@phdthesis{Prohaska2007, author = {Prohaska, Steffen}, title = {Skeleton-based visualization of massive voxel objects with network-like architecture}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14888}, year = {2007}, abstract = {This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation.}, language = {en} } @misc{RosanwoPetzProhaskaetal.2008, author = {Rosanwo, Olufemi and Petz, Christoph and Prohaska, Steffen and Hotz, Ingrid and Hege, Hans-Christian}, title = {Dual Streamline Seeding - Method and Implementation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11032}, number = {08-49}, year = {2008}, abstract = {This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces.}, language = {en} } @misc{ClasenPaarProhaska2011, author = {Clasen, Malte and Paar, Philip and Prohaska, Steffen}, title = {Level of Detail for Trees Using Clustered Ellipsoids}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-14251}, number = {11-41}, year = {2011}, abstract = {We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts.}, language = {en} } @misc{KlindtBaumProhaskaetal.2013, author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-17731}, year = {2013}, abstract = {We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar. The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage. The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer. The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".}, language = {en} } @inproceedings{ProhaskaHegeGiehletal.2003, author = {Prohaska, Steffen and Hege, Hans-Christian and Giehl, Michael and Gowin, Wolfgang}, title = {A Virtual Laboratory for Assessment of Bone Biopsies}, booktitle = {14th IAA Humans in Space Symposium}, address = {Banff, Alberta, Canada}, pages = {7}, year = {2003}, language = {en} } @inproceedings{SaparinGowinZaikinetal.2003, author = {Saparin, Peter and Gowin, Wolfgang and Zaikin, Alexei and Thomsen, Jesper and Prohaska, Steffen and Hege, Hans-Christian and Kurths, J{\"u}rgen}, title = {Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity}, booktitle = {14th IAA Humans in Space Symposium}, address = {Banff, Alberta, Canada}, year = {2003}, language = {en} } @inproceedings{ProhaskaHegeGiehletal.2003, author = {Prohaska, Steffen and Hege, Hans-Christian and Giehl, Michael and Gowin, Wolfgang}, title = {Interactive Visualization to Support Quantification of Bone Biopsies}, booktitle = {2nd European Congress 'Achievements in Space Medicine into Health Care Practice and Industry'}, address = {Berlin-Adlershof}, year = {2003}, language = {en} } @inproceedings{SaparinGowinZaikinetal.2003, author = {Saparin, Peter and Gowin, Wolfgang and Zaikin, Alexei and Prohaska, Steffen}, title = {Quantification of changes in human bone structure at different skeletal locations using measures of complexity}, booktitle = {2nd European Congress 'Achievements in Space Medicine into Health Care Practice and Industry'}, address = {Berlin-Adlershof}, year = {2003}, language = {en} } @inproceedings{GowinSaparinProhaskaetal.2003, author = {Gowin, Wolfgang and Saparin, Peter and Prohaska, Steffen and Hege, Hans-Christian and Belle, Stefan and Felsenberg, Dieter}, title = {Architectural Reasons for the Femoral Neck Fracture Location}, booktitle = {2nd European Congress 'Achievements in Space Medicine into Health Care Practice and Industry'}, address = {Berlin-Adlershof}, year = {2003}, language = {en} } @inproceedings{ZaikinSaparinProhaskaetal.2003, author = {Zaikin, Alexei and Saparin, Peter and Prohaska, Steffen and Kurths, J{\"u}rgen and Gowin, Wolfgang}, title = {2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures.