Bibtex
@ARTICLE{Moeller19_PS,
AUTHOR = {Birgit M{\"o}ller and Hongmei Chen and Tino Schmidt and Axel Zieschank and Roman Patzak and Manfred T{\"u}rke and Alexandra Weigelt and Stefan Posch},
TITLE = {rhizo{T}rak: A flexible open source {F}iji plugin for user-friendly manual annotation of time-series images from minirhizotrons},
JOURNAL = {Plant and Soil},
YEAR = {2019},
MONTH = {Sep},
DAY = {10},
ABSTRACT = {Background and aims: Minirhizotrons are commonly used to study root turnover which is essential for understanding ecosystem carbon and nutrient cycling. Yet, extracting data from minirhizotron images requires extensive annotation effort. Existing annotation tools often lack flexibility and provide only a subset of the required functionality. To facilitate efficient root annotation in minirhizotrons, we present the user-friendly open source tool rhizoTrak. Methods and results: rhizoTrak builds on TrakEM2 and is publicly available as Fiji plugin. It uses treelines to represent branching structures in roots and assigns customizable status labels per root segment. rhizoTrak offers configuration options for visualization and various functions for root annotation mostly accessible via keyboard shortcuts. rhizoTrak allows time-series data import and particularly supports easy handling and annotation of time-series images. This is facilitated via explicit temporal links (connectors) between roots which are automatically generated when copying annotations from one image to the next. rhizoTrak includes automatic consistency checks and guided procedures for resolving inconsistencies. It facilitates easy data exchange with other software by supporting open data formats. Conclusions: rhizoTrak covers the full range of functions required for user-friendly and efficient annotation of time-series images. Its flexibility and open source nature will foster efficient data acquisition procedures in root studies using minirhizotrons.},
ISSN = {1573-5036},
DOI = {10.1007/s11104-019-04199-3},
URL = {http://link.springer.com/article/10.1007/s11104-019-04199-3 }
hizo{T}rak: A flexible open source {F}iji plugin for user-friendly manual annotation of time-series images from minirhizotrons
rhizoTrak-MoellerChen-PLSO-D-19-00329-final-1.pdf
(2 MB) vom 16.09.2019
@INCOLLECTION{Moeller19_BPCM_cytoskeleton,
AUTHOR = {M{\"o}ller, Birgit and Zergiebel, Luise and B{\"u}rstenbinder, Katharina},
EDITOR = {Cvr{\v{c}}kov{\'a}, Fatima and {\v{Z}}{\'a}rsk{\'y}, Viktor},
TITLE = {Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D},
BOOKTITLE = {Plant Cell Morphogenesis: Methods and Protocols},
CHAPTER = {10},
YEAR = {2019},
PUBLISHER = {Springer New York},
ADDRESS = {New York, NY},
PAGES = {151--171},
ABSTRACT = {The microtubule cytoskeleton plays important roles in cell morphogenesis. To investigate the mechanisms of cytoskeletal organization, for example, during growth or development, in genetic studies, or in response to environmental stimuli, image analysis tools for quantitative assessment are needed. Here, we present a method for texture measure-based quantification and comparative analysis of global microtubule cytoskeleton patterns and subsequent visualization of output data. In contrast to other approaches that focus on the extraction of individual cytoskeletal fibers and analysis of their orientation relative to the growth axis, CytoskeletonAnalyzer2D quantifies cytoskeletal organization based on the analysis of local binary patterns. CytoskeletonAnalyzer2D thus is particularly well suited to study cytoskeletal organization in cells where individual fibers are difficult to extract or which lack a clearly defined growth axis, such as leaf epidermal pavement cells. The tool is available as ImageJ plugin and can be combined with publicly available software and tools, such as R and Cytoscape, to visualize similarity networks of cytoskeletal patterns.},
ISBN = {978-1-4939-9469-4},
DOI = {10.1007/978-1-4939-9469-4_10},
URL = {https://doi.org/10.1007/978-1-4939-9469-4_10 }
@INCOLLECTION{Moeller19_BPCM_pacequant,
AUTHOR = {M{\"o}ller, Birgit and Poeschl, Yvonne and Klemm, Sandra and B{\"u}rstenbinder, Katharina},
EDITOR = {Cvr{\v{c}}kov{\'a}, Fatima and {\v{Z}}{\'a}rsk{\'y}, Viktor},
TITLE = {Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant},
BOOKTITLE = {Plant Cell Morphogenesis: Methods and Protocols},
CHAPTER = {22},
YEAR = {2019},
PUBLISHER = {Springer New York},
ADDRESS = {New York, NY},
PAGES = {329--349},
ABSTRACT = {Morphological analysis of cell shapes requires segmentation of cell contours from input images and subsequent extraction of meaningful shape descriptors that provide the basis for qualitative and quantitative assessment of shape characteristics. Here, we describe the publicly available ImageJ plugin PaCeQuant and its associated R package PaCeQuantAna, which provides a pipeline for fully automatic segmentation, feature extractionFeature extraction, statistical analysis, and graphical visualization of cell shape properties. PaCeQuant is specifically well suited for analysis of jigsaw puzzle-like leaf epidermis pavement cells from 2D input images and supports the quantification of global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.},
ISBN = {978-1-4939-9469-4},
DOI = {10.1007/978-1-4939-9469-4_22},
URL = {https://doi.org/10.1007/978-1-4939-9469-4_22 }
@INPROCEEDINGS{Moeller19_ISBI,
TITLE = {Semi-automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level},
AUTHOR = {B.~M{\"o}ller and K.~B{\"u}rstenbinder},
BOOKTITLE = {Proc. of IEEE 16th International Symposium on Biomedical Imaging (ISBI)},
YEAR = {2019},
ADDRESS = {Venice, Italy},
MONTH = {April},
PAGES = {199-203},
ISBN = {978-1-5386-3640-4},
