@article{Song24_SR,
title = {A new approach to three-dimensional microstructure reconstruction of a polycrystalline solar cell using high-efficiency {C}u({I}n,{G}a){S}e2},
author = {Song, Chang-Yun and Maiberg, Matthias and Kempa, Heiko and Witte, Wolfram and Hariskos, Dimitrios and Abou-Ras, Daniel and Moeller, Birgit and Scheer, Roland and Gholinia, Ali},
year = {2024},
journal = {Scientific Reports},
volume = {14},
number = {1},
pages = {2036},
publisher = {Nature Publishing Group UK London},
doi = {10.1038/s41598-024-52436-2},
url = {https://www.nature.com/articles/s41598-024-52436-2},
abstract = {A new method for efficiently converting electron backscatter diffraction data obtained using serial sectioning by focused ion beam of a polycrystalline thin film into a computational, three-dimensional (3D) structure is presented. The reported data processing method results in a more accurate representation of the grain surfaces, reduced computer memory usage, and improved processing speed compared to traditional voxel methods. The grain structure of a polycrystalline absorption layer from a high-efficiency Cu(In,Ga)Se2 solar cell (19.5\%) is reconstructed in 3D and the grain size and surface distribution is investigated. The grain size distribution is found to be best fitted by a log-normal distribution. We further find that the grain size is determined by the [Ga]/([Ga] + [In]) ratio in vertical direction, which was measured by glow discharge optical emission spectroscopy. Finally, the 3D model derived from the structural information is applied in optoelectronic simulations, revealing insights into the effects of grain boundary recombination on the open-circuit voltage of the solar cell. An accurate 3D structure like the one obtained with our method is a prerequisite for a detailed understanding of mechanical properties and for advanced optical and electronic simulations of polycrystalline thin films.}
}
@incollection{Klemm23_TPC,
author = {Klemm, Sandra and Buhl, Jonas and M{\"o}ller, Birgit and B{\"u}rstenbinder, Katharina},
editor = {Hussey, Patrick J. and Wang, Pengwei},
title = {Quantitative Analysis of Microtubule Organization in Leaf Epidermis Pavement Cells},
booktitle = {The Plant Cytoskeleton: Methods and Protocols},
year = {2023},
publisher = {Springer US},
address = {New York, NY},
pages = {43--61},
abstract = {Leaf epidermis pavement cells form highly complex shapes with interlocking lobes and necks at their anticlinal walls. The microtubule cytoskeleton plays essential roles in pavement cell morphogenesis, in particular at necks. Vice versa, shape generates stress patterns that regulate microtubule organization. Genetic or pharmacological perturbations that affect pavement cell shape often affect microtubule organization. Pavement cell shape and microtubule organization are therefore closely interconnected. Here, we present commonly used approaches for the quantitative analysis of pavement cell shape characteristics and of microtubule organization. In combination with ablation experiments, these methods can be applied to investigate how different genotypes (or treatments) affect the organization and stress responsiveness of the microtubule cytoskeleton.},
isbn = {978-1-0716-2867-6},
doi = {10.1007/978-1-0716-2867-6_4},
url = {https://doi.org/10.1007/978-1-0716-2867-6_4}
}
@book{Moeller22_Habil,
title = {Image analysis in the life sciences: computational methods and tools},
author = {M{\"o}ller, Birgit},
year = {2022},
publisher = {Martin Luther University Halle-Wittenberg},
series = {Habilitation {T}hesis},
url = {https://search.ebscohost.com/login.aspx?direct=true&db=cat09315a&AN=ulb.1842691589&lang=de&site=eds-live&scope=site},
keywords = {image analysis, spot detection, segmentation, active contours, machine learning, Alida, MiToBo, life sciences, cells, roots},
abstract = {This habilitation thesis presents methodical and computational approaches for the analysis of image data in various application domains of the life sciences. Amongst others methods for the detection of punctiform structures in microscope images are described. A second research field deals with the segmentation of more complex objects like cells or plant roots. Here established methods like active contours have specifically been extended as well as new methods of machine learning with neural networks been applied. A third topic area comprises the extraction of quantitative data of objects. Here new measures for cell shape have been devised as well as protocols for the quantification and comparison of subcellular structures been developed. In addition to the methodical approaches the software libraries Alida and MiToBo are presented, which yield the basis for the implementation of most of the approaches, and the annotation tool rhizoTrak.}
}
@inproceedings{Moeller21_CVPPA,
title = {{Analysis of Arabidopsis Root Images - Studies on CNNs and Skeleton-Based Root Topology}},
author = {B.~M{\"o}ller and B.~Schreck and S.~Posch},
booktitle = {{Proc. of the IEEE/CVF International Conference on Computer Vision (ICCV) Workshops, 7th Workshop on Computer Vision in Plant Phenotyping and Agriculture (CVPPA)}},
year = {2021},
pages = {1294-1302},
month = {October},
doi = {10.1109/ICCVW54120.2021.00150},
url = {https://openaccess.thecvf.com/content/ICCV2021W/CVPPA/html/Moller_Analysis_of_Arabidopsis_Root_Images_--_Studies_on_CNNs_and_ICCVW_2021_paper.html},
abstract = {Roots and their temporal development play an important role in plant research. Over the decades image-based monitoring of root growth has become a key methodology in this research field. The growing amount of image data is often tackled with automatic image analysis approaches. In particular convolutional neural networks (CNNs) recently gained increasing interest for root segmentation. This segmentation of roots is usually only the first step of an analysis pipeline and needs to be supplemented by topological reconstruction of the complete root system architecture.
