84 results on '"Steffen Prohaska"'
Search Results
2. Microtubule reorganization during female meiosis in C. elegans
- Author
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Ina Lantzsch, Che-Hang Yu, Yu-Zen Chen, Vitaly Zimyanin, Hossein Yazdkhasti, Norbert Lindow, Erik Szentgyoergyi, Ariel M Pani, Steffen Prohaska, Martin Srayko, Sebastian Fürthauer, and Stefanie Redemann
- Subjects
Meiosis ,tomography ,mathematical modelling ,microtubules ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic Caenorhabditis elegans spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin.
- Published
- 2021
- Full Text
- View/download PDF
3. Quantitative PA tomography of high resolution 3-D images: Experimental validation in a tissue phantom
- Author
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Jens Buchmann, Bernhard Kaplan, Samuel Powell, Steffen Prohaska, and Jan Laufer
- Subjects
Physics ,QC1-999 ,Acoustics. Sound ,QC221-246 ,Optics. Light ,QC350-467 - Abstract
Quantitative photoacoustic tomography aims to recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. Keywords: Quantitative photoacoustic imaging, Blood oxygen saturation, Inverse problem, Model based inversion, Monte Carlo, Spectral unmixing
- Published
- 2020
- Full Text
- View/download PDF
4. Male meiotic spindle features that efficiently segregate paired and lagging chromosomes
- Author
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Gunar Fabig, Robert Kiewisz, Norbert Lindow, James A Powers, Vanessa Cota, Luis J Quintanilla, Jan Brugués, Steffen Prohaska, Diana S Chu, and Thomas Müller-Reichert
- Subjects
male meiosis ,chromosome segregation ,lagging chromosome ,spindle ,anaphase A ,anaphase B ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Chromosome segregation during male meiosis is tailored to rapidly generate multitudes of sperm. Little is known about mechanisms that efficiently partition chromosomes to produce sperm. Using live imaging and tomographic reconstructions of spermatocyte meiotic spindles in Caenorhabditis elegans, we find the lagging X chromosome, a distinctive feature of anaphase I in C. elegans males, is due to lack of chromosome pairing. The unpaired chromosome remains tethered to centrosomes by lengthening kinetochore microtubules, which are under tension, suggesting that a ‘tug of war’ reliably resolves lagging. We find spermatocytes exhibit simultaneous pole-to-chromosome shortening (anaphase A) and pole-to-pole elongation (anaphase B). Electron tomography unexpectedly revealed spermatocyte anaphase A does not stem solely from kinetochore microtubule shortening. Instead, movement of autosomes is largely driven by distance change between chromosomes, microtubules, and centrosomes upon tension release during anaphase. Overall, we define novel features that segregate both lagging and paired chromosomes for optimal sperm production.
- Published
- 2020
- Full Text
- View/download PDF
5. C. elegans chromosomes connect to centrosomes by anchoring into the spindle network
- Author
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Stefanie Redemann, Johannes Baumgart, Norbert Lindow, Michael Shelley, Ehssan Nazockdast, Andrea Kratz, Steffen Prohaska, Jan Brugués, Sebastian Fürthauer, and Thomas Müller-Reichert
- Subjects
Science - Abstract
A connection between centrosomes and chromosomes is a key feature of mitotic spindles. Here the authors generate 3D reconstructions of whole mitotic spindles in earlyC. elegansembryos and show that chromosomes are anchored by the entire spindle network and that connections through kinetochore microtubules are few and likely very transient.
- Published
- 2017
- Full Text
- View/download PDF
6. Automated segmentation of complex patterns in biological tissues: Lessons from stingray tessellated cartilage.
- Author
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David Knötel, Ronald Seidel, Steffen Prohaska, Mason N Dean, and Daniel Baum
- Subjects
Medicine ,Science - Abstract
Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays.Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size.Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.
- Published
- 2017
- Full Text
- View/download PDF
7. Automated stitching of microtubule centerlines across serial electron tomograms.
- Author
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Britta Weber, Erin M Tranfield, Johanna L Höög, Daniel Baum, Claude Antony, Tony Hyman, Jean-Marc Verbavatz, and Steffen Prohaska
- Subjects
Medicine ,Science - Abstract
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.
