TY - GEN A1 - Redemann, Stefanie A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Hyman, Anthony A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Müller-Reichert, Thomas T1 - The Segmentation of Microtubules in Electron Tomograms Using Amira T2 - Mitosis: Methods and Protocols Y1 - 2014 U6 - https://doi.org/10.1007/978-1-4939-0329-0_12 SP - 261 EP - 278 PB - Springer ER - TY - JOUR A1 - Rigort, Alexander A1 - Günther, David A1 - Hegerl, Reiner A1 - Baum, Daniel A1 - Weber, Britta A1 - Prohaska, Steffen A1 - Medalia, Ohad A1 - Baumeister, Wolfgang A1 - Hege, Hans-Christian T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks JF - Journal of Structural Biology Y1 - 2012 U6 - https://doi.org/10.1016/j.jsb.2011.08.012 VL - 177 SP - 135 EP - 144 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Weber, Britta A1 - Hege, Hans-Christian T1 - Probabilistic Marching Cubes JF - Computer Graphics Forum Y1 - 2011 U6 - https://doi.org/10.1111/j.1467-8659.2011.01942.x VL - 30 IS - 3 SP - 931 EP - 940 ER - TY - THES A1 - Weber, Britta T1 - Merkmalskurven auf triangulierten Oberflächen Y1 - 2008 ER - TY - JOUR A1 - Weber, Britta A1 - Greenan, Garrett A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Müller-Reichert, Thomas A1 - Hyman, Anthony A1 - Verbavatz, Jean-Marc T1 - Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos JF - Journal of Structural Biology Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1047847711003509 U6 - https://doi.org/10.1016/j.jsb.2011.12.004 VL - 178 IS - 2 SP - 129 EP - 138 ER - TY - THES A1 - Weber, Britta T1 - Reconstruction of Microtubule Centerlines from Electron Tomograms N2 - The organization of the mitotic spindle, a structure that separates the chromosomes during cell division, is an active research topic in molecular cell biology. It is composed of microtubules, elongated tubular macromolecules with a diameter of 25 nm. The only volumetric imaging technique that is available to a wide community and provides the required resolution to capture details about microtubules is electron tomography. However, the automatic detection of microtubules in electron tomograms is a difficult task due to the low contrast of the data. Furthermore, thick samples have to be cut into 300 nm thin sections before electron tomography can be applied. Software for automatically segmentation and stitching of the microtubules are not available and therefore these tasks have to be performed manually. Unfortunately, manual segmentation is time consuming for large samples and manual stitching of the tomograms is often infeasible due to the lack of prominent features for registration. Conclusions drawn from electron tomographic data is currently mostly based on either small samples containing few microtubules or single sections of complex structures. Consequently, simple properties, such as the length of microtubules in the spindle or their number, are still unknown for most model organisms. In this thesis, we present methods for 1) an automatic segmentation of microtubule centerlines in electron tomograms, and 2) an automatic stitching of the lines extracted from serial sections. For the centerline segmentation, we use 3D template matching and exploit knowledge about shape of microtubules and microscopy artifacts to design the templates. For the registration of the lines, we present a way to model the orientation of lines as a mixture of Fisher-Mises distributions where we estimate transformation parameters with the expectation maximization algorithm. The final line matching problem is formulated in terms of a probabilistic graphical model. To find the correct correspondences of line ends, we use belief propagation. We handle the poor convergence properties of this algorithm by detecting ambiguous and conflicting assignments of lines automatically. An expert can then influence the final output of the algorithm by solving conflicts manually. A detailed error analysis on true biological data and assessment of the reliability of the results is the prerequisite for analyzing the resulting line representations of the microtubules. To this end, the developed workflow for segmenting and stitching of microtubule centerlines is evaluated on plasticembedded samples of C. elegans early embryos and of spindles from X. laevis egg extracts. Our results suggest that the output of the presented algorithms together with little manual correction is of sufficient quality to allow a detailed analysis of dense microtubule networks. Finally, we exemplarily show results for the centrosome of a C. elegans mitotic spindle. KW - microtubules KW - electron tomography KW - c.elegans KW - image processing KW - graphical model KW - gaussian mixture model KW - template matching Y1 - 2015 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000100915 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - JOUR A1 - Sahner, Jan A1 - Weber, Britta A1 - Lamecker, Hans A1 - Prohaska, Steffen T1 - Extraction of feature Lines on surface meshes based on discrete Morse theory JF - Computer Graphics Forum Y1 - 2008 U6 - https://doi.org/10.1111/j.1467-8659.2008.01202.x VL - 27 IS - 3 SP - 735 EP - 742 CY - Eindhoven, Netherlands ER - TY - CHAP A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Prohaska, Steffen T1 - Fast Tracing of Microtubule Centerlines in Electron Tomograms T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - JOUR A1 - Torsney-Weir, Thomas A1 - Saad, Ahmed A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weber, Britta A1 - Verbavatz, Jean-Marc T1 - Tuner: Principled Parameter Finding for Image Segmentation Algorithms Using Visual Response Surface Exploration JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2011 VL - 17 IS - 12 SP - 1892 EP - 1901 ER -