In this paper we present a comprehensive study of different CNN architectures, loss functions and parameter settings for root image segmentation. In addition, we show how main and lateral roots can be identified based on the skeletons of segmented root components as a first step towards topological reconstruction of root system architecture. We present quantitative and qualitative results on data released in the course of the CVPPA Arabidopsis Root Segmentation Challenge 2021.}
}
@incollection{Poeschl20_MBC,
title = {User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools},
series = {Methods in Cell Biology},
publisher = {Academic Press},
volume = {160},
pages = {349-363},
year = {2020},
booktitle = {Plant Cell Biology},
issn = {0091-679X},
doi = {https://doi.org/10.1016/bs.mcb.2020.04.010},
url = {http://www.sciencedirect.com/science/article/pii/S0091679X20300741},
author = {Yvonne Poeschl and Birgit Möller and Lukas Müller and Katharina Bürstenbinder},
keywords = {Cell segmentation, Feature extraction, Pavement cells, ImageJ, MiToBo, PaCeQuant, Arabidopsis},
abstract = {Leaf epidermis pavement cells develop complex jigsaw puzzle-like shapes in many plant species, including the model plant Arabidopsis thaliana. Due to their complex morphology, pavement cells have become a popular model system to study shape formation and coordination of growth in the context of mechanically coupled cells at the tissue level. To facilitate robust assessment and analysis of pavement cell shape characteristics in a high-throughput fashion, we have developed PaCeQuant and a collection of supplemental tools. The ImageJ-based MiToBo plugin PaCeQuant supports fully automatic segmentation of cell contours from microscopy images and the extraction of 28 shape features for each detected cell. These features now also include the Largest Empty Circle criterion as a proxy for mechanical stress. In addition, PaCeQuant provides a set of eight features for individual lobes, including the categorization as type I and type II lobes at two- and three-cell junctions, respectively. The segmentation and feature extraction results of PaCeQuant depend on the quality of input images. To allow for corrections in case of local segmentation errors, the LabelImageEditor is provided for user-friendly manual postprocessing of segmentation results. For statistical analysis and visualization, PaCeQuant is supplemented with the R package PaCeQuantAna, which provides statistical analysis functions and supports the generation of publication-ready plots in ready-to-use R workflows. In addition, we recently released the FeatureColorMapper tool which overlays feature values over cell regions for user-friendly visual exploration of selected features in a set of analyzed cells.}
}
@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},
number = {444},
pages = {519-534},
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 = {https://doi.org/10.1007/s11104-019-04199-3}
}
@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. To identify cellular processes or genetic elements underlying stromule formation screens of large populations of mutant plants or plants under different treatments are carried out and stromule frequencies are extracted. Due to a lack of automatic methods, however, this quantification is usually done manually rendering this step a main bottleneck in stromule research. Here, we present a new approach for quantification of stromule frequencies. Plastids are extracted from microscope images using local wavelet analysis over multiple scales combined with statistical hypothesis testing to resolve competing detections from different scales. Subsequently, for each plastid region evidence for the existence of stromules in its vicinity is investigated applying ridge detection techniques and geometric criteria. Experimental results prove that our approach is suitable to properly identify stromules. Even in microscopy images with a high noise level and distracting signals extracted stromule counts are comparable to those of biological experts.}
}
@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 integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.}
}
@inproceedings{Moeller18_EMBL-01,
title = {{A}nalysis of {C}ell {M}orphology with the {I}mage{J} {P}lugin {P}a{C}e{Q}uant},
author = {B.~M{\"o}ller and Y.~Poeschl and K.~B{\"u}rstenbinder},
booktitle = {EMBL Conference: From Images to Knowledge with ImageJ \& Friends},
year = {2018},
address = {EMBL Heidelberg, Germany},
month = {December},
note = {Poster Presentation}
}
@inproceedings{Moeller18_EMBL-02,
title = {{M}inirhizotron {I}mage {A}nnotation in {F}iji with rhizo{T}rak},
author = {B.~M{\"o}ller and H.~Chen and T.~Schmidt and A.~Zieschank and R.~Patzak and B.~Schreck and M.~T{\"u}rke and A.~Weigelt and S.~Posch},
booktitle = {EMBL Conference: From Images to Knowledge with ImageJ \& Friends},
year = {2018},
address = {EMBL Heidelberg, Germany},
month = {December},
note = {Poster Presentation}
}
@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}
}
@article{Franke15_JECR,
title = {{T}he '{MTB} {C}ell {C}ounter' 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},
abstract = {Organelle morphology as well as subcellular organisation can drastically change in response to a changing cellular environment. However our knowledge about the functionality as well as the regulation of organelle form changes, such as plastid tubule formation (stromules) and organelle rearrangements, is limited. Monitoring changes to organelle morphology and subcellular organisation in response to experimental treatments and in different mutant backgrounds is a promising strategy to address open questions. However, for a detailed comparison of different treatments and mutants, the quantification of subcellular phenotypes is crucial. Unfortunately, for many specific subcellular parameters, such as stromule frequency, software tools supporting data extraction from images are not readily available or are highly specialized in their purpose. In order to quantify stromule frequency in a semi-automated manner we developed the 'MTB Cell Counter', which combines automated plastid detection with manual counting tools. We show that with the use of our plugin stromule frequency can be quantified up to 90% faster. We further demonstrate, with the detection of peroxisomes and nuclei, that due to its adaptable detection algorithm, which is based on scale-adaptive analysis of wavelet coefficients, the plugin can be used to reliably detect and count organelles of different size and brightness. In addition to the analysis of CLSM images, the 'MTB Cell Counter' is easily adapted to particle detection in challenging epifluorescence images, making it a versatile, semi-automated tool capable of quantifying a wide variety of subcellular phenotypes.},
file = {:http\://zs.thulb.uni-jena.de/servlets/MCRFileNodeServlet/jportal_derivate_00242396/ECR_2015_31-42_Franke.etal..pdf:PDF},
keywords = {plastid, nucleus, peroxisome, image analysis, ImageJ, MiToBo, stromule, cell biology},
owner = {moeller},
timestamp = {2015.06.17},
url = {http://zs.thulb.uni-jena.de/receive/jportal_jparticle_00342296}
}
@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},
address = {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},
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.},
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{Bley15_NAR,
title = {Stress granules are dispensable for {mRNA} stabilization during cellular stress},
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},
journal = {Nucleic Acids Research},
year = {2015},
month = {February},
note = {PubMed ID: 25488811, PubMed CID: PMC4344486},
number = {4},
pages = {e26},
volume = {43},
abstract = {During cellular stress, protein synthesis is severely reduced and bulk mRNA is recruited to stress granules (SGs). Previously, we showed that the SG-recruited IGF2 mRNA-binding protein 1 (IGF2BP1) interferes with target mRNA degradation during cellular stress. Whether this requires the formation of SGs remained elusive. Here, we demonstrate that the sustained inhibition of visible SGs requires the concomitant knockdown of TIA1, TIAR and G3BP1. FRAP and photo-conversion studies, however, indicate that these proteins only transiently associate with SGs. This suggests that instead of forming a rigid scaffold for mRNP recruitment, TIA proteins and G3BP1 promote SG-formation by constantly replenishing mRNPs. In contrast, RNA-binding proteins like IGF2BP1 or HUR, which are dispensable for SG-assembly, are stably associated with SGs and the IGF2BP1/HUR-G3BP1 association is increased during stress. The depletion of IGF2BP1 enhances the degradation of target mRNAs irrespective of inhibiting SG-formation, whereas the turnover of bulk mRNA remains unaffected when SG-formation is impaired. Together these findings indicate that the stabilization of mRNAs during cellular stress is facilitated by the formation of stable mRNPs, which are recruited to SGs by TIA proteins and/or G3BP1. Importantly, however, the aggregation of mRNPs to visible SGs is dispensable for preventing mRNA degradation.},
doi = {10.1093/nar/gku1275},
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 22nd Int.~Conf.~on Pattern Recognition (ICPR)},
year = {2014},
pages = {3251-3256},
address = {Stockholm, Sweden},
month = {August},
publisher = {IEEE},
abstract = {The analysis of F-actin organization in cells is a
key topic in many fields of biomedical research. While standard
protocols for imaging immunostained actin are well established,
assessment of the resulting microscopy images is most of the time
still performed manually and with a high degree of subjectivity.