ABSTRACT= {The structure of the microtubule cytoskeleton provides valuable information related to morphogenesis of cells. The cytoskeleton organizes into diverse patterns that vary in cells of different types and tissues, but also within a single tissue. To assess differences in cytoskeleton organization methods are needed that quantify cytoskeleton patterns within a complete cell and which are suitable for large data sets. A major bottleneck in most approaches, however, is a lack of techniques for automatic extraction of cell contours. Here, we present a semi-automatic pipeline for cell segmentation and quantification of microtubule organization. Automatic methods are applied to extract major parts of the contours and a handy image editor is provided to manually add missing information efficiently. Experimental results prove that our approach yields high-quality contour data with minimal user intervention and serves a suitable basis for subsequent quantitative studies.}, keywords = {Image segmentation;Organizations;Data mining;Feature extraction;Noise measurement;Pipelines;Standards organizations;cytoskeleton;cell segmentation;vesselness;gap closing;label editor;texture;clustering;ImageJ},
DOI = {10.1109/ISBI.2019.8759145},
ISSN = {1945-8452},
MONTH = {April},
URL = {https://ieeexplore.ieee.org/document/8759145 }
@INPROCEEDINGS{Moeller19_Bioimaging,
TITLE = {{Q}uantification of {S}tromule {F}requencies in {M}icroscope {I}mages of {P}lastids combining {R}idge {D}etection and {G}eometric {C}riteria},
AUTHOR = {B.~M{\"o}ller and M.~Schattat},
BOOKTITLE = {Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING,},
YEAR = {2019},
PAGES = {38-48},
PUBLISHER = {SciTePress},
ORGANIZATION = {INSTICC},
DOI = {10.5220/0007390300380048},
URL = {https://www.scitepress.org/PublicationsDetail.aspx?ID=H1fepfq9NBw=&t=1 },
ISBN = {978-989-758-353-7},
MONTH = {February},
ADDRESS= {Prague, Czech Republic},
ABSTRACT = {Plastids are involved in many fundamental biochemical pathways in plants. They can produce tubular membrane out-folds from their surface. These so-called stromules have initially been described over a century ago, but their functional role is still elusive.}
@ARTICLE{Moeller19_JEB,
AUTHOR = {Mitra, Dipannita and Klemm, Sandra and Kumari, Pratibha and Quegwer, Jakob and Möller, Birgit and Poeschl, Yvonne and Pflug, Paul and Stamm, Gina and Abel, Steffen and Bürstenbinder, Katharina},
TITLE = {Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana},
JOURNAL= {Journal of Experimental Botany},
VOLUME = {70},
NUMBER = {2},
PAGES = {529-543},
YEAR = {2019},
DOI = {10.1093/jxb/ery395},
URL = {http://dx.doi.org/10.1093/jxb/ery395 },
EPRINT = {https://www.biorxiv.org/content/biorxiv/early/2018/02/20/268466.full-text.pdf },
ABSTRACT = {Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that.}
@ARTICLE{Moeller17_PPhys,
TITLE = {{P}a{C}e{Q}uant: {A} {T}ool for {H}igh-{T}hroughput {Q}uantification of {P}avement {C}ell {S}hape {C}haracteristics},
AUTHOR = {Birgit M{\"o}ller and Yvonne Poeschl and Romina Pl{\"o}tner and Katharina B{\"u}rstenbinder},
JOURNAL = {Plant Physiology},
YEAR = {2017},
MONTH = {November},
NUMBER = {3},
PAGES = {998--1017},
VOLUME = {175},
ABSTRACT = {Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitat.},
DOI = {10.1104/pp.17.00961},
FILE = {:http\://www.plantphysiol.org/content/175/3/998.full.pdf:URL},
OWNER= {moeller},
TIMESTAMP = {2017.09.22},
URL = {http://www.plantphysiol.org/content/175/3/998 }
@ARTICLE{Posch17_JORS,
TITLE = {Alida - {A}dvanced {L}ibrary for {I}ntegrated {D}evelopment of {D}ata {A}nalysis {A}pplications},
AUTHOR = {Stefan Posch and Birgit M{\"o}ller},
JOURNAL = {Journal of Open Research Software},
YEAR = {2017},
NUMBER = {1},
PAGES = {7},
VOLUME = {5},
ABSTRACT = {Data analysis procedures can often be modeled as a set of manipulation operations applied to input data and resulting in transformed intermediate and result data. The Java library Alida is providing an advanced development framework to support programmers in developing data analysis applications adhering to such a scheme. The main intention of Alida is to foster re-usability by offering well-defined, unified, modular APIs and execution procedures for operators, and to ease development by releasing developers from tedious tasks. Alida features automatic generation of handy graphical and command line user interfaces, a built-in graphical editor for workflow design, and an automatic documentation of analysis pipelines. Alida is available from its project webpage http://www.informatik.uni-halle.de/alida, on Github and via our Maven server.},
DOI = {http://doi.org/10.5334/jors.124 },
KEYWoRDS = {Data Analysis, Programming Framework, Implementation, Reusability, Graphical User Interfaces, Command Line Interface, Processing History, Java Software Library},
OWNER = {moeller},
TIMESTAMP = {2017.02.13},
URL = {http://openresearchsoftware.metajnl.com/articles/10.5334/jors.124/ }
@ARTICLE{Buerste17_PPhys,
TITLE = {{T}he {IQD} {F}amily of {C}almodulin-{B}inding {P}roteins {L}inks {C}alcium {S}ignaling to {M}icrotubules, {M}embrane {S}ubdomains, and the {N}ucleus},
AUTHOR = {Katharina B{\"u}rstenbinder and Birgit M{\"o}ller and Romina Pl{\"o}tner and Gina Stamm and Gerd Hause and Dipannita Mitra and Steffen Abel},
JOURNAL = {Plant Physiology},
YEAR = {2017},
VOLUME = {173},
NUMBER = {3},
MONTH = {March},
PAGES = {1692-1708},
ABSTRACT = {Calcium (Ca2+) signaling and dynamic reorganization of the cytoskeleton are essential processes for the coordination and control of plant cell shape and cell growth. Calmodulin (CaM) and closely related calmodulin-like (CML) polypeptides are principal sensors of Ca2+ signals. CaM/CMLs decode and relay information encrypted by the second messenger via differential interactions with a wide spectrum of targets to modulate their diverse biochemical activities. The plant-specific IQ67 DOMAIN (IQD) family emerged as possibly the largest class of CaM-interacting proteins with undefined molecular functions and biological roles. Here, we show that the 33 members of the IQD family in Arabidopsis (Arabidopsis thaliana) differentially localize, using green fluorescent protein (GFP)-tagged proteins, to multiple and distinct subcellular sites, including microtubule (MT) arrays, plasma membrane subdomains, and nuclear compartments. Intriguingly, the various IQD-specific localization patterns coincide with the subcellular patterns of IQD-dependent recruitment of CaM, suggesting that the diverse IQD members sequester Ca2+-CaM signaling modules to specific subcellular sites for precise regulation of Ca2+-dependent processes. Because MT localization is a hallmark of most IQD family members, we quantitatively analyzed GFP-labeled MT arrays in Nicotiana benthamiana cells transiently expressing GFP-IQD fusions and observed IQD-specific MT patterns, which point to a role of IQDs in MT organization and dynamics. Indeed, stable overexpression of select IQD proteins in Arabidopsis altered cellular MT orientation, cell shape, and organ morphology. Because IQDs share biochemical properties with scaffold proteins, we propose that IQD families provide an assortment of platform proteins for integrating CaM-dependent Ca2+ signaling at multiple cellular sites to regulate cell function, shape, and growth.},