}, booktitle = {2nd European Congress 'Achievements in Space Medicine into Health Care Practice and Industry'}, address = {Berlin-Adlershof}, year = {2003}, language = {en} } @inproceedings{ThomsenKollerLaibetal.2003, author = {Thomsen, Jesper and Koller, Bruno and Laib, Andreas and Prohaska, Steffen and Giehl, Michael and Gowin, Wolfgang}, title = {Comparison between Static Histomorphometric Measures Conducted by Traditionally 2D Histomorphometry and 3D μ-CT in Human Tibial Biopsies}, booktitle = {2nd European Congress 'Achievements in Space Medicine into Health Care Practice and Industry'}, address = {Berlin-Adlershof}, year = {2003}, language = {en} } @inproceedings{HegeWeinkaufProhaskaetal.2004, author = {Hege, Hans-Christian and Weinkauf, Tino and Prohaska, Steffen and Hutanu, Andrei}, title = {Distributed visualization and analysis of fluid dynamics data}, booktitle = {Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration}, address = {Sendai, Japan}, pages = {145 -- 150}, year = {2004}, language = {en} } @inproceedings{HegeSchirmacherWesterhoffetal.2002, author = {Hege, Hans-Christian and Schirmacher, Hartmut and Westerhoff, Malte and Lamecker, Hans and Prohaska, Steffen and Zachow, Stefan}, title = {From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models}, booktitle = {Proceedings of the Japan Korea Computer Graphics Conference 2002}, publisher = {Kanazawa University}, address = {Kanazawa City, Ishikawa, Japan}, year = {2002}, language = {en} } @article{ProhaskaHegeGiehletal.2002, author = {Prohaska, Steffen and Hege, Hans-Christian and Giehl, Michael and Gowin, Wolfgang}, title = {Visual Analysis of Trabecular Bone Structure}, volume = {9 (1)}, journal = {Journal of Gravitational Physiology}, pages = {171 -- 172}, year = {2002}, language = {en} } @misc{GowinSaparinFelsenbergetal.2002, author = {Gowin, Wolfgang and Saparin, Peter and Felsenberg, Dieter and Kurths, J{\"u}rgen and Zaikin, Alexei and Prohaska, Steffen and Hege, Hans-Christian}, title = {Regional Structural Skeletal Discordance Assessed by Measures of Complexity}, year = {2002}, language = {en} } @article{ZaikinSaparinProhaskaetal.2002, author = {Zaikin, Alexei and Saparin, Peter and Prohaska, Steffen and Kurths, J{\"u}rgen and Gowin, Wolfgang}, title = {Bone Modeling and Structural Measures of Complexity}, volume = {9}, journal = {Journal of Gravitational Physiology}, doi = {10.1016/j.actaastro.2005.01.007}, pages = {175 -- 176}, year = {2002}, language = {en} } @article{GowinSaparinProhaskaetal.2002, author = {Gowin, Wolfgang and Saparin, Peter and Prohaska, Steffen and Hege, Hans-Christian and Felsenberg, Dieter}, title = {Femoral Neck Fractures: Reasons for the Most Common Location of Fractures}, volume = {73}, journal = {Acta Orthop. Scand. (Suppl. 304)}, pages = {26}, year = {2002}, language = {en} } @article{CassotLauwersFouardetal.2006, author = {Cassot, Francis and Lauwers, Frederic and Fouard, C{\´e}line and Prohaska, Steffen and Lauwer-Cances, Valerie}, title = {A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex}, volume = {13}, journal = {Microcirculation}, pages = {15 -- 32}, year = {2006}, language = {en} } @inproceedings{ProhaskaHege2002, author = {Prohaska, Steffen and Hege, Hans-Christian}, title = {Fast Visualization of Plane-Like Structures in Voxel Data}, booktitle = {Proceedings of IEEE Visualization 2002}, editor = {J. Moorhead, Robert and Gross, Markus and I. Joy, Kenneth}, publisher = {IEEE Computer Society Press}, address = {Boston MA, USA}, doi = {10.1109/VISUAL.2002.1183753}, pages = {29 -- 36}, year = {2002}, language = {en} } @misc{HombergBaumWiebeletal.2013, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, year = {2013}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} } @article{BuchmannKaplanPowelletal.2019, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent}, volume = {24}, journal = {Journal of Biomedical Optics}, number = {6}, doi = {10.1117/1.JBO.24.6.066001}, pages = {066001}, year = {2019}, abstract = {Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Gr{\"u}neisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.}, language = {en} } @misc{BuchmannKaplanPowelletal.2019, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent}, issn = {1438-0064}, doi = {10.1117/1.JBO.24.6.066001}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72995}, year = {2019}, abstract = {Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Gr{\"u}neisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.