In this paper, we present a new approach for the analysis of
actin structures in microscopy images and the quantification of
differences and similarities in actin organization between cells.
Compared to existing methods, our approach does not require any
previous knowledge about the cells or structures to be analyzed.
It works in an unsupervised fashion, combining statistical texture
measures and clustering techniques. By this, our method yields
large flexibility and allows for application in a wide range of ex-
perimental scenarios, and also to heterogeneous cell populations.
Experimental evaluation on sample data proves that our method
yields meaningful results for biomedical investigations.},
keywords = {cellular biophysics;medical image processing;molecular biophysics;molecular configurations;pattern clustering;proteins;statistical analysis;F-actin organization analysis;actin structure quantification;biomedical investigation;biomedical research;cell biology;clustering techniques;heterogeneous cell populations;imaging immunostained actin;microscopy images;statistical texture;unsupervised pattern analysis;Feature extraction;Image segmentation;Microscopy;Organizations;Sociology;Statistics;Vectors;actin structures;clustering;quantification;texture},
doi = {10.1109/ICPR.2014.560},
issn = {1051-4651},
url = {http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=6977272&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6977272}
}
@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},
abstract = {The function of complex networks in the nervous system relies on the
proper formation of neuronal contacts and their remodeling. To decipher
the molecular mechanisms underlying these processes, it is essential
to establish unbiased automated tools allowing the correlation of
neurite morphology and the subcellular distribution of molecules
by quantitative means.
We developed NeuronAnalyzer2D, a plugin for ImageJ, which allows the
extraction of neuronal cell morphologies from two dimensional high
resolution images, and in particular their correlation with protein
profiles determined by indirect immunostaining of primary neurons.
The prominent feature of our approach is the ability to extract subcellular
distributions of distinct biomolecules along neurites. To extract
the complete areas of neurons, required for this analysis, we employ
active contours with a new distance based energy. For locating the
structural parts of neurons and various morphological parameters
we adopt a wavelet based approach. The presented approach is able
to extract distinctive profiles of several proteins and reports detailed
morphology measurements on neurites.
We compare the detected neurons from NeuronAnalyzer2D with those obtained
by NeuriteTracer and Vaa3D-Neuron, two popular tools for automatic
neurite tracing. The distinctive profiles extracted for several proteins,
for example, of the mRNA binding protein ZBP1, and a comparative
evaluation of the neuron segmentation results proves the high quality
of the quantitative data and proves its practical utility for biomedical
analyses.},
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}
}
@inproceedings{Moeller13_IbPRIA,
author = {Armagan Elibol and Stefan Posch and Andreas Maurer and Klaus Pillen
and Birgit M{\"o}ller},
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},
address = {Madeira, Portugal},
month = {June},
abstract = {For multi-view 3D reconstruction robust standard procedures have been
established and can directly be applied to many scenarios. However,
the extraction of point correspondences as a prerequisite for reconstruction
is demanding for various applications. Here we present a new analysis
pipeline for 3D reconstruction in the field of barley plant monitoring.
Barley plants show a significant structural and textural similarity
rendering the application of standard procedures to extract correspondences
impossible. Our new approach overcomes these problems by combining
information from various cues over different stages. Experiments
on real data prove the suitability of our approach to generate 3D
models of the plants from which phenotypical data can easily be derived.},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/978-3-642-38628-2_48}
}
@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},
address = {Kyoto, Japan},
month = {May},
pages = {447-450},
abstract = {Solving image analysis problems not only requires the development of
suitable sets of algorithms to produce desired result data, but also demands
for suitable user interfaces (UIs) to foster use in practice. Here we present
our library Alida which aims to promote the deployment of UIs by featuring their
automatic generation from algorithm code. Alida supports command line and
graphical UIs (GUIs), and ships with a graphical editor for designing more complex
workflows. Enforcing only a small set of rules to obey Alida significantly reduces
implementation overhead for developers and allows for focusing on algorithm rather
than UI design. The suitability of Alidaâs concept for real-life applications is
shown by the library MiToBo for biomedical image analysis implemented based on Alida.}
}
@inproceedings{Elibol08_ISCIS,
author = {A. Elibol and B. M{\"o}ller and R. Garcia},
title = {Perspectives of Auto-Correcting Lens Distortions in Mosaic-Based
Underwater Navigation"},
booktitle = {Proc. of 23rd IEEE Int. Symposium on Computer and Information Sciences
(ISCIS)},
year = {2008},
address = {Istanbul, Turkey},
month = {October},
publisher = {IEEE},
abstract = {When unmanned underwater vehicles (UUVs) perform missions near the
ocean floor, optical sensors can be used to improve local navigation.
Video mosaics allow to efficiently process the images acquired by
the vehicle, and also to obtain position estimates. We discuss in
this paper the role of lens distortions in this context, proving
that degenerate mosaics have their origin not only in the selected
motion model or in registration errors, but also in the cumulative
effect of radial distortion residuals. Additionally, we present results
on the accuracy of different feature-based approaches for self-correction
of lens distortions that may guide the choice of appropriate techniques
for correcting distortions.},
url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4717863}
}
@inproceedings{Glass12_ImageJ,
author = {M. Gla{\ss} and B. M{\"o}ller and S. Posch},
title = {Scratch Assay Analysis in ImageJ},
booktitle = {Proc. of ImageJ User \& Developer Conference},
year = {2012},
pages = {211-214},
address = {Mondorf-les-Bains, Luxembourg},
month = {October},
abstract = {Scratch assays are a widely used technique for assessing the migratory
potential of cells. However, due to a lack of appropriate tools these assays
are often analyzed manually. Here we present a plugin for the automatic
segmentation and analysis of scratch assay images. The input images
are segmented using a topology-preserving non-PDE level set approach.