- Published
- 2014
- Full Text
- View/download PDF
8. Image-Error-Based Level of Detail for Landscape Visualization.
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Malte Clasen and Steffen Prohaska
- Published
- 2010
- Full Text
- View/download PDF
9. TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory.
- Author
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Jan Reininghaus, David Günther, Ingrid Hotz, Steffen Prohaska, and Hans-Christian Hege
- Published
- 2010
- Full Text
- View/download PDF
10. Automatic Alignment of Stacks of Filament Data.
- Author
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Vincent J. Dercksen, Britta Weber, David Günther, Marcel Oberländer, Steffen Prohaska, and Hans-Christian Hege
- Published
- 2009
- Full Text
- View/download PDF
11. Dual streamline seeding.
- Author
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Olufemi Rosanwo, Christoph Petz, Steffen Prohaska, Hans-Christian Hege, and Ingrid Hotz
- Published
- 2009
- Full Text
- View/download PDF
12. Near-Wall Flow Visualization in Flattened Surface Neighborhoods.
- Author
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Christoph Petz, Steffen Prohaska, Leonid Goubergrits, Ulrich Kertzscher, and Hans-Christian Hege
- Published
- 2008
13. Ontology-Based Visualization of Hierarchical Neuroanatomical Structures.
- Author
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Anja Kuß, Steffen Prohaska, Björn Meyer, Jürgen Rybak, and Hans-Christian Hege
- Published
- 2008
- Full Text
- View/download PDF
14. Semi‐automatic stitching of filamentous structures in image stacks from serial‐section electron tomography
- Author
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Gunar Fabig, Florian N. Brünig, Thomas Müller-Reichert, Robert Kiewisz, Steffen Prohaska, Norbert Lindow, Vincent J. Dercksen, Daniel Baum, and Stefanie Redemann
- Subjects
Electron Microscope Tomography ,Histology ,Computer science ,business.industry ,Histological Techniques ,3D reconstruction ,Process (computing) ,Spindle Apparatus ,Tracing ,Microtubules ,Pipeline (software) ,Pathology and Forensic Medicine ,Visualization ,Image stitching ,Imaging, Three-Dimensional ,Software ,Electron tomography ,Image Processing, Computer-Assisted ,Computer vision ,Tomography ,Artificial intelligence ,business ,Interactive visualization - Abstract
We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, 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 labour. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists 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 dealing with imperfect data 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 visualisation of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialised, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualisation and interaction tools for each processing step to guarantee real-time response, and an optimised workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists. LAY DESCRIPTION: Electron tomography of biological samples is used for a three-dimensional (3D) reconstruction of filamentous structures, such as microtubules (MTs) in mitotic and meiotic spindles. Large-scale electron tomography can be applied to increase the reconstructed volume for the visualisation of full spindles. For this, each spindle is cut into a series of semi-thick physical sections, from 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. Previously, we presented fully automatic approaches for this 3D reconstruction pipeline. However, large volumes often suffer from imperfections (ie physical distortions) caused by the image acquisition process, making it difficult to apply fully automatic approaches for matching and stitching of numerous tomograms. Therefore, we developed an interactive, semi-automatic solution that considers all requirements for large-scale stitching of microtubules in image stacks of consecutive sections. We achieved this by combining automatic methods, visual validation and interactive error correction, thus allowing the user to continuously improve the result by interactively correcting landmarks or matches of filaments. We present large-scale reconstructions of spindles in which the automatic workflow failed and where different steps of manual corrections were needed. Our approach is also applicable to other biological samples showing 3D distributions of MTs in a number of different cellular contexts.
- Published
- 2021
15. Visualization of Time-Dependent Remote Adaptive Mesh Refinement Data.
- Author
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Ralf Kähler, Steffen Prohaska, Andrei Hutanu, and Hans-Christian Hege
- Published
- 2005
- Full Text
- View/download PDF
16. Fast Cross-sectional Display of Large Data Sets.
- Author
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Vincent J. Dercksen, Steffen Prohaska, and Hans-Christian Hege
- Published
- 2005
17. Skeletonzation by Blocks for Large 3D Datasets: Application To Brain Microcirculation.
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Céline Fouard, Grégoire Malandain, Steffen Prohaska, Malte Westerhoff, Francis Cassot, Christophe Mazel, Didier Asselot, and Jean-Pierre Marc-Vergnes
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- 2004
- Full Text
- View/download PDF
18. Interactive Exploration of Large Remote Micro-CT Scans.
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Steffen Prohaska, Andrei Hutanu, Ralf Kähler, and Hans-Christian Hege
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- 2004
- Full Text
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19. Fast Visualization of Plane-Like Structures in Voxel Data.