}, language = {en} } @article{OzelKulkarniHasanetal.2019, author = {Ozel, Mehmet Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, Ferdi Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, volume = {50}, journal = {Developmental Cell}, number = {4}, doi = {10.1016/j.devcel.2019.06.014}, pages = {447 -- 461}, year = {2019}, abstract = {Following 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.}, language = {en} } @article{ZhukovaHiepenKnausetal.2017, author = {Zhukova, Yulia and Hiepen, Christian and Knaus, Petra and Osterland, Marc and Prohaska, Steffen and Dunlop, John W. C. and Fratzl, Peter and Skorb, Ekaterina V.}, title = {The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration}, journal = {Advanced Healthcare Materials}, doi = {10.1002/adhm.201601244}, year = {2017}, abstract = {Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered - mesoporous titania (TMS), and ordered - titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.}, language = {en} } @inproceedings{RitterProhaskaBrandetal.2011, author = {Ritter, Zully and Prohaska, Steffen and Brand, R. and Friedmann, A. and Hege, Hans-Christian and Goebbels, J{\"u}rgen and Felsenberg, Dieter}, title = {Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study}, booktitle = {Proc. ISB 2011}, year = {2011}, language = {en} } @inproceedings{StreicherPaetschSeileretal.2011, author = {Streicher, Doreen and Paetsch, Olaf and Seiler, Robert and Prohaska, Steffen and Krause, Martin and Boller, Christian}, title = {3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira}, booktitle = {Proc. DGZfP-Jahrestagung 2011}, year = {2011}, language = {de} } @inproceedings{PaetschBaumEhrigetal.2012, author = {Paetsch, Olaf and Baum, Daniel and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {Vergleich automatischer 3D-Risserkennungsmethoden f{\"u}r die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie}, booktitle = {Tagungsband der DACH Jahrestagung 2012}, year = {2012}, language = {de} } @inproceedings{PaetschBaumBressleretal.2013, author = {Paetsch, Olaf and Baum, Daniel and Breßler, David and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben}, booktitle = {Tagungsband der DGZfP Jahrestagung 2013}, year = {2013}, language = {de} } @inproceedings{PaetschBaumEhrigetal.2012, author = {Paetsch, Olaf and Baum, Daniel and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography}, booktitle = {Proceedings of Conference on Industrial Computed Tomography}, pages = {321 -- 330}, year = {2012}, language = {en} } @misc{CostaMantonOstrovskyetal.2016, author = {Costa, Marta and Manton, James D. and Ostrovsky, Aaron D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, issn = {1438-0064}, doi = {10.1016/j.neuron.2016.06.012}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59672}, year = {2016}, abstract = {Neural circuit mapping is generating datasets of 10,000s 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 1052 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.}, language = {en} } @article{CostaMantonOstrovskyetal.2016, author = {Costa, Marta and Manton, James D. and Ostrovsky, Aaron D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases}, volume = {91}, journal = {Neuron}, number = {2}, doi = {10.1016/j.neuron.2016.06.012}, pages = {293 -- 311}, year = {2016}, abstract = {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.}, language = {en} } @misc{RedemannLantzschLindowetal.2018, author = {Redemann, Stefanie and Lantzsch, Ina and Lindow, Norbert and Prohaska, Steffen and Srayko, Martin and M{\"u}ller-Reichert, Thomas}, title = {A switch in microtubule orientation during C. elegans meiosis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69855}, year = {2018}, abstract = {In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1-5]. 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.}, language = {en} } @article{RedemannLantzschLindowetal.2018, author = {Redemann, Stefanie and Lantzsch, Ina and Lindow, Norbert and Prohaska, Steffen and Srayko, Martin and M{\"u}ller-Reichert, Thomas}, title = {A switch in microtubule orientation during C. elegans meiosis}, journal = {Current Biology}, issn = {0960-9822}, doi = {10.1016/j.cub.2018.07.012}, year = {2018}, abstract = {In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1-5]. 