To exclude images where the scratch has already been completely closed a support
vector machine separates images containing a scratch from such that
do not. As our method requires adjustment of only two parameters,
it is easy to use and has already been successfully applied in practice.},
comment = {ISBN 2-919941-18-6},
keywords = {Scratch assay, Level sets, SVM, Entropy, Topology preservation}
}
@inproceedings{Glass11_IbPRIA,
author = {M. Gla{\ss} and B. M{\"o}ller and A. Zirkel and K. W{\"a}chter and
S. H{\"u}ttelmaier 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 Vitri{\`a} and Jo{\~a}o M. Sanches and Mario Hern{\'a}ndez},
number = {6669},
series = {LNCS},
pages = {100-108},
address = {Gran Canaria, Spain},
publisher = {Springer},
abstract = {Scratch assays are widely used for cell motility and migration assessment
in biomedical research. However, quantitative data is very often
extracted manually. Here, we present a fully automated analysis pipeline
for detecting scratch boundaries and measuring areas in scratch assay
images based on level set techniques. In particular, non-PDE level
sets are extended for topology preservation and applied to entropy
data of scratch assay microscope images. Compared to other algorithms
our approach, implemented in Java as ImageJ plugin based on the extension
package MiToBo, relies on a minimal set of configuration parameters.
Experimental evaluations show the high-quality of extracted assay
data and their suitability for biomedical investigations.},
doi = {10.1007/978-3-642-21257-4},
keywords = {Scratch assay, level set segmentation, texture, topology},
url = {http://www.springerlink.com/content/978-3-642-21256-7/#section=910893&page=1&locus=0}
}
@article{Glass12_PR,
author = {M. Gla{\ss} and B. M{\"o}ller and A. Zirkel and K. W{\"a}chter and
S. H{\"u}ttelmaier and S. 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}
}
@inproceedings{Gress10_BVM,
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},
booktitle = {{Bildverarbeitung f{\"u}r die Medizin}},
year = {2010},
editor = {Hans-Peter Meinzer and Thomas Martin Deserno and Heinz Handels and
Thomas Tolxdorff},
series = {Informatik Aktuell},
pages = {266-270},
address = {Berlin},
publisher = {Springer},
note = {ISBN 978-3-642-11967-5},
abstract = {Stress granules and processing bodies play a major role in analysing
the physiology of cells under various environmental conditions. We
present a fully automatic approach to detect such particles in fluorescence
labeled microscope images. The detection is based on scale-adaptive
analysis of wavelet coefficients allowing for an accurate detection
of particles with a large variety in size. Results on real images
illustrate the appropriateness of our approach and proof high quality.},
location = {Aachen},
url = {http://ceur-ws.org/Vol-574/bvm2010_54.pdf}
}
@inproceedings{Kirchner12_IJ,
author = {S. Kirchner and S. Posch and B. M{\"o}ller},
title = {Graphical Programming in Alida and ImageJ 2.0 with Grappa},
booktitle = {Proc. of ImageJ User \& Developer Conference},
year = {2012},
pages = {138-143},
address = {Mondorf-les-Bains, Luxembourg},
month = {October},
abstract = {Solving challenging image analysis problems usually requires to combine
several individual analysis steps into comprehensive workflows.
To find a suitable combination of algorithms is often quite elaborate and accomplished
interactively. In this paper we present our graphical program editor
''Grappa'' (Graphical Program Editor for Alida) supporting the design of workflows
from individual image analysis operators in a graphical manner.
Grappa is built on top of Alida and takes full advantage of Alida's
operator annotation and generic execution mechanisms, as well as of its functionality
to automatically generate graphical user interfaces for operators.
Grappa is under active development and available as prototypical plugin
for ImageJ and ImageJ 2.0.},
comment = {ISBN 2-919941-18-6}
}
@inproceedings{Misiak09_GCB,
author = {D. Misiak and S. Posch and N. St{\"o}hr and S. H{\"u}ttelmaier and
B. M{\"o}ller},
title = {Automatic Detection of Fluorescence Labeled Neurites in Microscope
Images},
booktitle = {German Conf. on Bioinformatics (GCB)},
year = {2009},
address = {Halle (Saale), Germany},
month = {September},
note = {Poster Presentation}
}
@inproceedings{Misiak09_WACV,
author = {Danny Misiak and Stefan Posch and Nadine St{\"o}hr and Stefan H{\"u}ttelmaier
and Birgit M{\"o}ller},
title = {Automatic Analysis of Fluorescence Labeled Neurites in Microscope
Images},
booktitle = {IEEE Workshop on Applications of Computer Vision (WACV '09)},
year = {2009},
pages = {118-124},
address = {Snowbird, Utah, USA},
month = {December},
publisher = {IEEE},
note = {ISBN: 978-1-4244-5496-9, IEEE Catalog Number: CFP09082-CDR},
abstract = {Microscope imaging technologies have turned out to yield an indispensable
tool in modern biomedical research. Combined with fluorescence labeling
techniques they not only provide new perspectives on tissues and
cells as a whole, but also on processes at the cellular level, and
will be one important experimental technique of systems biology.