- Author
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Steffen Prohaska and Hans-Christian Hege
- Published
- 2002
- Full Text
- View/download PDF
20. Accelerated Visualization of Dynamic Molecular Surfaces.
- Author
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Norbert Lindow, Daniel Baum, Steffen Prohaska, and Hans-Christian Hege
- Published
- 2010
- Full Text
- View/download PDF
21. Effective Techniques to Visualize Filament-Surface Relationships.
- Author
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Anja Kuß, M. Gensel, Björn Meyer, Vincent J. Dercksen, and Steffen Prohaska
- Published
- 2010
- Full Text
- View/download PDF
22. Hierarchical Vortex Regions in Swirling Flow.
- Author
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Christoph Petz, Jens Kasten, Steffen Prohaska, and Hans-Christian Hege
- Published
- 2009
- Full Text
- View/download PDF
23. Extraction Of Feature Lines On Surface Meshes Based On Discrete Morse Theory.
- Author
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Jan Sahner, Britta Weber, Steffen Prohaska, and Hans Lamecker
- Published
- 2008
- Full Text
- View/download PDF
24. Blockwise processing applied to brain microvascular network study.
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Céline Fouard, Grégoire Malandain, Steffen Prohaska, and Malte Westerhoff
- Published
- 2006
- Full Text
- View/download PDF
25. Distributed and collaborative visualization of large data sets using high-speed networks.
- Author
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Andrei Hutanu, Gabrielle Allen, Stephen David Beck, Petr Holub, Hartmut Kaiser, Archit Kulshrestha, Milos Liska, Jon MacLaren, Ludek Matyska, Ravi Paruchuri, Steffen Prohaska, Edward Seidel, Brygg Ullmer, and Shalini Venkataraman
- Published
- 2006
- Full Text
- View/download PDF
26. Modeling Bone Resorption in 2D CT and 3D muct Images.
- Author
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Alexey Zaikin, Jürgen Kurths, Peter Saparin, W. Gowin, and Steffen Prohaska
- Published
- 2005
- Full Text
- View/download PDF
27. Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition.
- Author
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Marco Klindt, Steffen Prohaska, Daniel Baum, and Hans-Christian Hege
- Published
- 2012
- Full Text
- View/download PDF
28. Microtubule reorganization during female meiosis in C. elegans
- Author
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Ariel M. Pani, Ina Lantzsch, Stefanie Redemann, Norbert Lindow, Sebastian Fürthauer, Vitaly Zimyanin, Che-Hang Yu, Hossein Yazdkhasti, Yu-Zen Chen, Steffen Prohaska, Erik Szentgyoergyi, and Martin Srayko
- Subjects
QH301-705.5 ,Science ,Female meiosis ,Katanin ,tomography ,Biology ,General Biochemistry, Genetics and Molecular Biology ,microtubules ,03 medical and health sciences ,0302 clinical medicine ,Meiosis ,Microtubule ,mathematical modelling ,Biology (General) ,Metaphase ,030304 developmental biology ,Anaphase ,Microtubule severing ,0303 health sciences ,General Immunology and Microbiology ,General Neuroscience ,Chromosome ,General Medicine ,Cell biology ,biology.protein ,Medicine ,030217 neurology & neurosurgery - Abstract
The female meiotic spindles of most animals are acentrosomal and undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of acentrosomal spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic C. elegans spindles undergoing the transition from metaphase to anaphase. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over on second time scales. The results show that the transition from metaphase to anaphase correlates with an increase in the number of microtubules and a decrease in their average length. Detailed analysis of the tomographic data revealed that the length of microtubules changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for those microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the observed large-scale reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those that are closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe alone. In anaphase, even microtubules close to the chromosomes show no signs of cutting. This suggests that the most prominent drivers of spindle rearrangements from metaphase to anaphase are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on the presence of katanin.
- Published
- 2021
29. Author response: Microtubule reorganization during female meiosis in C. elegans
- Author
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Vitaly Zimyanin, Hossein Yazdkhasti, Ina Lantzsch, Che-Hang Yu, Martin Srayko, Yu-Zen Chen, Erik Szentgyoergyi, Ariel M. Pani, Norbert Lindow, Steffen Prohaska, Sebastian Fürthauer, and Stefanie Redemann
- Subjects
Microtubule ,Female meiosis ,Biology ,Cell biology - Published
- 2021
30. Microtubule re-organization during female meiosis in C. elegans
- Author
-
Ina Lantzsch, Che-Hang Yu, Yu-Zen Chen, Vitaly Zimyanin, Hossein Yazdkhasti, Norbert Lindow, Erik Szentgyörgyi, Ariel Pani, Steffen Prohaska, Martin Srayko, Sebastian Fürthauer, and Stefanie Redemann
- Subjects
Meiosis ,Electron tomography ,Microtubule ,Female meiosis ,Length distribution ,Biology ,Metaphase ,Anaphase ,Cell biology - Abstract
The female meiotic spindles of most animals are acentrosomal and undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of acentrosomal spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown.To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic C. elegans spindles undergoing the transition from metaphase to anaphase. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over on second time scales. The results show that the transition from metaphase to anaphase correlates with an increase in the number of microtubules and a decrease in their average length. Detailed analysis of the tomographic data revealed that the length of microtubules changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for those microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the observed large-scale reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those that are closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe alone. In anaphase, even microtubules close to the chromosomes show no signs of cutting. This suggests that the most prominent drivers of spindle rearrangements from metaphase to anaphase are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on the presence of katanin.