DOI = {10.1104/pp.16.01743},
URL = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338658/# }
@ARTICLE{Moeller16_JORS,
TITLE = {MiToBo - A Toolbox for Image Processing and Analysis},
AUTHOR = {Birgit M{\"o}ller and Markus Gla{\ss} and Danny Misiak and Stefan Posch},
JOURNAL = {Journal of Open Research Software},
YEAR = {2016},
NUMBER = {1},
Pages = {e17},
VOLUME = {4},
ABSTRACT = {MiToBo is a toolbox and Java library for solving basic as well as advanced image processing and analysis tasks. It features a rich collection of fundamental, intermediate and high-level image processing operators and algorithms as well as a couple of sophisticated tools for specific biological and biomedical applications. These tools include operators for elucidating cellular morphology and locomotion as well as operators for the characterization of certain intracellular particles and structures. MiToBo builds upon and integrates into the widely-used image analysis software packages ImageJ and Fiji [11, 10], and all of its operators can easily be run in ImageJ and Fiji via a generic operator runner plugin. Alternatively MiToBo operators can directly be run from command line, and using its functionality as a library for developing own applications is also supported. Thanks to the Alida library [8] forming the base of MiToBo all operators share unified APIs fostering reusability, and graphical as well as command line user interfaces for operators are automatically generated. MiToBo is available from its website http://www.informatik.uni-halle.de/mitobo, on Github, via an Apache Archiva Maven repository server, and it can easily be activated in Fiji via its own update site.},
DOI = {http://dx.doi.org/10.5334/jors.103 },
FILE = {:http\://openresearchsoftware.metajnl.com/articles/10.5334/jors.103/galley/153/download/:URL},
KEYWORDS = {Image Analysis, Image Processing, Toolbox, Java Library, ImageJ, Fiji, Microscope Images, Biomedical Imaging, Wound Closure, Actin Microfilament, Morphology, Protein Profile},
URL = {http://openresearchsoftware.metajnl.com/articles/10.5334/jors.103/ }
@ARTICLE{Posch16_JPRIA,
TITLE = {Design and implementation of the Alida framework to ease the development of image analysis algorithms},
AUTHOR = {Posch, S. and M{\"o}ller, B.},
JOURNAL = {Pattern Recognition and Image Analysis},
YEAR = {2016},
NUMBER = {1},
PAGES = {181--189},
VOLUME = {26},
ABSTRACT = {Solving image analysis problems is not restricted to the pure delineation of algorithms suitable to tackle the task at hand. Rather these also need to be made available to the users promptly and equipped with handy user interfaces to foster progress in the intended field of application. Alida is a software framework to advance the integrated development of algorithms and appropriate user interfaces. It automatically generates user interfaces for implemented algorithms, offers an automatic documentation of analysis procedures, and ships with a graphical editor for designing complex workflows. Alida's Java implementation is licensed under GPL 3.0 and publicly available at http://www.informatik.uni-halle.de/alida.},
DOI = {10.1134/S105466181601020X},
ISSN = {1555-6212},
KEYWORDS = {image analysis, user interface, process documentation, workflow design, software development},
URL = {http://dx.doi.org/10.1134/S105466181601020X }
@INPROCEEDINGS{Posch14_OGRW,
TITLE = {{D}esign and {I}mplementation of the {A}lida {F}ramework to {E}ase the {D}evelopment of {I}mage {A}nalysis {A}lgorithms},
AUTHOR = {Stefan Posch and Birgit M{\"o}ller},
BOOKTITLE = {9th Open German-Russian Workshop on Pattern Recognition and Image Understanding ({OGRW} 2014), Proceedings},
YEAR = {2015},
ADRESS = {Koblenz},
EDITOR = {Dietrich Paulus and Christian Fuchs and Detlev Droege},
MONTH = {5},
NOTE = {Workshop Chairs: Heinrich Niemann, Yuri Zhuravlev},
PAGES = {75-81},
PUBLISHER = {University of Koblenz-Landau},
FILE = {:http\://kola.opus.hbz-nrw.de/volltexte/2015/1136/pdf/OGRW_2014_Proceedings.pdf:URL},
SHORTTITLE = {{OGRW}},
URL = {http://kola.opus.hbz-nrw.de/volltexte/2015/1136/pdf/OGRW_2014_Proceedings.pdf#82},
URN = {urn:nbn:de:hbz:kob7-2015051206} }
@ARTICLE{Franke15_JECR,
TITLE = {The 'MTB Cell Counter' a versatile tool for the semi-automated quantification of sub-cellular phenotypes in fluorescence microscopy images. A case study on plastids, nuclei and peroxisomes},
AUTHOR = {Lars Franke and Benjamin Storbeck and Jessica Lee Erickson and Daniela R{\"o}del and Daniel Schr{\"o}ter and Birgit M{\"o}ller and Martin Hartmut Schattat},
JOURNAL = {Journal of Endocytobiosis and Cell Research},
YEAR = {2015},
PAGES = {31-42},
VOLUME = {26},
KEYWORDS = {plastid, nucleus, peroxisome, image analysis, ImageJ, MiToBo, stromule, cell biology},
URL = {http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296 } }
@ARTICLE{Bley14_NAR,
AUTHOR = {N. Bley and M. Lederer and B. Pfalz and C. Reinke and T. Fuchs and M. Gla{\ss} and B. M{\"o}ller and S. H{\"u}ttelmaier},
TITLE = {Stress granules are dispensable for {mRNA} stabilization during cellular stress},
JOURNAL = {Nucleic Acids Research},
YEAR = {2014},
VOLUME = {43},
NUMBER = {4},
PAGES = {e26},
MONTH = {December},
DOI = {10.1093/nar/gku1275},
NOTE = {PubMed PMID: 25488811},
