it, and use it to segment coral polyp cavities by integrating it into the ambient occlusion framework. Moreover, we combine the ambient curvature with other ambient information in a Gaussian mixture model, trained from a few user scribbles, resulting in a significantly improved cavity segmentation. We showcase the superiority of our approach using four coral colonies of very different morphological types. While in this paper we restrict ourselves to coral data, we believe that the concept of ambient curvature is also useful for other data. Furthermore, our approach is not restricted to curvature but can be easily extended to exploit any properties given on an object's surface, thereby adjusting it to specific applications.}, language = {en} } @article{VohraHerreraTavhelidseSucketal., author = {Vohra, Sumit Kumar and Herrera, Kristian and Tavhelidse-Suck, Tinatini and Knoblich, Simon and Seleit, Ali and Boulanger-Weill, Jonathan and Chambule, Sydney and Aspiras, Ariel and Santoriello, Cristina and Randlett, Owen and Wittbrodt, Joachim and Aulehla, Alexander and Lichtman, Jeff W. and Fishman, Mark and Hege, Hans-Christian and Baum, Daniel and Engert, Florian and Isoe, Yasuko}, title = {Multi-species community platform for comparative neuroscience in teleost fish}, doi = {10.1101/2024.02.14.580400}, abstract = {Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community's research and its easy extensibility will encourage contributions to its continuous expansion.}, language = {en} }