@article{KaltdorfSchulzeHelmprobstetal.2017, author = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian}, title = {Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms}, series = {PLoS Computational Biology}, volume = {13}, journal = {PLoS Computational Biology}, number = {1}, doi = {10.1371/journal.pcbi.1005317}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172112}, year = {2017}, abstract = {Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.}, language = {en} } @article{vonMammenWagnerKnoteetal.2017, author = {von Mammen, Sebastian Albrecht and Wagner, Daniel and Knote, Andreas and Taskin, Umut}, title = {Interactive simulations of biohybrid systems}, series = {Frontiers in Robotics and AI}, volume = {4}, journal = {Frontiers in Robotics and AI}, issn = {2296-9144}, doi = {10.3389/frobt.2017.00050}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195755}, year = {2017}, abstract = {In this article, we present approaches to interactive simulations of biohybrid systems. These simulations are comprised of two major computational components: (1) agent-based developmental models that retrace organismal growth and unfolding of technical scaffoldings and (2) interfaces to explore these models interactively. Simulations of biohybrid systems allow us to fast forward and experience their evolution over time based on our design decisions involving the choice, configuration and initial states of the deployed biological and robotic actors as well as their interplay with the environment. We briefly introduce the concept of swarm grammars, an agent-based extension of L-systems for retracing growth processes and structural artifacts. Next, we review an early augmented reality prototype for designing and projecting biohybrid system simulations into real space. In addition to models that retrace plant behaviors, we specify swarm grammar agents to braid structures in a self-organizing manner. Based on this model, both robotic and plant-driven braiding processes can be experienced and explored in virtual worlds. We present an according user interface for use in virtual reality. As we present interactive models concerning rather diverse description levels, we only ensured their principal capacity for interaction but did not consider efficiency analyzes beyond prototypic operation. We conclude this article with an outlook on future works on melding reality and virtuality to drive the design and deployment of biohybrid systems.}, language = {en} } @article{FisselerMuellerWeichert2017, author = {Fisseler, Denis and M{\"u}ller, Gerfrid G. W. and Weichert, Frank}, title = {Web-Based scientific exploration and analysis of 3D scanned cuneiform datasets for collaborative research}, series = {Informatics}, volume = {4}, journal = {Informatics}, number = {4}, issn = {2227-9709}, doi = {10.3390/informatics4040044}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197958}, pages = {44}, year = {2017}, abstract = {The three-dimensional cuneiform script is one of the oldest known writing systems and a central object of research in Ancient Near Eastern Studies and Hittitology. An important step towards the understanding of the cuneiform script is the provision of opportunities and tools for joint analysis. This paper presents an approach that contributes to this challenge: a collaborative compatible web-based scientific exploration and analysis of 3D scanned cuneiform fragments. The WebGL -based concept incorporates methods for compressed web-based content delivery of large 3D datasets and high quality visualization. To maximize accessibility and to promote acceptance of 3D techniques in the field of Hittitology, the introduced concept is integrated into the Hethitologie-Portal Mainz, an established leading online research resource in the field of Hittitology, which until now exclusively included 2D content. The paper shows that increasing the availability of 3D scanned archaeological data through a web-based interface can provide significant scientific value while at the same time finding a trade-off between copyright induced restrictions and scientific usability.}, language = {en} }