- Published
- 2020
31. Microtubule reorganization during female meiosis in
- Author
-
Ina, Lantzsch, Che-Hang, Yu, Yu-Zen, Chen, Vitaly, Zimyanin, Hossein, Yazdkhasti, Norbert, Lindow, Erik, Szentgyoergyi, Ariel M, Pani, Steffen, Prohaska, Martin, Srayko, Sebastian, Fürthauer, and Stefanie, Redemann
- Subjects
Electron Microscope Tomography ,Bayes Theorem ,Spindle Apparatus ,Cell Biology ,Models, Theoretical ,tomography ,Microtubules ,Chromosomes ,Meiosis ,Chromosome Segregation ,Oocytes ,C. elegans ,Animals ,Female ,mathematical modelling ,Anaphase ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Katanin ,Metaphase ,Research Article ,Computational and Systems Biology - Abstract
Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic Caenorhabditis elegans spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin.
- Published
- 2020
32. Author response: Male meiotic spindle features that efficiently segregate paired and lagging chromosomes
- Author
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Diana S Chu, Jan Brugués, Steffen Prohaska, Norbert Lindow, James A. Powers, Thomas Müller-Reichert, Luis J Quintanilla, Vanessa Cota, Gunar Fabig, and Robert Kiewisz
- Subjects
Genetics ,Meiosis ,Biology ,Lagging - Published
- 2020
33. Quantitative PA tomography of high resolution 3-D images: Experimental validation in a tissue phantom
- Author
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Jens, Buchmann, Bernhard, Kaplan, Samuel, Powell, Steffen, Prohaska, and Jan, Laufer
- Subjects
Physics::Medical Physics ,lcsh:QC221-246 ,530 Physik ,blood oxygen saturation ,lcsh:QC1-999 ,spectral unmixing ,lcsh:Acoustics. Sound ,inverse problem ,lcsh:QC350-467 ,quantitative photoacoustic imaging ,ddc:530 ,model based inversion ,Monte Carlo ,lcsh:Physics ,lcsh:Optics. Light ,Research Article - Abstract
Quantitative photoacoustic tomography aims to recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. Keywords: Quantitative photoacoustic imaging, Blood oxygen saturation, Inverse problem, Model based inversion, Monte Carlo, Spectral unmixing
- Published
- 2020
34. Male meiotic spindle features that efficiently segregate paired and lagging chromosomes
- Author
-
Steffen Prohaska, Jan Brugués, Leslie J. Mateo, Thomas Müller-Reichert, James A. Powers, Gunar Fabig, Robert Kiewisz, Vanessa Cota, Diana S Chu, and Norbert Lindow
- Subjects
Male ,X Chromosome ,QH301-705.5 ,Science ,chromosome segregation ,Spindle Apparatus ,Spermatocyte ,Biology ,General Biochemistry, Genetics and Molecular Biology ,male meiosis ,Chromosome segregation ,Kinetochore microtubule ,03 medical and health sciences ,0302 clinical medicine ,Meiosis ,Spermatocytes ,anaphase B ,anaphase A ,medicine ,Animals ,lagging chromosome ,Biology (General) ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,X chromosome ,030304 developmental biology ,Anaphase ,Structure formation and active systems ,0303 health sciences ,General Immunology and Microbiology ,Kinetochore ,General Neuroscience ,030302 biochemistry & molecular biology ,Cell Biology ,General Medicine ,spindle ,Cell biology ,Chromosome Pairing ,medicine.anatomical_structure ,Centrosome ,C. elegans ,Medicine ,030217 neurology & neurosurgery ,Research Article - Abstract
Chromosome segregation during male meiosis is tailored to rapidly generate multitudes of sperm. Little, however, is known about the mechanisms that efficiently segregate chromosomes to produce sperm. Using live imaging inCaenorhabditis elegans, we find that spermatocytes exhibit simultaneous pole-to-chromosome shortening (anaphase A) and pole-to-pole elongation (anaphase B). Electron tomography unexpectedly revealed that spermatocyte anaphase A does not stem from kinetochore microtubule shortening. Instead, movement is driven by changes in distance between chromosomes, microtubules, and centrosomes upon tension release at anaphase onset. We also find that the lagging X chromosome, a distinctive feature of anaphase I inC. elegansmales, is due to lack of chromosome pairing. The unpaired chromosome remains tethered to centrosomes by continuously lengthening kinetochore microtubules which are under tension, suggesting a ‘tug of war’ that can reliably resolve chromosome lagging. Overall, we define features that partition both paired and lagging chromosomes for optimal sperm production.