To handle this steadily increasing amount of image data, in this
paper we propose a new and fully automatic approach for neurite segmentation
and protein quantification. Our technique combines three phases of
automatic neuron cell localization, neurite segmentation and protein
analysis. In the second stage active contour models based on hierarchical
Gradient Vector Flow fields are employed, enabling precise neurite
segmentation despite inhomogeneous texture. Neurite segmentation
results as well as protein quantification profiles from a set of
test images demonstrate the appropriateness of our approach for practical
biomedical research.},
city = {Snowbird, Utah, USA},
isbn = {978-1-4244-5496-9},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=5403112&contentType=Conference+Publications&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A5403027%29}
}
@phdthesis{Moeller05_PhD,
author = {M{\"o}ller, B.},
title = {Multi-Mosaikbilder - Ein Ansatz zur ikonischen Repr{\"a}sentation
von Bilddaten aktiver Kameras},
school = {Martin-Luther-Universit{\"a}t Halle-Wittenberg},
year = {2005},
abstract = {Die Dissertation stellt das neue Konzept der so genannten Multi-Mosaikbilder
zur effizienten Repr{\"a}sentation von Bildsequenzen aktiver Kameras
vor. Das Konzept zielt darauf ab, interaktiven Systemen ein visuelles
Ged{\"a}chtnis f{\"u}r ikonische Daten zur Verf{\"u}gung zu stellen,
das eine flexiblere Nutzung visueller Informationen erlaubt und damit
zu einer Erh{\"o}hung der Leistungsf{\"a}higkeit und einer Verbesserung
der Kommunikationsm{\"o}glichkeiten interaktiver Systeme beitragen
kann.
Mosaikbilder sind ein Mechanismus, der eine kompakte Darstellung von
Bildfolgen erm{\"o}glicht. Dabei werden alle Bilder einer Folge unter
Eliminierung redundanter Anteile und einer signifikanten Reduktion
des Datenvolumens zu einem Bild verschmolzen. Der Einsatz existierender
Verfahren zur Mosaikbildberechnung in interaktiven Systemen ist allerdings
h{\"a}ufig aufgrund der verwendeten Koordinatensysteme und der gew{\"a}hlten
Verarbeitungsstrategien mit Schwierigkeiten verbunden. Das neue Konzept
der Multi-Mosaikbilder erweitert und erg{\"a}nzt daher g{\"a}ngige
Ans{\"a}tze, um einen Einsatz dieser Techniken auch in ressourcenbeschr{\"a}nkten,
interaktiven Systemen zu erm{\"o}glichen.
Das neue Konzept gr{\"u}ndet im Kern auf der Verwendung polyedrischer
Koordinaten, in denen Bilddaten station{\"a}rer rotierender Kameras
weitgehend verzerrungsfrei repr{\"a}sentiert werden k{\"o}nnen. Gleichzeitig
wird die direkte Anwendung existierender Bildverarbeitungsalgorithmen
auf die Bilddaten erm{\"o}glicht. Dies gew{\"a}hrleistet einen einfachen
Zugriff auf die gespeicherten Informationen und erlaubt interaktiven
Systemen einen flexiblen Umgang mit der Datenstruktur. Dar{\"u}ber
hinaus unterst{\"u}tzt das neue Konzept eine inkrementelle Online-Berechnung
der Mosaikbilder, die Verarbeitung von Bildfolgen mit statischen
und dynamischen Inhalten, und die ad{\"a}quate Darstellung von Bilddaten
mit verschiedenen Zoomstufen innerhalb einer Aufl{\"o}sungshierarchie.
Die praktische Relevanz des entwickelten Konzeptes wurde durch die
Realisierung einer aktiven Szenenexploration auf Basis der Multi-Mosaikbilder
belegt, die den Kreislauf aus Datenrepr{\"a}sentation und aktiver
Akquisition schlie{\ss}t. Au{\ss}erdem erfolgte eine prototypische
Integration des visuellen Speichers in die Architektur des interaktiven,
mobilen Roboters BIRON, dessen F{\"a}higkeiten zum Lernen und Wiedererkennen
von Objekten auf diese Weise verbessert werden sollen.},
keywords = {Visueller Speicher, Interaktive Systeme, Multi-Mosaikbilder, Polyeder,
Online-Mosaikbildberechnung, Dynamische Szenen, Aktive Szenenexploration,
Mensch-Roboter-Interaktion, Objektlernen},
url = {http://sundoc.bibliothek.uni-halle.de/diss-online/05/05H124/index.htm}
}
@mastersthesis{Moeller01_Master,
author = {Birgit M{\"o}ller},
title = {Detektion von Bewegung bei der Berechnung von Mosaikbildern},
school = {Universit{\"a}t Bielefeld, Technische Fakult{\"a}t, AG Angewandte
Informatik},
year = {2001},
type = {Diploma Thesis},
address = {Bielefeld, Germany},
month = {March},
url = {http://aiweb.techfak.uni-bielefeld.de/pubs/2007/detektion-von-bewegung-bei-der-berechnung-von-mosaikbildern}
}
@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)},
year = {2007},
pages = {233-240},
address = {Barcelona, Spain},
month = {March},
abstract = {Geometric registration of visual images is a fundamental intermediate
processing step in a wide variety of computer vision applications
that deal with image sequence analysis. 2D motion recovery and mosaicing,
3D scene reconstruction and also motion detection approaches strongly
rely on accurate registration results. However, automatically assessing
the overall quality of a registration is a challenging task. In particular,
optimization criteria used in registration are not necessarily closely
linked to the final quality of the result and often show a lack of
local sensitivity. In this paper we present a new approach for an
objective quality metric in 2D image registration. The proposed method
is based on local structure analysis and facilitates voting-techniques
for error pooling, leading to an objective measure that correlates
well with the visual appearance of registered images. Since observed
differences are furthermore classified in more detail according to
various underlying error sources, the new measure not only yields
a suitable base for objective quality assessment, but also opens
perspectives towards an automatic and optimally adjusted correction
of errors.}
}
@inproceedings{Moeller08_GCB,
author = {B. M{\"o}ller and O. Gre{\ss} and S. Posch},
title = {A Comparative Study of Robust Feature Detectors for 2D Electrophoresis
Gel Image Registration},
booktitle = {Proc. of German Conference on Bioinformatics (GCB)},
year = {2008},
editor = {Andreas Beyer and Michael Schroeder},
volume = {P-136},
series = {Lecture Notes in Informatics},
pages = {138-147},
address = {Dresden, Germany},
month = {September},
abstract = {In this study we consider the performance of different feature detectors
used as the basis for the registration of images from two-dimensional
gel electrophoresis. These are three spot detectors also used to
identify proteins, and two domain independent keypoint detectors.