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.}, language = {en} } @incollection{LindowRedemannBruenigetal.2018, author = {Lindow, Norbert and Redemann, Stefanie and Br{\"u}nig, Florian and Fabig, Gunar and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen}, title = {Quantification of three-dimensional spindle architecture}, volume = {145}, booktitle = {Methods in Cell Biology Part B}, publisher = {Academic Press}, issn = {0091-679X}, doi = {10.1016/bs.mcb.2018.03.012}, pages = {45 -- 64}, year = {2018}, 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.}, language = {en} } @misc{BuchmannKaplanPowelletal.2019, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms}, issn = {1438-0064}, doi = {10.1016/j.pacs.2019.100157}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-75416}, year = {2019}, abstract = {Quantitative photoacoustic tomography aims 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.}, language = {en} } @article{BuchmannKaplanPowelletal.2020, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms}, volume = {17}, journal = {Photoacoustics}, doi = {10.1016/j.pacs.2019.100157}, pages = {100157}, year = {2020}, abstract = {Quantitative photoacoustic tomography aims 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.}, language = {en} } @article{FabigKiewiszLindowetal.2020, author = {Fabig, Gunar and Kiewisz, Robert and Lindow, Norbert and Powers, James A. and Cota, Vanessa and Quintanilla, Luis J. and Brugu{\´e}s, Jan and Prohaska, Steffen and Chu, Diana S. and M{\"u}ller-Reichert, Thomas}, title = {Sperm-specific meiotic chromosome segregation in C. elegans}, volume = {9}, journal = {eLife}, doi = {10.7554/eLife.50988}, pages = {e50988}, year = {2020}, language = {en} } @article{LindowBruenigDercksenetal.2020, author = {Lindow, Norbert and Br{\"u}nig, Florian and Dercksen, Vincent J. and Fabig, Gunar and Kiewisz, Robert and Redemann, Stefanie and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen and Baum, Daniel}, title = {Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography}, journal = {bioRxiv}, doi = {10.1101/2020.05.28.120899}, year = {2020}, abstract = {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.}, language = {en} } @article{JinKiralOzeletal.2018, author = {Jin, Eugene Jennifer and Kiral, Ferdi Ridvan and Ozel, Mehmet Neset and Burchardt, Lara Sophie and Osterland, Marc and Epstein, Daniel and Wolfenberg, Heike and Prohaska, Steffen and Hiesinger, Peter Robin}, title = {Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals}, volume = {28}, journal = {Current Biology}, number = {7}, doi = {10.1016/j.cub.2018.02.032}, pages = {1027 -- 1038.e4}, year = {2018}, abstract = {Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains. We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ''hub'' compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent, whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body.}, language = {en} } @misc{KnoetelSeidelZaslanskyetal.2017, author = {Kn{\"o}tel, David and Seidel, Ronald and Zaslansky, Paul and Prohaska, Steffen and Dean, Mason N. and Baum, Daniel}, title = {Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material)}, doi = {10.12752/4.DKN.1.0}, year = {2017}, abstract = {Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens.}, language = {en} } @misc{LindowRedemannFabigetal.2018, author = {Lindow, Norbert and Redemann, Stefanie and Fabig, Gunar and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen}, title = {Quantification of Three-Dimensional Spindle Architecture}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66562}, year = {2018}, 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 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. Three-dimensional reconstruction of microtubules, however, is only the first step towards 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.}, language = {en} } @misc{OezelKulkarniHasanetal.2019, author = {{\"O}zel, M. Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, F. Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, issn = {1438-0064}, doi = {10.1016/j.devcel.2019.06.014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74397}, year = {2019}, abstract = {Following 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.