- Published
- 2019
- Full Text
- View/download PDF
35. Serial synapse formation through filopodial competition for synaptic seeding factors
- Author
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Ferdi Ridvan Kiral, Vincent J. Dercksen, Max von Kleist, Steffen Prohaska, Heike Wolfenberg, Mehmet Neset Özel, Josephine Brummer, Marian Moldenhauer, P. Robin Hiesinger, Abhishek Kulkarni, Martin Weiser, Ilsa-Maria Daumann, and Amr Hasan
- Subjects
Neurogenesis ,Growth Cones ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Live cell imaging ,medicine ,Synapse formation ,Animals ,Drosophila Proteins ,Computer Simulation ,Pseudopodia ,Axon ,Growth cone ,Molecular Biology ,Analysis method ,030304 developmental biology ,0303 health sciences ,Synapse assembly ,GTPase-Activating Proteins ,Intracellular Signaling Peptides and Proteins ,Gene Expression Regulation, Developmental ,Cell Biology ,Phosphoproteins ,Axons ,medicine.anatomical_structure ,Entire axon ,Drosophila melanogaster ,Synapses ,Axon guidance ,Seeding ,Neuroscience ,Filopodia ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
SummaryFollowing axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a ‘serial synapse formation’ model, where at any time point only a single ‘synaptogenic’ filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial ‘winner-takes-all’ mechanism that ensures the formation of an appropriate number of synapses.
- Published
- 2019
36. Quantitative inversion of 3D multiwavelength photoacoustic images using an adjoint radiance Monte Carlo model (Conference Presentation)
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Samuel Powell, Steffen Prohaska, Jens Buchmann, Jan Laufer, and Bernhard Kaplan
- Subjects
Wavelength ,Scanner ,Materials science ,Optics ,Scattering ,business.industry ,Monte Carlo method ,Radiance ,Tomography ,Chromophore ,Inverse problem ,business - Abstract
Quantitative photoacoustic (PA) tomography aims to recover absolute chromophore concentrations from multiwavelength PA images. Challenges include the accurate prediction of the fluence, the accuracy of the initial pressure distribution reconstructed from measured data, and the large scale of the inverse problem involving high resolution 3D images. In this study, a radiance Monte-Carlo (RMC) light model was used to predict the fluence inside tissue phantoms. Gradients of the scattering coefficient and the chromophore concentrations were calculated using the adjoint formalism. The gradient descent efficiency was significantly improved by using adaptive moment estimation. 3D maps of chromophore concentrations and the scattering coefficient were recovered from measured PA images. The inversion scheme was validated on measured images of a tissue phantom consisting of a scattering liquid and chromophore-filled polymer tubes immersed at different depths. The images were acquired at visible and near-infrared wavelengths using a Fabry-Perot scanner with a planar detection geometry. Amplitude mismatches in the reconstructed initial pressure images due to limited view detection were corrected using an ad hoc correction method. The inversion was stabilized by introducing a calibrated absorber in the imaged volume, or an absolute calibration of the setup. 3D maps of absolute chromophore concentrations, their ratios, and the global scattering coefficient were accurately recovered. The recovery of chromophore concentrations in the image background where SNR is low was identified as a significant new challenge for quantitative PA imaging.
- Published
- 2019
37. Quantification of three-dimensional spindle architecture
- Author
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Norbert, Lindow, Stefanie, Redemann, Florian, Brünig, Gunar, Fabig, Thomas, Müller-Reichert, and Steffen, Prohaska
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Electron Microscope Tomography ,Meiosis ,Animals ,Mitosis ,Spindle Apparatus ,Microtubules ,Chromosomes - Abstract
Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.
- Published
- 2018
38. Quantification of Chromophore Concentrations from Multispectral 3D Photoacoustic Images Using an Adjoint Monte-Carlo-based Inversion
- Author
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Steffen Prohaska, Jan Laufer, Samuel Powell, Jens Buchmann, and Bernhard Kaplan
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Materials science ,Deep tissue ,Attenuation coefficient ,Multispectral image ,Monte Carlo method ,Radiative transfer ,Photoacoustic imaging in biomedicine ,Tomography ,Chromophore ,Biological system - Abstract
An adjoint Monte-Carlo model was used to recover absolute chromophore concentrations and their ratios from 3D photoacoustic (PA) images. The method is an important step towards functional quantitative PA tomography (qPAT) in deep tissue.