We conduct a case study with images from a publically available data
set which are synthetically distorted using thin plate splines. The
performance is assessed by the repeatability score, the probability
of an image structure to be detected in original and distorted images
with reasonable localization accuracy.},
url = {http://subs.emis.de/LNI/Proceedings/Proceedings136/article2249.html}
}
@inproceedings{Moeller11_ICVS,
author = {Birgit M{\"o}ller and Oliver Gre{\ss} 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 and B.A. Draper and M. Thonnat},
volume = {6962},
series = {LNCS},
pages = {1-10},
address = {Sophia Antipolis, France},
publisher = {Springer},
abstract = {Proper archiving or later reconstruction and verification of results
in data analysis requires thorough logging of all manipulative actions
on the data and corresponding parameter settings. Unfortunately such
documentation tasks often enforce extensive and error prone manual
activities by the user. To overcome these problems we present Alida,
an approach for fully automatic documentation of data analysis procedures.
Based on an unified operator interface all operations on data including
their sequence and configurations are registered during analysis.
Subsequently these data are made explicit in XML graph representations
yielding a suitable base for visual and analytic inspection. As example
for the application of Alida in practice we present MiToBo, a toolbox
for image analysis implemented on the basis of Alida and demonstrating
the advantages of automatic documentation for image analysis procedures.},
doi = {10.1007/978-3-642-23968-7_1},
keywords = {automatic documentation, meta data, XML, processing graph, image analysis},
url = {http://www.springerlink.com/content/m331u047758nn84l/}
}
@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. M{\"o}ller and O. Gre{\ss} and N. St{\"o}hr and S. H{\"u}ttelmaier
and S. Posch},
volume = {229},
series = {Communications in Computer and Information Science},
note = {ISBN 978-3-642-25381-2},
abstract = {Analysis of biomolecules in cells essentially relies on fluorescence
microscopy. In combination with fully automatic image analysis it
allows for insights into biological processes on the sub-cellular level and thus
provides valuable information for systems biology studies. In this paper we present
two new techniques for automatic segmentation of cell areas and included sub-cellular
particles. A new cascaded and intensity-adaptive segmentation scheme
based on coupled active contours is used to segment cell areas. Structures on
the sub-cellular level, i.e. stress granules and processing bodies, are detected applying
a scale-adaptive wavelet-based detection technique. Combining these results
yields fully automated analyses of biological processes, and allows for new insights
into interactions between different cellular structures and their distributions
among different cells. We present an experimental evaluation based on ground-truth
data that confirms the high-quality of our segmentation results regarding
these aims and opens perspectives towards deeper insights into biological systems
for other problems from systems biology.},
doi = {10.1007/978-3-642-25382-9},
keywords = {Segmentation, wavelets, a contrario, active contours, fluorescent
microscope imaging, cells, granules},
url = {http://www.springer.com/computer/image+processing/book/978-3-642-25381-2 }
}
@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},
volume = {2},
pages = {97-106},
address = {Angers, France},
month = {May},
abstract = {Microscope imaging is an indispensable tool in modern systems biology.
In combination with fully automatic image analysis it allows for
valuable insights into biological processes on the sub-cellular level
and fosters understanding of biological systems. In this paper we
present two new techniques for automatic segmentation of cell areas
and included sub-cellular particles. A new cascaded and intensity-adaptive
segmentation scheme based on coupled active contours is used to segment
cell areas. Structures on the sub-cellular level, i.e. stress granules
and processing bodies, are detected applying a scale-adaptive wavelet-based
detection technique. Combining these results allows for complementary
analysis of biological processes. It yields new insights into interactions
between different particles and distributions of particles among
different cells. Our experimental evaluations based on ground-truth
data prove the high-quality of our segmentation results regarding
these aims and open perspectives towards deeper insights into biological
systems on the sub-cellular level.}
}
@inproceedings{Moeller12_IJ,
author = {B. M{\"o}ller and D. Misiak},
title = {Snake Optimizer - Object Segmentation with Parametric Active Contours
in ImageJ},
booktitle = {Proc. of ImageJ User \& Developer Conference},
year = {2012},
pages = {215-217, 222},
address = {Mondorf-les-Bains, Luxembourg},
month = {October},
abstract = {Parametric active contour models, commonly denoted as snakes, provide
an integrated framework for transforming object segmentation tasks into
well-founded mathematical optimization problems. Over the years snakes
have proven large flexibility in segmenting a great variety of different
objects in lots of setups. Nevertheless, each new object segmentation problem
again raises the question if snakes are capable of solving the problem
and if so, which combination of energies to apply. Here we present
our ImageJ plugin 'SnakeOptimizer' which implements object segmentation
based on 2D parametric active contours. It is well-suited to support users in
answering the above questions during rapid-prototyping stages, as
well as for being integrated into productive analysis workflows.
The functional core of the implementation can easily be extended with new energy models
based on functionality provided by Alida.1 The ImageJ plugin features
a handy GUI for interactive use, and the optimizer can also be run headless from
command line or on the programming level using its intuitive API.},
comment = {ISBN 2-919941-18-6},
keywords = {Image Segmentation, Active Contours, Snakes, ImageJ, Alida}
}
@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},
pages = {1-4},
address = {Tampa, Florida, USA},
month = {December},
publisher = {IEEE},
abstract = {Ensembles of multiple (active) cameras yield an important ingredient
in modern tracking and surveillance applications. They overcome the
limited fields-of-view of single cameras, however, require robust
procedures for handing over tracking tasks from one camera to another.
In this paper a calibration-free procedure is proposed that allows
for fast and reliable camera hand-over in Ambient Intelligence (AmI)
applications. The approach is based on online acquisition of scenario-specific
target models and especially solves the problem of significant changes
in object view during hand-over. Real-world results acquired in an
AmI environment prove the effectiveness of our technique.},
url = {http://figment.csee.usf.edu/~sfefilat/data/papers/TuAT9.19.pdf}
}
@inproceedings{Moeller02_DAGM,
author = {Birgit M{\"o}ller and Stefan Posch},
title = {Analysis of Object Interactions in Dynamic Scenes},
booktitle = {Pattern Recognition, Proc. of 24th DAGM Symposium},
year = {2002},
editor = {L. van Gool},
series = {LNCS 2449},
pages = {361-369},
address = {Zurich, Switzerland},
month = {September},
publisher = {Springer},
abstract = {One important source of information in scene understanding is given
by actions performed either by human actors or robots. In this paper
an approach to recognition and low-level interpretation of actions
is presented. Since actions are characterized by specific motion
patterns of moving objects, recognition is done by detecting such
motion patterns as specific constellations of interactions between
moving objects. First of all, motion detection and tracking algorithms
are applied to extract correspondences between moving objects in
consecutive images of a sequence. Subsequently these are represented
with a graph data-structure for further analysis. To detect interactions
of moving objects robustly a short history of motion of objects is
traced using a finite-state automaton. Finally activities are segmented
based on detected interactions. Since robust motion data are required
consistency checks and corrections of the acquired motion data are
performed in parallel.},
isbn = {3-540-44209-X},
numpages = {9},
url = {http://www.springerlink.com/content/1fgrp9l90vjac9f1/fulltext.pdf}
}
@inproceedings{Moeller05_Koblenz,
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},
year = {2005},
editor = {Dietrich Paulus and Detlev Droege},
pages = {27-32},
address = {Koblenz},
organization = {Universit{\"a}t Koblenz-Landau, Institut f{\"u}r Informatik},
abstract = {Visual data acquired with active cameras yields an important source
of information for interactive systems. However, since image sequences
usually comprise large data volumes and notable portions of redundant
information analysis is often diffcult. Hence, data structures are
required that allow for compact representation of image sequences.