TIMESTAMP = {2014.02.04},
URL = {http://nar.oxfordjournals.org/content/43/4/e26.long } }
@INPROCEEDINGS{Moeller14_ICPR,
AUTHOR = {B. M{\"o}ller and E. Piltz and N. Bley},
TITLE = {Quantification of Actin Structures using Unsupervised Pattern Analysis Techniques},
BOOKTITLE = {Proceedings of Int.~Conf.~on Pattern Recognition (ICPR)},
YEAR = {2014},
PAGES = {3251-3256},
ADDRESS = {Stockholm, Sweden},
MONTH = {August},
PUBLISHER = {IEEE} }
@ARTICLE{Misiak14_JNM, author = {Danny Misiak and Stefan Posch and Marcell Lederer and Claudia Reinke and Stefan H{\"u}ttelmaier and Birgit M{\"o}ller},
TITLE= {Extraction of protein profiles from primary neurons using active contour models and wavelets},
JOURNAL= {Journal of Neuroscience Methods},
YEAR= {2014},
VOLUME= {225},
PAGES= {1-12},
MONTH= {March},
DOI= {http://dx.doi.org/10.1016/j.jneumeth.2013.12.009 },
KEYWORDS= {Active contours; Fluorescence microscopy; High-content analysis; Neuron morphology; Protein distribution; Segmentation; Wavelets},
URL= {http://www.sciencedirect.com/science/article/pii/S0165027013004330 } }
@ARTICLE{grau13talenoffer,
AUTHOR= {Jan Grau, Jens Boch and Stefan Posch},
JOURNAL= {Bioinformatics},
TITLE= {TALENoffer: genome-wide TALEN off-target prediction},
YEAR= {2013}}
@ARTICLE{grau13a-general,
AUTHOR= {Jan Grau, Stefan Posch, Ivo Grosse and Jens Keilwagen},
JOURNAL= {Nucleic Acids Research},
TITLE= {A general approach for discriminative de-novo motif discovery from high-throughput data},
YEAR= {2013, doi: 10.1093/nar/gkt831}}
@ARTICLE{grau13computational,
AUTHOR= {Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch and Jens Boch},
JOURNAL= {PLoS Comput Biol},
MONTH= {03},
NUMBER= {3},
PAGES = {e1002962},
TITLE= {Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites},
VOLUME= {9},
YEAR= {2013}}
@ARTICLE{grau13dispom,
AUTHOR = {Jan Grau, Jens Keilwagen, Andr{\'e} Gohr, Ivan A. Paponov, Stefan Posch, Michael Seifert, Marc Strickert and Ivo Grosse},
JOURNAL= {Journal of Bioinformatics and Computational Biology},
NUMBER= {1},
TITLE= {Dispom: A Discriminative De-novo Motif Discovery Tool Based On The Jstacs Library},
VOLUME= {11},
YEAR= {2013}}
@INPROCEEDINGS{Elibol13_IbPRIA,
AUTHOR = {Armagan Elibol, Stefan Posch, Andreas Maurer, Klaus Pillen and Birgit Möller},
TITLE = {Vision-Based 3D-Reconstruction of Barley Plants},
BOOKTITLE = {Proc. of 6th Iberian Conference on Pattern Recognition and Image Analysis},
YEAR = {2013},
PAGES = {406-415},
EE = {http://dx.doi.org/10.1007/978-3-642-38628-2_48 },
CROSSREF = {DBLP:conf/ibpria/2013},
BIBSOURCE = {DBLP, http://dblp.uni-trier.de }}
@INPROCEEDINGS{Moeller13_MVA,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces},
BOOKTITLE = {Proc. of 13th IAPR International Conference on Machine Vision Applications (MVA)},
YEAR = {2013},
PAGES = {447-450},
ADDRESS = {Kyoto, Japan},
MONTH = {May},
TIMESTAMP = {2013.02.26}}
@INPROCEEDINGS{Moeller12_ImageJEditor,
AUTHOR = {S. Kirchner, S. Posch and B. Möller},
TITLE = {Graphical Programming in Alida and ImageJ 2.0},
MONTH = {October},
BOOKTITLE = {Proc. of ImageJ User \& Developer Conference},
YEAR = {2012},
PAGES = {138-143},
COMMENT = {ISBN 2-919941-18-6},
ADDRESS = {Mondorf-les-Bains, Luxembourg}}
@INPROCEEDINGS{Moeller12_ImageJSnakes,
AUTHOR = {B. Möller and D. Misiak},
TITLE = {SnakeOptimizer - Object Segmentation with Parametric Active Contours
in ImageJ},
BOOKTITLE= {Proc. of ImageJ User \& Developer Conference},
YEAR = {2012},
ADDRESS= {Mondorf-les-Bains, Luxembourg},
MONTH = {October},
PAGES = {215-217, 222},
COMMENT = {ISBN 2-919941-18-6},
KEYWORDS = {Image Segmentation, Active Contours, Snakes, ImageJ, Alida}}
@INPROCEEDINGS{Glass12_ImageJ,
AUTHOR = {M. Glaß, B. Möller and S. Posch},
TITLE = {Scratch Assay Analysis in ImageJ},
BOOKTITLE = {Proc. of ImageJ User \& Developer Conference},
YEAR = {2012},
ADDRESS = {Mondorf-les-Bains, Luxembourg},
MONTH = {October},
PAGES = {211-214},
COMMENT = {ISBN 2-919941-18-6},
KEYWORDS = {Scratch assay, Level sets, SVM, Entropy, Topology preservation}}
@INPROCEEDINGS{Posch12_ImageJ,
AUTHOR = {S. Posch and B. Möller},
TITLE = {Automatic Generation of Processing Histories using Alida},
BOOKTITLE = {Proc. of ImageJ User \& Developer Conference},
YEAR = {2012},
ADDRESS = {Mondorf-les-Bains, Luxembourg},
MONTH = {October},
PAGES = {218-221},
COMMENT = {ISBN 2-919941-18-6},
NOTE = {Best Scientific Poster Award, 1st place},
KEYWORDS = {Process Documentation, Processing Graph, XML, Alida, ImageJ}}
@ARTICLE{Glass12_PR,
AUTHOR= {Markus Glaß, Birgit Möller, A. Zirkel, K. Wächter, Stefan Hüttelmaier and Stefan Posch},
TITLE = {Cell Migration Analysis: Segmenting Scratch Assay Images with Level Sets and Support Vector Machines},
JOURNAL= {Pattern Recognition},
YEAR = {2012},
VOLUME = {45},
PAGES = {3154-3165},
NUMBER= {9},
MONTH = {September},
ABSTRACT = {Cell migration assessment is often done by scratch assay experiments for which quantitative evaluations are usually performed manually. Here we present an automatic analysis pipeline detecting scratch boundaries and measuring areas based on level sets. We extend non-PDE level sets for topology-preservation and use an entropy-based energy functional. This approach by design segments a scratch in every image, hence, we employ support vector machines to identify images showing no scratch at all. Compared to other algorithms our approach, implemented as ImageJ plugin, relies on a minimal set of parameters. Experimental evaluations show the high quality of results and their suitability for biomedical investigations.},
DOI = {10.1016/j.patcog.2012.03.001},
KEYWORDS = {Scratch assay, Segmentation, Level sets, Texture, Topology, SVM},
URL = {http://www.sciencedirect.com/science/article/pii/S0031320312001173 }}
@ARTICLE{grau12jstacs,
AUTHOR= {Jan Grau, Jens Keilwagen, Andr\'{e} Gohr, Berit Haldemann, Stefan Posch and Ivo Grosse},
JOURNAL= {Journal of Machine Learning Research},
NUMBER= {Jun},
PAGES= {1967-1971},
TITLE= {Jstacs: A Java Framework for Statistical Analysis and Classification of Biological Sequences},
VOLUME= {13},
YEAR= {2012}}
@INPROCEEDINGS{moeller12_isbi,