- Published
- 2018
39. Chromosome Segregation in C. Elegans Female Meiosis is Accompanied by a Switch in Lateral to End-On Microtubule Orientation
- Author
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Ina Lantzsch, Martin Srayko, Stefanie Redemann, Steffen Prohaska, Norbert Lindow, and Thomas Müller-Reichert
- Subjects
Chromosome segregation ,Meiosis ,Microtubule ,Female meiosis ,Chromosome ,Biology ,Orientation (graph theory) ,Metaphase ,Cell biology ,Anaphase - Abstract
Acentrosomal female meiotic spindles of many organisms undergo a transition of the microtubule cytoskeleton from a bipolar spindle in metaphase to an inter-chromosomal array in anaphase. Two opposing modes of microtubule-to-chromosome orientation have been previously proposed during chromosome partitioning in C. elegans oocytes, i.e., lateral attachment of microtubule bundles to chromosomes versus inter-chromosomal organization of microtubules. Here we applied large-scale electron tomography of staged C. elegans oocytes in meiosis to show that the re-organization of microtubules is accompanied by a switch from a lateral to an end-on orientation of microtubules to chromosomes. We further show that this transition in microtubule orientation involves the microtubule depolymerase KLP-7 to remove laterally associated microtubules around chromosomes, thus contributing to a high fidelity in chromosome segregation. These results indicate that both modes of microtubule-to-chromosome orientation operate successively in oocyte meiosis to segregate chromosomes.
- Published
- 2018
40. Quantification of three-dimensional spindle architecture
- Author
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Steffen Prohaska, Norbert Lindow, Thomas Müller-Reichert, Florian N. Brünig, Stefanie Redemann, and Gunar Fabig
- Subjects
0301 basic medicine ,business.industry ,3D reconstruction ,Biology ,Image stitching ,03 medical and health sciences ,030104 developmental biology ,Software ,Electron tomography ,Microtubule ,Automatic segmentation ,business ,Biological system ,Mitosis - Abstract
Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.
- Published
- 2018
41. Cell Adhesion: The Role of Titanium Surface Nanostructuring on Preosteoblast Morphology, Adhesion, and Migration (Adv. Healthcare Mater. 15/2017)
- Author
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Ekaterina V. Skorb, Petra Knaus, John W. C. Dunlop, Steffen Prohaska, Marc Osterland, Peter Fratzl, Christian Hiepen, and Yulia Zhukova
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Biomaterials ,Materials science ,Morphology (linguistics) ,chemistry ,Biomedical Engineering ,Pharmaceutical Science ,chemistry.chemical_element ,Nanotopography ,Titanium surface ,Nanotechnology ,Adhesion ,Cell adhesion ,Titanium - Published
- 2017
42. C. elegans chromosomes connect to centrosomes by anchoring into the spindle network
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Thomas Mueller-Reichert, Steffen Prohaska, Ehssan Nazockdast, Andrea Kratz, Sebastian Fuerthauer, Johannes Baumgart, Norbert Lindow, Stefanie Redemann, Jan Brugués, and Michael Shelley
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0301 basic medicine ,Embryo, Nonmammalian ,Science ,Biophysics ,General Physics and Astronomy ,Anchoring ,Spindle Apparatus ,Biology ,Microtubules ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Article ,Chromosomes ,03 medical and health sciences ,0302 clinical medicine ,Imaging, Three-Dimensional ,Microtubule ,Animals ,Caenorhabditis elegans ,Kinetochores ,Mitosis ,030304 developmental biology ,Centrosome ,0303 health sciences ,Stochastic Processes ,Multidisciplinary ,Kinetochore ,Extramural ,General Chemistry ,Living matter ,Spindle apparatus ,Cell biology ,030104 developmental biology ,Electron tomography ,Astral microtubules ,030217 neurology & neurosurgery - Abstract
The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient., A connection between centrosomes and chromosomes is a key feature of mitotic spindles. Here the authors generate 3D reconstructions of whole mitotic spindles in early C. elegans embryos and show that chromosomes are anchored by the entire spindle network and that connections through kinetochore microtubules are few and likely very transient.
- Published
- 2017
43. Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography
- Author
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Jens Buchmann, Bernhard Kaplan, Jan Laufer, and Steffen Prohaska
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Physics ,business.industry ,Physics::Medical Physics ,Monte Carlo method ,Partial volume ,Image segmentation ,Inverse problem ,01 natural sciences ,030218 nuclear medicine & medical imaging ,Computational physics ,010309 optics ,03 medical and health sciences ,0302 clinical medicine ,Optics ,Planar ,Region of interest ,0103 physical sciences ,Boundary value problem ,Coordinate descent ,business - Abstract
The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.
