TY - JOUR A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms JF - PLoS ONE Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0113222 SP - e113222 ER - TY - GEN A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms N2 - Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts’ opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort. T3 - ZIB-Report - 14-41 KW - electron tomography KW - microtubules KW - serial sectioning KW - image analysis KW - geometry reconstruction KW - image and geometry alignment KW - point correspondence Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52958 SN - 1438-0064 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 - 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 - 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 - 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 - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie T2 - Tagungsband der DACH Jahrestagung 2012 Y1 - 2012 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2012 SP - 321 EP - 330 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Breßler, David A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben T2 - Tagungsband der DGZfP Jahrestagung 2013 Y1 - 2013 ER - TY - JOUR 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 A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - bioRxiv N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining 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. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. Y1 - 2020 U6 - https://doi.org/10.1101/2020.05.28.120899 ER -