AUTHOR = {Birgit Möller and Stefan Posch},
TITLE = {Comparing Active Contours for the Segmentation of Biomedical Images},
BOOKTITLE = {Proc. of IEEE International Symposium on Biomedical Imaging: From Nano to Macro(ISBI), IEEE Catalog No.: CFP12BIS-CDR ISBN: 978-1-4577-1856-4},
YEAR = {2012},
ADDRESS = {Barcelona, Spain},
MONTH = {May}},
PAGES= {736-739}}
@INPROCEEDINGS{posch12_isbi,
AUTHOR = {Stefan Posch and Birgit Möller},
TITLE = {Alida - Automatic Generation of User Interfaces for Data Analysis Algorithms},
BOOKTITLE = {Proc. of IEEE International Symposium on Biomedical Imaging (ISBI), Bioimage Analysis Workshop},
YEAR = {2012},
ADDRESS = {Barcelona, Spain},
MONTH = {May}}
@ARTICLE{thum12mass,
AUTHOR = {Steffen Neumann, Andrea Thum and Cristoph Böttcher},
JOURNAL= {Metabolomics},
TITLE = {Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data}, YEAR= {2012},
ISSN= {1573-3882},
PAGES= {1-8},
URL= {http://dx.doi.org/10.1007/s11306-012-0401-0 },
AFFILIATION= {Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany},
NOTE= {10.1007/s11306-012-0401-0},
PUBLISHER= {Springer Boston}}
@INPROCEEDINGS{gress2012parametric,
AUTHOR = {Oliver Gre{\ss} and Stefan Posch},
TITLE = {Parametric Data Association Prior for Multi-Target Tracking based on Rao-Blackwellized Monte Carlo Data Association},
BOOKTITLE = {VISAPP 2012 - International Conference on Computer Vision Theory and Applications},
YEAR= {2012},
VOLUME= {2},
PAGES= {387-394},
MONTH= {February},
ADRESS= {Rome, Italy},
EDITOR= {Gabriela Csurka and José Braz},
PUBLISHER= {SciTePress} }
@INBOOK{Moeller11_VISIGRAPP,
CHAPTER = {Adaptive Segmentation of Particles and Cells for Fluorescent Microscope Imaging},
PAGES = {154-169},
TITLE = {VISIGRAPP 2010, Revised Selected Papers of Int. Joint Conf. on Computer Vision, Imaging and Computer Graphics. Theory and Applications},
PUBLISHER = {Springer},
YEAR = {2011},
EDITOR = {P. Richard and J. Braz},
AUTHOR = {B. Möller, O. Greß, N. Stöhr, S. Hüttelmaier, S. Posch},
VOLUME = {229},
SERIES = {Communications in Computer and Information Science},
URL = {http://www.springer.com/computer/image+processing/book/978-3-642-25381-2 } }
@INPROCEEDINGS{moeller11:miaab,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {{MiCA} - Easy Cell Image Analysis with Normalized Snakes},
BOOKTITLE = {International Workshop on Microscopic Image Analysis with Applications in Biology},
YEAR = {2011},
MONTH = {September},
DAY = {2},
CITY = {Heidelberg} }
@ARTICLE{springerlink:10.1007/s11033-011-0796-0,
AUTHOR = {Hesse, Manuela and Willscher, Edith and Schmiedel, Benjamin and Posch, Stefan and Golbik, Ralph and Staege, Martin},
AFFILIATION = {Department of Pediatrics, Childrenâ<80><99>s Cancer Research Centre, Martin-Luther-University Halle-Wittenberg, Ernst Grube Str. 40, 06097 Halle, Germany},
TITLE = {Sequence and expression of the chicken membrane-associated phospholipases A1 alpha (LIPH) and beta (LIPI)},
JOURNAL = {Molecular Biology Reports},
PUBLISHER = {Springer Netherlands},
ISSN = {0301-4851},
KEYWORD = {Biomedical and Life Sciences},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1007/s11033-011-0796-0 },
NOTE = {10.1007/s11033-011-0796-0}, YEAR = {2011} }
@INPROCEEDINGS{Moeller11_ICVS,
AUTHOR = {Birgit Möller and Oliver Greß and Stefan Posch},
TITLE = {Knowing what happened - Automatic Documentation of Image Analysis Processes},
BOOKTITLE = {Proceedings of 8th International Conference on Computer Vision Systems},
YEAR = {2011},
EDITOR = {J.L. Crowley, B.A. Draper, and M. Thonnat},
VOLUME = {6962},
SERIES = {LNCS},
PAGES = {1-10},
ADRESS = {Sophia Antipolis, France},
PUBLISHER = {Springer},
KEYWORDS = {automatic documentation, meta data, XML, processing graph, image analysis},
OWNER = {moeller},
TIMESTAMP = {2011.09.26},
URL = {http://www. springerlink. com/content/m331u047758nn84l/ } }
@INPROCEEDINGS{Glass11_IbPRIA,
AUTHOR = {M. Glaß and B. Möller and A. Zirkel and K. Wächter and S. Hüttelmaier and S. Posch},
TITLE = {Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures},
BOOKTITLE = {Proc. of 5th Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA '11)},
YEAR = {2011},
EDITOR = {Jordi Vitrià and João M. Sanches and Mario Hernández},
NUMBER = {6669},
SERIES = {LNCS},
PAGES = {100-108},
ADDRESS = {Gran Canaria, Spain},
PUBLISHER = {Springer},
ABSTRACT = {},
KEYWORDS = {Scratch assay, level set segmentation, texture, topology},
OWNER = {moeller},
TIMESTAMP = {2011.07.01}
}
@ARTICLE{keilwagen11:dispomm,
AUTHOR = {Keilwagen, Jens AND Grau, Jan AND Paponov, Ivan A. AND Posch, Stefan AND Strickert, Marc AND Grosse, Ivo},
JOURNAL = {PLoS Comput Biol},
PUBLISHER = {Public Library of Science},
TITLE = {De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference},
YEAR = {2011},
MONTH = {February},
VOLUME = {7},
URL = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1001070 },
PAGES = {e1001070},
}
@INPROCEEDINGS{Moeller10:icpr,
AUTHOR = {Birgit M{\"o}ller and Nadine St{\"o}hr and Stefan H{\"u}ttelmaier and Stefan Posch },
TITLE = {Cascaded Segmentation of Grained Cell Tissue with Active Contour Models},
BOOKTITLE = {Proceedings International Conference on Pattern Recognition},
YEAR = {2010},
PAGES = {1481-1484}
}
@INPROCEEDINGS{Gress10:bvm,
EDITOR = {Hans-Peter Meinzer and Thomas Martin Deserno and Heinz Handels and Thomas Tolxdorff},
ADDRESS = {Berlin},
LOCATION = {Aachen},
BOOKTITLE = {{Bildverarbeitung f{\"u}r die Medizin}},
AUTHOR = {Oliver Gre{\ss} and Birgit M{\"o}ller and Nadine St{\"o}hr and Stefan H{\"u}ttelmaier and Stefan Posch},
TITLE = {Scale-adaptive Wavelet-based Particle Detection in Microscopy Images},
YEAR = {2010},
PAGES = {266-270},
PUBLISHER = {Springer}
}
@INPROCEEDINGS{Moeller10:visapp,
AUTHOR = {Birgit M{\"o}ller and Oliver Gre{\ss} and Nadine St{\"o}hr and Stefan H{\"u}ttelmaier and Stefan Posch },
TITLE = {Adaptive Segmentation of cells and particles in fluorescent microscope images},
BOOKTITLE = {Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '10)},
YEAR = {2010},
NOTE = {accepted}
}
@INCOLLECTION{bookchapter10,