- Published
- 2017
44. NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases
- Author
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Marta Costa, Aaron D. Ostrovsky, Steffen Prohaska, James D. Manton, Gregory S.X.E. Jefferis, Manton, James [0000-0001-9260-3156], Jefferis, Gregory [0000-0002-0587-9355], and Apollo - University of Cambridge Repository
- Subjects
0301 basic medicine ,Time Factors ,Databases, Factual ,Nerve net ,Computer science ,Neuroscience(all) ,Statistics as Topic ,03 medical and health sciences ,0302 clinical medicine ,Similarity (network science) ,medicine ,Animals ,Cluster Analysis ,Cluster analysis ,030304 developmental biology ,Structure (mathematical logic) ,Neurons ,0303 health sciences ,business.industry ,General Neuroscience ,NBLAST ,Probabilistic logic ,Brain ,Computational Biology ,Pattern recognition ,Neuroinformatics ,cell type ,online resource ,neuroinformatics ,NeuroResource ,030104 developmental biology ,medicine.anatomical_structure ,neuron similarity ,nervous system ,Pairwise comparison ,Neuron ,Artificial intelligence ,Nerve Net ,business ,Neuroscience ,030217 neurology & neurosurgery ,Algorithms ,clustering - Abstract
Summary Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. Video Abstract, Highlights • NBLAST is a fast and sensitive algorithm to measure pairwise neuronal similarity • NBLAST can distinguish neuronal types at the finest level without training • Automated clustering of 16,129 Drosophila neurons identifies 1,052 classes • Online search tool for databases of single neurons or genetic driver lines, Thousands of single-neuron images are being generated by efforts to map circuits and define neuronal types. Costa et al. validate a new neuronal similarity algorithm, NBLAST, demonstrating that it can distinguish neuronal types and organize huge datasets.
- Published
- 2016
- Full Text
- View/download PDF
45. A Switch in Microtubule Orientation during C. elegans Meiosis
- Author
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Norbert Lindow, Thomas Müller-Reichert, Martin Srayko, Ina Lantzsch, Stefanie Redemann, and Steffen Prohaska
- Subjects
0301 basic medicine ,Kinesins ,Spindle Apparatus ,Biology ,Microtubules ,General Biochemistry, Genetics and Molecular Biology ,Spindle pole body ,Chromosome segregation ,03 medical and health sciences ,0302 clinical medicine ,Meiosis ,Microtubule ,Chromosome Segregation ,medicine ,Animals ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Metaphase ,Anaphase ,Oocyte ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Centrosome ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
Summary In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [ 1 , 2 , 3 , 4 , 5 ]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter-chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter-chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [ 6 , 7 ]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [ 8 , 9 ]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here, we applied large-scale electron tomography [ 10 ] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this, we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.
- Published
- 2018
46. Effective Techniques to Visualize Filament-Surface Relationships
- Author
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Vincent J. Dercksen, B. Meyer, Maria Gensel, Anja Kuß, and Steffen Prohaska
- Subjects
Surface (mathematics) ,Structure (mathematical logic) ,genetic structures ,Computer science ,business.industry ,Line (geometry) ,Computer vision ,Glyph ,Artificial intelligence ,business ,Computer Graphics and Computer-Aided Design ,Intersection (Euclidean geometry) ,Visualization - Abstract
Combined visualizations of filamentous structures and surrounding volumetric objects are common in biological and medical applications. Often, the structures' spatial relationships remain unclear to the viewer. In this paper, we discuss and evaluate techniques to emphasize spatial relationships. We concentrate on the visualization of transparent objects and intersecting lines. Among various techniques, participants of an exploratory user study preferred coloring of lines, marking of line-surface intersections by glyphs, and the combination of both. These techniques were additionally evaluated in a confirmatory study in which participants were asked to judge whether a filament runs through a transparent structure. We found that the evaluated techniques significantly improve the participants' performance in terms of the number of correct responses and response time. The best performance was found for the combination of line coloring and intersection glyph display.
- Published
- 2010
47. Automated segmentation of complex patterns in biological tissues: Lessons from stingray tessellated cartilage
- Author
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Daniel Baum, Steffen Prohaska, David Knötel, Ronald Seidel, and Mason N. Dean
- Subjects
0301 basic medicine ,Computer science ,Anisotropic diffusion ,lcsh:Medicine ,Distance Measurement ,01 natural sciences ,Pattern Recognition, Automated ,Diagnostic Radiology ,010104 statistics & probability ,Medicine and Health Sciences ,Segmentation ,Skates, Fish ,lcsh:Science ,Tomography ,Measurement ,Ground truth ,Multidisciplinary ,Geography ,Physics ,Radiology and Imaging ,Software Engineering ,Condensed Matter Physics ,Thresholding ,Connective Tissue ,Physical Sciences ,Pattern recognition (psychology) ,Engineering and Technology ,Anatomy ,Watersheds ,Algorithms ,Smoothing ,Research Article ,Computer and Information Sciences ,Watershed ,Imaging Techniques ,Materials Science ,Material Properties ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Neuroimaging ,Image Analysis ,Research and Analysis Methods ,03 medical and health sciences ,Diagnostic Medicine ,Animals ,0101 mathematics ,Preprocessing ,business.industry ,lcsh:R ,Biology and Life Sciences ,Pattern recognition ,X-Ray Microtomography ,Image segmentation ,Computed Axial Tomography ,Cartilage ,Biological Tissue ,030104 developmental biology ,Physical Geography ,Earth Sciences ,Anisotropy ,lcsh:Q ,Artificial intelligence ,business ,Distance transform ,Neuroscience - Abstract
Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.
