@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} }