In this paper we introduce our concept of a visual scene memory.
The memory is based on mosaic images enabling compact image sequence
representation by fusing all sequence images into one single frame
while eliminating redundancies. Since interactive systems put special
demands on mosaicing techniques we developed a new mosaic concept
called multi-mosaics well-suited to be used with interactive systems.
The memory is focussed on adaquate representation of iconic data,
however, not restricted to it. Rather higher-level data, particularly
motion data as well as data suitable for active camera control are
additionally included completing the visual scene representation.},
isbn = {1860-4471}
}
@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},
editor = {B. Radig and S. Florczyk},
series = {LNCS 2191},
pages = {208-215},
address = {Munich, Germany},
month = {September},
publisher = {Springer},
abstract = {Mosaic images provide an efficient representation of image sequences
and simplify scene exploration and analysis. However, the application
of conventional methods to generate mosaics of scenes with moving
objects causes integration errors and a loss of dynamic information.
In this paper a method to compute mosaics of dynamic scenes is presented
addressing the above mentioned problems. Moving pixels are detected
in the images and not integrated in the mosaic yielding a consistent
representation of the static scene background. Furthermore, dynamic
object information is extracted by tracking moving regions. To account
for unavoidable variances in region segmentation topologically neighboring
regions are grouped into sets before tracking. The regions' and objects'
motion characteristics are described by trajectories. Along with
the background mosaic they provide a complete representation of the
underlying scene which is idealy suited for further analysis.},
isbn = {3-540-42596-9},
numpages = {8},
url = {http://dl.acm.org/citation.cfm?id=756114}
}
@inproceedings{Moeller12_ISBI,
author = {B. M{\"o}ller and S. Posch},
title = {Comparing Active Contours for the Segmentation of Biomedical Images},
booktitle = {Proc. of IEEE International Symposium on Biomedical Imaging (ISBI)},
year = {2012},
pages = {736-739},
address = {Barcelona, Spain},
month = {May},
note = {IEEE Catalog No.: CFP12BIS-CDR, ISBN: 978-1-4577-1856-4},
abstract = {Application of active contours for image segmentation raises the question
of contour representation, i.e. whether to use snakes or level sets.
The representation directly affects is- sues like topology-preservation
and energy optimization. In this paper we aim to contribute to the
understanding of spe- cific characteristics of contour representations
with a detailed comparison of snakes vs. non-PDE level sets. Based
on the same energy functional and applied to different kinds of real-
world data our experiments show minor differences in seg- mentation
quality, but outline important distinctions regarding implementation,
parameter settings and computational effort.},
keywords = {Snakes, non-PDE level sets, comparison},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6235653&contentType=Conference+Publications&sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A6235468%29%26pageNumber%3D8}
}
@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},
address = {Heidelberg, Germany},
month = {September},
abstract = {Quantitative analysis of microscopy cell images requires accurate
detection of cell boundaries, nuclei and sub-cellular structures.
Accordingly, tools for integrated cell image analysis are required
which not only provide a variety of different segmentation and detection
algorithms, but at the same time support easy usage also by life
scientists. In this paper we present our integrated cell analysis
tool MiCA offering different segmentation techniques, e.g., based
on wavelets or snakes. Iterative optimization of snake energies depends
on a variety of parameters that require thorough adjustment for optimal
results. To facilitate easy use of these techniques MiCA provides
a new energy normalization scheme for snakes allowing for intuitive
interpretation of energy parameters and, thus, simplified cell image
analysis. The high quality of the result data of MiCA is proven on
two sample data sets by qualitative assessments and ground-truth
comparisons.},
city = {Heidelberg},
pdf = {http://www.miaab.org/miaab-2011-heidelberg-papers/miaab-2011-h-moeller.pdf}
}
@article{Moeller09_Elec,
author = {Birgit M{\"o}ller and Stefan Posch},
title = {Robust Features for 2-D Electrophoresis Gel Image Registration},
journal = {Electrophoresis},
year = {2009},
volume = {30},
pages = {4137-4148},
abstract = {Proteomics is a rapidly growing field of modern biology. Since quantitative
data of proteins involved in dynamic processes of living organisms
are essential for understanding the basics of life, techniques like
2-DE and related procedures for automatic data interpretation are
at the heart of this research field. They are strongly required to
enable analysis and interpretation of the emerging amount of available
data. Analyzing and interpreting gel image data usually requires
the comparison of gels from different experiments and, thus, a prior
registration of gels. This can be accomplished using featureless,
feature-based or hybrid registration approaches combining both techniques.