TITLE = {Probabilistic Approaches to Transcription Factor Binding Site Prediction},
AUTHOR = {Stefan Posch and Jan Grau and Andr{\'e} Gohr and Jens Keilwagen and Ivo Grosse},
BOOKTITLE = {The Computational Biology of Transcription Factor Binding},
EDITOR = {Istvan Ladunga},
PUBLISHER = {Springer Press},
SERIES = {Methods in Molecular Biology},
CITY = {Berlin},
NOTE = {in preparation},
YEAR = {2010}
}
@ARTICLE{Keilwagen2010gendisPaper,
AUTHOR = {Keilwagen, Jens and Grau, Jan and Posch, Stefan and Strickert, Marc and Grosse, Ivo},
TITLE = {Unifying generative and discriminative learning principles},
JOURNAL = {BMC Bioinformatics},
VOLUME = {11},
YEAR = {2010},
NUMBER = {1},
PAGES = {98},
URL = {http://www.biomedcentral.com/1471-2105/11/98 },
DOI = {10.1186/1471-2105-11-98},
PUBMEDID = {20175896},
ISSN = {1471-2105},
}
@ARTICLE{Keilwagen:2010:prior,
AUTHOR = {Keilwagen, Jens and Grau, Jan and Posch, Stefan and Grosse, Ivo},
TITLE = {Apples and oranges: avoiding different priors in {B}ayesian {DNA} sequence analysis},
JOURNAL = {BMC Bioinformatics},
VOLUME = {11},
YEAR = {2010},
NUMBER = {1},
PAGES = {149},
URL = {http://www.biomedcentral.com/1471-2105/11/149 },
DOI = {10.1186/1471-2105-11-149},
ISSN = {1471-2105},
}
@INPROCEEDINGS{Grau10:gcb,
ADDRESS = {Bonn},
AUTHOR = {Jan Grau and Daniel Arend and Ivo Grosse and Artemis G. Hatzigeorgiou and Jens Keilwagen and Manolis Maragkakis and Claus Weinholdt and Stefan Posch},
BOOKTITLE = {German Conference on Bioinformatics},
EDITOR = {Dietmar Schomburg and Andreas Grote},
PAGES = {81-91},
PUBLISHER = {Gesellschaft f{\"u}r Informatik},
SERIES = {Lecture Notes in Informatics (LNI) - Proceedings},
TITLE = {{Predicting miRNA targets utilizing an extended profile HMM}},
VOLUME = {P-173},
YEAR = {2010} }
@ARTICLE{moeller09:JEP,
TITLE = {Robust Features for 2-D Electrophoresis Gel Image Registration},
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
JOURNAL = {Electrophoresis},
PAGES = {4137-4148},
VOLUME = {30},
YEAR = {2009}
}
@INPROCEEDINGS{misiak09:wacv,
TITLE = {Automatic Analysis of Fluorescence Labeled Neurites in Microscope Images},
AUTHOR = {Danny Misiak and Stefan Posch and Nadine St{\"o}hr and Stefan H{\"u}ttelmaier and Birgit M{\"o}ller},
BOOKTITLE = {IEEE Workshop on Applications of Computer Vision (WACV '09)},
PAGES = {118-124},
YEAR = {2009},
CITY = {Snowbird, Utah, USA},
ISBN = {978-1-4244-5496-9},
NOTE = {IEEE Catalog Number: CFP09082-CDR}
}
@PROCEEDINGS{gcb09,
EDITOR = {Ivo Grosse and Steffen Neumann and Stefan Posch and Falk Schreiber and Peter F. Stadler},
TITLE = {German Conference on Bioinformatics 2009},
DATE = {28th to 30th September},
CITY = {Halle (Saale); Germany},
PUBLISHER = {GI},
SERIES = {LNI},
VOLUME = {157},
YEAR = {2009},
ISBN = {978-3-88579-251-2}
}
@INPROCEEDINGS{Moeller08_ICPR,
AUTHOR = {Birgit M{\"o}ller and Thomas Pl{\"o}tz and Gernot Fink},
TITLE = {Calibration-free Camera Hand-Over for Fast and Reliable Person Tracking in Multi-Camera Setups},
BOOKTITLE = {Proc. of Int. Conf. on Pattern Recognition (ICPR '08)},
YEAR = {2008},
MONTH = {December},
ADDRESS = {Tampa, Florida, USA},
NOTE = {to appear},
ABSTRACT = { }
}
@PROCEEDINGS{gcb09,
EDITOR = {Ivo Grosse and Steffen Neumann and Stefan Posch and Falk Schreiber and Peter F. Stadler},
TITLE = {German Conference on Bioinformatics 2009},
DATE = {28th to 30th September},
CITY = {Halle (Saale); Germany},
PUBLISHER = {GI},
SERIES = {LNI},
VOLUME = {157},
YEAR = {2009},
ISBN = {978-3-88579-251-2}
}
@INPROCEEDINGS{Moeller07_BMVC,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Identifying Lens Distortions in Image Registration by Learning from Examples},
BOOKTITLE = {Proc. of British Machine Vision Conference (BMVC '07)},
YEAR = {2007},
MONTH = {September},
ADDRESS = {University of Warwick, Coventry, UK},
PAGES = {I:152-161},
PDF = {http://www.dcs.warwick.ac.uk/bmvc2007/proceedings/CD-ROM/papers/paper-123.pdf },
ABSTRACT = { }
}
@ARTICLE{Wensch07:ivc,
AUTHOR = {J{\"o}rg Wensch and Alf Gerisch and Stefan Posch},
TITLE = {Optimised coupling of hierarchies in image registration},
JOURNAL = {Image and Vision Computing},
YEAR = {2008},
VOLUME = {26},
NUMBER = {7},
PAPGES = {1000-1011},
PUBLISHER = {Elsevier},
ABSTRACT = {}
}
@ARTICLE{Moeller08:PRIA,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {An Integrated Analysis Concept for Errors in Image Registration},
JOURNAL = {Int. Journal on Pattern Recognition and Image Analysis (PRIA)},
YEAR = {2008},
PUBLISHER = {Springer},
VOLUME = {18},
NUMBER = {2},
PAGES = {201-206}
}
@TECHREPORT{Moeller07_TR,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {An Iconic Scene Memory Approach for Mobile Robots Interacting with Humans},
INSTITUTION = {Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany},
YEAR = {2007},
MONTH = {December},
TYPE = {Technical Report},
PS = {https://nirvana.informatik.uni-halle.de/~funke/TR/2007_03.pdf},
NUMBER = {2007-03}
}
@INPROCEEDINGS{Moeller07_BMVC,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Identifying Lens Distortions in Image Registration by Learning from Examples},
BOOKTITLE = {Proc. of British Machine Vision Conference (BMVC '07)},
YEAR = {2007},
MONTH = {September},
ADDRESS = {University of Warwick, Coventry, UK},
PAGES = {I:152-161},
PDF = {http://www.dcs.warwick.ac.uk/bmvc2007/proceedings/CD-ROM/papers/paper-123.pdf },
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller07_OGRW,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {An Integrated Analysis Concept for Errors in Image Registration},
BOOKTITLE = {Proc. of 7th Open German/Russian Workshop on Pattern Recognition and Image Understanding (OGRW '07)},
YEAR = {2007},
MONTH = {August},
ADDRESS = {Ettlingen, Germany},
PDF = {PDF/Moeller07_OGRW.pdf},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller07_CCMVS,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Automatic Analysis of Lens Distortions in Image Registration},
BOOKTITLE = {Proc. of Int. Conf. on Computer Vision Systems (ICVS '07), Workshop on Camera Calibration Methods for
Computer Vision Systems (CCMVS '07)},
YEAR = {2007},
MONTH = {March},
ADDRESS = {Bielefeld, Germany},
