TY - GEN A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures N2 - In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor. The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection. Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures. T3 - ZIB-Report - 19-30 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73739 SN - 1438-0064 ER - TY - JOUR A1 - Lang, Stefan A1 - Dercksen, Vincent J. A1 - Sakmann, Bert A1 - Oberlaender, Marcel T1 - Simulation of signal flow in 3D reconstructions of an anatomically realistic neural network in rat vibrissal cortex JF - Neural Networks Y1 - 2011 U6 - https://doi.org/doi:10.1016/j.neunet.2011.06.013 VL - 24 IS - 9 SP - 998 EP - 1011 ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sakmann, Bert A1 - Hege, Hans-Christian T1 - Light Microscopy-Based Reconstruction and Interactive Structural Analysis of Cortical Neural Networks T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Oberlaender, Marcel A1 - Sakmann, Bert A1 - Hege, Hans-Christian ED - Linsen, Lars ED - Hagen, Hans ED - Hamann, Bernd ED - Hege, Hans-Christian T1 - Interactive Visualization – a Key Prerequisite for Reconstruction of Anatomically Realistic Neural Networks T2 - Visualization in Medicine and Life Sciences II Y1 - 2012 UR - http://www.zib.de/visual/publications/sources/src-2012/DercksenVMLS2012web.pdf SP - 27 EP - 44 PB - Springer, Berlin ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Egger, Robert A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Synaptic Connectivity in Anatomically Realistic Neural Networks: Modeling and Visual Analysis T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) Y1 - 2012 U6 - https://doi.org/10.2312/VCBM/VCBM12/017-024 SP - 17 EP - 24 CY - Norrköping, Sweden ER - TY - GEN A1 - Pfister, Hanspeter A1 - Kaynig, Verena A1 - Botha, Charl A1 - Bruckner, Stefan A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Roerdink, Jos T1 - Visualization in Connectomics Y1 - 2012 U6 - https://doi.org/10.1007/978-1-4471-6497-5_21 ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Brüß, Cornelia A1 - Stalling, Detlev A1 - Gubatz, Sabine A1 - Seiffert, Udo A1 - Hege, Hans-Christian T1 - Towards automatic generation of 3D models of biological objects based on serial sections T2 - Visualization in Medicine and Life Sciences Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-72630-2 SP - 3 EP - 25 PB - Springer-Verlag Berlin Heidelberg ER - TY - GEN A1 - Oberlaender, Marcel A1 - Dercksen, Vincent J. A1 - Lang, Stefan A1 - Sakmann, Bert T1 - 3D mapping of synaptic connections within “in silico” microcircuits of full compartmental neurons in extended networks on the example of VPM axons projecting into S1 of rats. T2 - Conference Abstract, Neuroinformatics Y1 - 2009 U6 - https://doi.org/10.3389/conf.neuro.11.2009.08.092 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Binner, Richard A1 - Prohaska, Steffen A1 - Dercksen, Vincent J. A1 - Kuß, Anja A1 - Kalbe, Ute T1 - Determining Geometric Grain Structure from X-Ray Micro-Tomograms of Gradated Soil T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 37 EP - 52 ER -