}, language = {en} } @misc{LindowBruenigDercksenetal.2019, author = {Lindow, Norbert and Br{\"u}nig, Florian and Dercksen, Vincent J. and Fabig, Gunar and Kiewisz, Robert and Redemann, Stefanie and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen}, title = {Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73739}, year = {2019}, abstract = {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.}, language = {en} } @misc{HombergBaumWiebeletal.2014, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, journal = {Topological Methods in Data Analysis and Visualization III}, editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald}, publisher = {Springer}, doi = {10.1007/978-3-319-04099-8_15}, pages = {235 -- 248}, year = {2014}, language = {en} } @inproceedings{KlindtProhaskaBaumetal.2012, author = {Klindt, Marco and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian}, title = {Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition}, booktitle = {VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers}, editor = {Arnold, David and Kaminski, Jaime and Niccolucci, Franco and Stork, Andre}, publisher = {Eurographics Association}, address = {Brighton, UK}, doi = {10.2312/PE/VAST/VAST12S/025-028}, pages = {25 -- 28}, year = {2012}, language = {en} } @inproceedings{KlindtBaumProhaskaetal.2012, author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, booktitle = {EVA 2012 Berlin}, publisher = {Gesellschaft zur F{\"o}rderung angewandter Informatik e.V.}, address = {Volmerstraße 3, 12489 Berlin}, pages = {150 -- 155}, year = {2012}, language = {en} } @article{KleinfeldBhariokeBlinderetal.2011, author = {Kleinfeld, David and Bharioke, Arjun and Blinder, Pablo and Bock, David and Briggman, Kevin and Chklovskii, Dmitri and Denk, Winfried and Helmstaedter, Moritz and Kaufhold, John and Lee, Wei-Chung and Meyer, Hanno and Micheva, Kristina and Oberlaender, Marcel and Prohaska, Steffen and Reid, R. and Smith, Stephen and Takemura, Shinya and Tsai, Philbert and Sakmann, Bert}, title = {Large-scale automated histology in the pursuit of connectomes}, volume = {31}, journal = {Journal of Neuroscience}, number = {45}, doi = {10.1523/JNEUROSCI.4077-11.2011}, pages = {16125 -- 16138}, year = {2011}, language = {en} } @article{RigortGuentherHegerletal.2012, author = {Rigort, Alexander and G{\"u}nther, David and Hegerl, Reiner and Baum, Daniel and Weber, Britta and Prohaska, Steffen and Medalia, Ohad and Baumeister, Wolfgang and Hege, Hans-Christian}, title = {Automated segmentation of electron tomograms for a quantitative description of actin filament networks}, volume = {177}, journal = {Journal of Structural Biology}, doi = {10.1016/j.jsb.2011.08.012}, pages = {135 -- 144}, year = {2012}, language = {en} } @inproceedings{HombergBaumProhaskaetal.2012, author = {Homberg, Ulrike and Baum, Daniel and Prohaska, Steffen and Kalbe, Ute and Witt, Karl Josef}, title = {Automatic Extraction and Analysis of Realistic Pore Structures from µCT Data for Pore Space Characterization of Graded Soil}, booktitle = {Proceedings of the 6th International Conference on Scour and Erosion (ICSE-6)}, pages = {345 -- 352}, year = {2012}, language = {en} } @article{WeberGreenanProhaskaetal.2012, author = {Weber, Britta and Greenan, Garrett and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian and M{\"u}ller-Reichert, Thomas and Hyman, Anthony and Verbavatz, Jean-Marc}, title = {Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos}, volume = {178}, journal = {Journal of Structural Biology}, number = {2}, doi = {10.1016/j.jsb.2011.12.004}, pages = {129 -- 138}, year = {2012}, language = {en} } @inproceedings{EhrigGoebbelsMeineletal.2011, author = {Ehrig, Karsten and Goebbels, J{\"u}rgen and Meinel, Dietmar and Paetsch, Olaf and Prohaska, Steffen and Zobel, Valentin}, title = {Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography}, booktitle = {International Symposium on Digital Industrial Radiology and Computed Tomography}, year = {2011}, language = {en} }