PDF = {http://www.icvs2007.org/ccmvs/CCMVS2007-174.pdf },
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller07_VISAPP,
AUTHOR = {Birgit M{\"o}ller and Rafael Garcia and Stefan Posch},
TITLE = {Towards Objective Quality Assessment of Image Registration Results},
BOOKTITLE = {Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '07)},
PAGES = {233-240},
YEAR = {2007},
MONTH = {March},
ADDRESS = {Barcelona, Spain},
ABSTRACT = { }
}
@INPROCEEDINGS{Opitz07_insitu,
TITLE = {Joint Analysis of In-situ Hybridization and Gene Expression Data},
AUTHOR = {Lennart Opitz and Alexander Schliep and Stefan Posch},
BOOKTITLE = {Advances in Data Analysis: Proceedings of the 30th Annual Conference of the Gesellschaft f{\"u}r Klassifikation e.V.,},
EDITOR = {Reinhold Decker and Hans -J. Lenz},
PAGES = {577-584},
YEAR = {2007},
PUBLISHER = {Springer},
CITY = {Berlin, Heidelberg},
ISBN = {978-3-540-70980-0 (Print) 978-3-540-70981-7 (Online)},
ABSTRACT = {}
}
@ARTICLE{posch07:jbcb,
AUTHOR = {Stefan Posch and Jan Grau and Andre Gohr and Irad Ben-Gal and Alexander Kel and Ivo Grosse},
TITLE = {Recognition of cis-regulatory elements with {VOMBAT}},
JOURNAL = {Journal of Bioinformatics and Computational Biology},
YEAR = {2007},
PAGES = {561-577},
VOLUME = {5},
NUMBER = {02B},
URL = {http://www.worldscinet.com/jbcb/05/0502b/S0219720007002886.html },
ABSTRACT = {}
}
@INPROCEEDINGS{Grau07:gcb,
AUTHOR = {Jan Grau and Jens Keilwagen and Alexander Kel and Ivo Grosse and Stefan Posch},
TITLE = {Supervised posteriors for DNA-motif classification},
BOOKTITLE = {German Conference on Bioinformtics},
YEAR = {2007},
PAGES = {123-134},
ABSTRACT = {}
}
@PROCEEDINGS{gcb09,
EDITOR = {Ivo Grosse and Steffen Neumann and Stefan Posch and Falk Schreiber and Peter F. Stadler},
TITLE = {German Conference on Bioinformatics 2009},
DATE = {28th to 30th September},
CITY = {Halle (Saale); Germany},
PUBLISHER = {GI},
SERIES = {LNI},
VOLUME = {157},
YEAR = {2009},
ISBN = {978-3-88579-251-2}
}
@INPROCEEDINGS{Moeller06_VISAPP,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {A Space- and Time-Efficient Mosaic-Based Iconic Memory for Interactive Systems},
BOOKTITLE = {Proc. of International Conference on Computer Vision Theory and Applications (VISAPP '06)},
PAGES = {413--421},
YEAR = {2006},
MONTH = {February},
ADDRESS = {Set{\'u}bal, Portugal},
ABSTRACT = { }
}
@INPROCEEDINGS{Grau06:gcb-etfbs,
AUTHOR = {Jan Grau and Irad Ben-Gal and Andre Gohr and Alexander Kel and Olga Kel-Margoulis and Stefan Posch and Ivo Grosse},
TITLE = {Prediction of eukaryotic transcription factor binding sites using Variable Order Markov models},
BOOKTITLE = {GCB},
YEAR = {2006},
PAGES = {5-6}
}
@INPROCEEDINGS{Grau06:gcb-vombat,
AUTHOR = {Jan Grau and Irad Ben-Gal and Ivo Grosse and Stefan Posch},
TITLE = {VOMBAT: A web-server for predicting transcription factor binding sites using Variable Order Markov Models and Variable Order Bayesian Trees},
BOOKTITLE = {GCB, Short paper},
YEAR = {2006}
}
@INPROCEEDINGS{Poeschl06:gcb,
AUTHOR = {Yvonne P{\"o}schl and Christoph B{\"o}ttcher and Stephan Clemens and Dierk Scheel and Stefan Posch and Steffen Neumann},
TITLE = {Analysis of Metabolite relations in LCMS data using Bayesian Networks},
BOOKTITLE = {GCB, Short paper},
YEAR = {2006},
PAGES = {17-18}
}
@ARTICLE{VOMBAT06,
AUTHOR = {Jan Grau and Irad Ben-Gal and Stefan Posch and Ivo Grosse},
TITLE = {{VOMBAT}: Prediction of Transcription Factor Binding Sites using Variable Order Bayesian Trees},
JOURNAL = {Nucleic Acids Research},
VOLUME = {34},
NUMBER = {suppl_2},
YEAR = {2006},
PAGES = {W529-533},
DOI = {10.1093/nar/gkl212},
URL = {http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_2/W529?ijkey=f29UCw2WfY47dcX&keytype=ref }
}
@INPROCEEDINGS{Erz05:Eurocon,
AUTHOR = {Gregor Erz and Stefan Posch},
TITLE = {Root Detection By Hierarchical Seed Expansion},
BOOKTITLE = {Proceedings of Eurocon 2005},
YEAR = {2005},
MONTH = {November},
PUBLISHER = {IEEE Computer Society Press},
ADDRESS = {Belgrade},
PAGES = {963-966}
}
@INPROCEEDINGS{Moeller05_IROS,
AUTHOR = {Birgit Möller and Stefan Posch and Axel Haasch and Jannik Fritsch and Gerhard Sagerer},
TITLE = {Interactive Object Learning for Robot Companions using Mosaic Images},
BOOKTITLE = {Proc. IEEE/RSJ Int. Conf. on Intelligent Robots and Systems},
MONTH = {August},
YEAR = {2005},
ADDRESS = {Edmonton, Alberta, Canada},
PAGES = {371-376},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller05_Mirage,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {A Mosaic-based Visual Memory with Applications to Active Scene Exploration},
BOOKTITLE = {Proc. of Mirage, Computer Vision / Computer Graphics Collaboration Techniques and Applications},
YEAR = {2005},
MONTH = {March},
PAGES = {117-125},
ADDRESS = {INRIA Rocquencourt, France},
PDF = {PDF/Moeller05_Mirage.pdf},
ABSTRACT = { }
}
@INPROCEEDINGS{posch05:KI,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Visual Scene Memory Based on Multi-Mosaics},
BOOKTITLE = {Mixed-reality as a challenge to image understanding and artificial intelligence},
EDITOR = {Dietrich Paulus and Detlev Droege},
ORGANIZATION = {Universit{\"a}t Koblenz-Landau, Institut f{\"u}r Informatik},
ADDRESS = {Koblenz},
YEAR = {2005},
PAGES = {27-32},
ISBN = {1860-4471},
PDF = {PDF/posch05:KI.pdf},
ABSTRACT = { }
}
@ARTICLE{Erz05,
AUTHOR = {Gregor Erz and Maik Veste and Heiko Anlauf and Siegmar-Walter Breckle and Stefan Posch},
TITLE = {A region and contour based technique for automatic detection of of tomatoe roots in minirhizotron images},
JOURNAL = {Journal of Applied Botany and Food Quality},
YEAR = {2005},
VOLUME = {79},
PAGES = {83-88}
}
@ARTICLE{Bengal05:sigma70,
AUTHOR = {I. Ben-Gal and A. Shani and A. Gohr and J. Grau and S. Arviv and A. Shmilovici and S. Posch and I. Grosse},
TITLE = {Identification of transcription factor binding sites with variable-order Bayesian networks},
JOURNAL = {Bioinformatics},
VOLUME = {21},
YEAR = {2005},
PAGES = {2657-2666},
URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/11/2657 }
}
@INPROCEEDINGS{ismb04,
AUTHOR = {Irad Ben-Gal and Sigal Arviv and Andre Gohr and Jan Grau an