- Published
- 2017
48. Extraction Of Feature Lines On Surface Meshes Based On Discrete Morse Theory
- Author
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Steffen Prohaska, Britta Weber, Jan Sahner, and Hans Lamecker
- Subjects
Computer science ,Feature (computer vision) ,ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION ,Scalar (mathematics) ,Discrete Morse theory ,Polygon mesh ,Local feature size ,Topology ,Computer Graphics and Computer-Aided Design ,ComputingMethodologies_COMPUTERGRAPHICS ,Vertex (geometry) - Abstract
We present an approach for extracting extremal feature lines of scalar indicators on surface meshes, based on discrete Morse Theory. By computing initial Morse-Smale complexes of the scalar indicators of the mesh, we obtain a candidate set of extremal feature lines of the surface. A hierarchy of Morse-Smale complexes is computed by prioritizing feature lines according to a novel criterion and applying a cancellation procedure that allows us to select the most significant lines. Given the scalar indicators on the vertices of the mesh, the presented feature line extraction scheme is interpolation free and needs no derivative estimates. The technique is insensitive to noise and depends only on one parameter: the feature significance. We use the technique to extract surface features yielding impressive, non photorealistic images.
- Published
- 2008
49. Registering 2D and 3D imaging data of bone during healing
- Author
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Daniel Baum, Wolfgang Wagermaier, Hans-Christian Hege, Steffen Prohaska, Rebecca M. Hoerth, Peter Fratzl, David Knötel, Georg N. Duda, and Bettina M. Willie
- Subjects
Fracture Healing ,Computer science ,Micro computed tomography ,Experimental data ,Cell Biology ,X-Ray Microtomography ,Backscattered electron ,Biochemistry ,Imaging data ,Bone and Bones ,Rats ,Imaging, Three-Dimensional ,Rheumatology ,Three dimensional visualization ,Calcium content ,Image Processing, Computer-Assisted ,Microscopy, Electron, Scanning ,Animals ,Orthopedics and Sports Medicine ,Research questions ,Tomography ,Tomography, X-Ray Computed ,Molecular Biology ,Biomedical engineering - Abstract
PURPOSE/AIMS OF THE STUDY: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro-computed tomography (µCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure.We investigated bone during healing by means of µCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties.We present an approach for the registration of 2D data in a 3D µCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into µCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way.By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.
- Published
- 2015
50. Blockwise processing applied to brain microvascular network study
- Author
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Grégoire Malandain, Malte Westerhoff, C. Fouard, Steffen Prohaska, Analysis and Simulation of Biomedical Images (ASCLEPIOS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB), Zuse Institute Berlin (ZIB), and MicroVisu3D
- Subjects
digital topology ,Computer science ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Information Storage and Retrieval ,Computing Methodologies ,Sensitivity and Specificity ,Skeletonization ,Mosaic ,Pattern Recognition, Automated ,medial axis ,Image (mathematics) ,Imaging, Three-Dimensional ,topological thinning ,Artificial Intelligence ,Medial axis ,Image Interpretation, Computer-Assisted ,[INFO.INFO-IM]Computer Science [cs]/Medical Imaging ,Humans ,skeleton ,Computer vision ,Electrical and Electronic Engineering ,Representation (mathematics) ,Digital topology ,Microscopy, Confocal ,Radiological and Ultrasound Technology ,image mosaic ,business.industry ,Microcirculation ,Homotopy ,Brain ,Reproducibility of Results ,Image Enhancement ,Computer Science Applications ,Cerebrovascular Circulation ,Chamfer map ,Artificial intelligence ,Focus (optics) ,business ,Algorithms ,Software - Abstract
International audience; The study of cerebral microvascular networks requires high-resolution images. However, to obtain statistically relevant results, a large area of the brain (several square millimeters) must be analyzed. This leads us to consider huge images, too large to be loaded and processed at once in the memory of a standard computer. To consider a large area, a compact representation of the vessels is required. The medial axis is the preferred tool for this application. To extract it, a dedicated skeletonization algorithm is proposed. Numerous approaches already exist which focus on computational efficiency. However, they all implicitly assume that the image can be completely processed in the computer memory, which is not realistic with the large images considered here. We present in this paper a skeletonization algorithm that processes data locally (in subimages) while preserving global properties (i.e., homotopy). We then show some results obtained on a mosaic of three-dimensional images acquired by confocal microscopy.
- Published
- 2006
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