d Stefan Posch and Armin Shmilovici and Ivo Grosse},
TITLE = {Computational identification of transcription factor binding si
tes with Variable-Order Markov Models},
BOOKTITLE = {ISMB/ECCB, Poster Abstract},
YEAR = {2004}
}
@INPROCEEDINGS{gcb04,
AUTHOR = {Andreas Stephanik and Steffen Neumann and Lothar Altschmied
and David L. Müller and Stefan Posch and Ivo Grosse},
TITLE = {{SMArrT}: SMArrT: An integrated Workflow for Array An integrate
d Workflow for Array Analysis},
BOOKTITLE = {GCB, Poster Abstract},
YEAR = {2004}
}
@ARTICLE{Moeller04_PRIA,
AUTHOR = {Birgit M{\"o}ller and Denis Williams and Stefan Posch},
TITLE = {Towards a Mosaic-based Visual Representation of Large Scenes},
JOURNAL = {Int. Journal on Pattern Recognition and Image Analysis (PRIA), Spec. Issue},
YEAR = {2004},
VOLUME = {14(2)},
PAGES = {262-266},
ABSTRACT = { }
}
@INPROCEEDINGS{Erz03_DAGM,
AUTHOR = {Gregor Erz and Stefan Posch},
TITLE = {A Region Based Seed Detection for Root Detection in Minirhizotron Images},
BOOKTITLE = {Pattern Recognition, Proc. of 25th DAGM Symposium},
YEAR = {2003},
MONTH = {September},
EDITOR = {B. Michaelis and G. Krell},
ADDRESS = {Magdeburg, Germany},
SERIES = {LNCS 2781},
PAGES = {482-489},
PUBLISHER = {Springer},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller03:DAGM,
AUTHOR = {Birgit M{\"o}ller and Denis Williams and Stefan Posch},
TITLE = {Robust Image Sequence Mosaicing},
BOOKTITLE = {Pattern Recognition, Proc. of 25th DAGM Symposium},
YEAR = {2003},
MONTH = {September},
EDITOR = {B. Michaelis and G. Krell},
ADDRESS = {Magdeburg, Germany},
SERIES = {LNCS 2781},
PAGES = {386-293},
PUBLISHER = {Springer},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller03:OGRW,
AUTHOR = {Birgit M{\"o}ller and Denis Williams and Stefan Posch},
TITLE = {Towards a Mosaic-based Visual Representation of Large Scenes},
BOOKTITLE = {Proc. of 6th Open German-Russian Workshop (IAPR)},
YEAR = {2003},
MONTH = {25.-30. August},
ADDRESS = {Katun Village, Altai Region, Russian Federation},
PAGES = {108-111},
ABSTRACT = { }
}
@INPROCEEDINGS{posch03:iasted,
AUTHOR = {J{\"o}rg Weitzenberg and Stefan Posch},
TITLE = {{Using Hidden-Markov-Models to analyze Concentrations from Biosensor Curves}},
BOOKTITLE = {Proc. Int. Conference Signal Processing, Pattern Recognition, \& Applications},
PUBLISHER = {IASTED},
PAGES = {98-103},
YEAR = {2003},
ADDRESS = {Rhodes},
PDF = {PDF/posch03:iasted.pdf},
ABSTRACT = { }
}
@INPROCEEDINGS{Williams03_CISST,
AUTHOR = {Denis Williams and Birgit M{\"o}ller and Stefan Posch},
TITLE = {Integrated System for a Visual Memory Based on Mosaics},
BOOKTITLE = {Proc. of International Conference on Imaging Science, Systems, and Technology (CISST'03)},
PUBLISHER = {CSREA Press},
EDITOR = {H.R. Arabnia and Youngsong Mun},
PAGES = {II: 633-639},
YEAR = {2003},
MONTH = {23.-26.June},
ADDRESS = {Las Vegas, USA},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller02:dagm,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Analysis of Object Interactions in Dynamic Scenes},
BOOKTITLE = {Pattern Recognition. 24.~DAGM-Symposium},
YEAR = {2002},
MONTH = {September},
EDITOR = {L. van Gool},
ADDRESS = {Zurich, Switzerland},
PAGES = {361-369},
SERIES = {LNCS 2449},
PUBLISHER = {Springer},
PDF = {PDF/Moeller02:dagm.pdf},
ABSTRACT = { }
}
@INPROCEEDINGS{Weitzenberg02:dagm,
AUTHOR = {J{\"o}rg Weitzenberg and Stefan Posch and Manfred Rost},
TITLE = {Analysis of Amperometric Biosensor Curves Using Hidden-Markov-Modells},
EDITOR = {Luc Van Gool},
BOOKTITLE = {Pattern Recognition. 24.~DAGM-Symposium},
YEAR = {2002},
PAGES = {182-189},
ABSTRACT = { }
}
@INPROCEEDINGS{Moeller01:dagm,
AUTHOR = {Birgit M{\"o}ller and Stefan Posch},
TITLE = {Detection and Tracking of Moving Objects for Mosaic Image Generation},
BOOKTITLE = {Pattern Recognition, Proc. of 23rd DAGM Symposium},
YEAR = {2001},
MONTH = {September},
EDITOR = {B. Radig and S. Florczyk},
ADDRESS = {Munich, Germany},
PAGES = {208-215},
SERIES = {LNCS 2191},
PUBLISHER = {Springer},
PDF = {PDF/Moeller01:dagm.pdf},
ABSTRACT = { }
}
@INPROCEEDINGS{Weitzenberg01:sensor,
AUTHOR = {J. Weitzenberg and S. Posch and C. Bauer and M. Rost and B. Gr{\"u}ndig},
TITLE = {Analysis of Amperometric Biosensor Data Using Fuzzy Logic and Discrete Hidden-Markov-Models},
BOOKTITLE = {SENSOR 2001},
YEAR = {2001},
EDITOR = {Tr{\"a}nkler, H.R.},
PAGES = {Volume II: 493-498},
ABSTRACT = { }
}
@INPROCEEDINGS{Schlueter00:icip,
AUTHOR = {Daniel Schl{\"u}ter and Sven Wachsmuth and Gerhard Sagerer and Stefan Posch},
TITLE = {Towards an Integrated Framework for Contour-Based Grouping and Object Recognition using Markov Random Fields},
BOOKTITLE = {Proc. International Conference on Image Processing},
YEAR = {2000},
ORGANIZATION = {IEEE},
PAGES = {100-103},
PS = {PS/Schlueter00:icip.ps},
VOLUME = {II}
}
@INPROCEEDINGS{Schlueter00:icpr,
AUTHOR = {Daniel Schl{\"u}ter and Franz Kummert and Gerhard Sagerer and Stefan Posch},
TITLE = {Integration of Regions and Contours for Object Recognition},
BOOKTITLE = {Proc. International Conference on Pattern Recognition},
YEAR = {2000},
ORGANIZATION = {IEEE},
PAGES = {944-947},
PS = {PS/Schlueter00:icpr.ps},
VOLUME = {1}
}
@INPROCEEDINGS{Williams00:dagm,
AUTHOR = {Denis Williams and Stefan Posch},
TITLE = {Stereozuordnung von hierachischen {K}onturgruppen mit {M}arkov {R}andom {F}ields},
BOOKTITLE = {Mustererkennug 2000. Proceedings 22.~DAGM-Symposium},
YEAR = {2000},
EDITOR = {Gerald Sommer and Norbert Kr{\"u}ger and Christian Perwass},
SERIES = {Informatik Aktuell},
ADRESS = {Berlin},
PUBLISHER = {Springer},
PAGES = {7-16}
}
@INPROCEEDINGS{Weitzenberg00:dagm,
AUTHOR = {J{\"o}rg Weitzenberg and Stefan Posch and Manfred Rost},
TITLE = {Diskrete {H}idden {M}arkov {M}odelle zur {A}nalyse von {M}e{\ss}kurven amperometrischer {B}iosensoren},
BOOKTITLE = {Mustererkennug 2000. Proceedings 22.~DAGM-Symposium},
YEAR = {2000},
EDITOR = {Gerald Sommer and Norbert Kr{\"u}ger and Christian Perwass},
SERIES = {Informatik Aktuell},
ADRESS = {Berlin},
PUBLISHER = {Springer},
PAGES = {317-324},
PS = {PS/Weitzenberg00:dagm.ps}
}