Recently, the latter ones have shown high performance, and it is
undoubtful that in general robust and reliable features are an essential
ingredient and valuable source of information for high-quality image
registration. In this paper we provide a thorough overview and elaborate
analysis of the capabilities of available feature detectors for gel
image registration. Particularly, a detailed and extensive comparative
study is presented where common spot-specific detectors are included
as well as image-content independent detectors that were not applied
to the task of gel image registration until now. The study incorporates
tests on several thousand synthetically deformed images from different
experimental conditions. As a result it provides valuable quantitative
data allowing for direct objective comparisons of various detectors,
and is well suited to guide the design of new registration algorithms.},
doi = {10.1002/elps.200900293},
keywords = {2-DE; Comparative study; Feature detectors; Image registration; Keypoints},
url = {http://onlinelibrary.wiley.com/doi/10.1002/elps.200900293/full}
}
@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},
volume = {18},
pages = {201-206},
number = {2},
abstract = {Image registration is an important ingredient in a wide variety of
computer vision applications. Over the years countless algorithms
emerged that allow for robust registration of image sequences. Unfortunately,
high quality results still cannot be guaranteed in any case. Especially
in interactive online systems that strongly rely on results of unsupervised
registration algorithms, techniques for automatic quality analysis
and failure compensation are indispensable. In this paper we present
a new concept for an integrated and fully automatic detection and
analysis of errors in registration. Based on a new metric for registration
quality assessment, image differences are robustly detected. In addition,
a hierarchical analysis scheme is proposed that allows distinguishing
between various underlying error sources, all having different impacts
on a registration result and requesting for individual compensation
strategies.},
doi = {10.1134/S105466180802003X},
publisher = {Springer},
pdf = {http://www.springerlink.com/content/94j30064x573x783/fulltext.pdf}
}
@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},
pages = {I:152-161},
address = {University of Warwick, Coventry, UK},
month = {September},
abstract = {Automatic quality assessment of image registration results is an important
issue in image processing. Many applications strongly depend on accurate
registration results, sometimes even requiring automatic self-recovery
from registration failures. In doing so it is not sufficient just
to detect registration errors. Also a distinction between different
error sources is necessary, as each source has an individual impact
on the final registration result and requires specific compensation
strategies. We present a new approach to automatically identify lens
distortions in image pairs, known to have a significant impact on
registration. The key idea is to analyse registration residuals and
to learn a model of spatial residual distributions typical for distorted
images. Our approach relies on a new metric for registration quality
assessment and implements a regression scheme based on SVMs for predicting
distortions in unknown data. The potential of the approach is demonstrated
by experimental results on synthetic as well as real image data.},
pdf = {http://www.dcs.warwick.ac.uk/bmvc2007/proceedings/CD-ROM/papers/paper-123.pdf }
}
@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},
address = {Bielefeld, Germany},
month = {March},
abstract = {Geometric image registration by estimating homographies is an important
processing step in a wide variety of computer vision applications.
The 2D registration of two images does not require an explicit reconstruction
of intrinsic or extrinsic camera parameters. However, correcting
images for non-linear lens distortions is highly recommended. Unfortunately,
standard calibration techniques are sometimes difficult to apply
and reliable estimations of lens distortions can only rarely be obtained.
In this paper we present a new technique for automatically detecting
and categorising lens distortions in pairs of images by analysing
registration results. The approach is based on a new metric for registration
quality assessment and facilitates a PCA-based statistical model
for classifying distortion effects. In doing so the overall importance
for lens calibration and image corrections can be checked, and a
measure for the efficiency of accordant correction steps is given.},
doi = {10.2390/biecoll-icvs2007-174},
keywords = {Camera Calibration, Lens Distortions, Image Registration, Automatic
Assessment, Statistical Classification},
pdf = {http://www.icvs2007.org/ccmvs/CCMVS2007-174.pdf },
url = {http://biecoll.ub.uni-bielefeld.de//frontdoor.php?source_opus=98&la=en}
}
@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},
address = {Ettlingen, Germany},
month = {August},
abstract = {Image registration is an important ingredient in a wide variety of
computer vision applications. Over the years countless algorithms
emerged that allow for robust registration of image sequences. Unfortunately,
high quality results still cannot be guaranteed in any case. Especially
in interactive online systems that strongly rely on results of unsupervised
registration algorithms, techniques for automatic quality analysis
and failure compensation are indispensable. In this paper we present
a new concept for an integrated and fully automatic detection and
analysis of errors in registration. Based on a new metric for registration
quality assessment, image differences are robustly detected. In addition,
a hierarchical analysis scheme is proposed that allows to distinguish
between various underlying error sources, all having different impacts
on a registration result and requesting for individual compensation
strategies.}
}
@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},
type = {Technical Report},
number = {2007-03},
month = {December},
abstract = {Robots that support humans in their private homes by carrying out
tasks of everyday life require sophisticated skills. Among others
they have to provide multi-modal communication facilities, and also
generic recognition and learning capabilities are indispensable.
However, several of these skills, e.g., the recognition of objects,
cannot be seen in isolation. Rather cognitive motivated approaches
are on demand that integrate aspects of perception, reasoning and
learning. Since all of these processes strongly rely on memorising
and recalling data a visual memory component yields a fundamental
building block of cognitive motivated system architectures.
Such a memory usually subsumes different levels of abstraction ranging
from low-level iconic to high-level categorial data and will often
be organised hierarchically. Within this paper we propose an extended
iconic scene representation for low level visual data, the SMARD
memory module.
It is particularly designed to meet the requirements of interactive
and mobile robotic systems. These systems significantly benefit from
such a memory component, however, at the same time they enforce strict
constraints on its architecture, e.g., regarding flow of data and
control or resource management strategies. Our approach is based
on mosaic images that are computed following an incremental strategy.
Due to polytopial coordinate frames they support easy data access
and a direct analysis. The practical relevance of our approach is
outlined by two example applications that illustrate its benefits
with regard to intuitive and efficient human-robot interaction.},
pdf = {http://wcms-neu1.urz.uni-halle.de/download.php?down=5355&elem=1555433}
}
@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)},
year = {2006},
pages = {413-421},
address = {Set{\'u}bal, Portugal},
month = {February},
note = {to appear.},
abstract = {One basic capability of interactive and mobile systems to cope with
unknown situations and environments is active, sequence-based visual
scene analysis. Image sequences provide static as well as dynamic
and also 2D as well as 3D information about a certain scene. However,
at the same time they require efficient mechanisms to handle their
large data volumes. In this paper we introduce a new concept of a
visual scene memory for interactive mobile systems that supports
these systems with a space- and time-efficient data structure for
representing iconic information. The memory is based on a new kind
of mosaic images called multi-mosaics and allows to efficiently store
and process sequences of stationary rotating and zooming cameras.
Its main key features are polytopial reference coordinate frames
and an online data processing strategy. The polytopes provide euclidean
coordinates and thus allow the application of standard image analysis
algorithms directly to the data yielding easy access and analysis,
while online data processing preserves system interactivity. Additionally,
mechanisms are included to properly handle multi-resolution data
and to deal with dynamic scenes. The concept has been implemented
in terms of an integrated system that can easily be included as an
additional module in the architecture of interactive and mobile systems.
As one prototypical example for possible fields of application the
integration of the memory into the architecture of an interactive
multi-modal robot is discussed emphasizing the practical relevancy
of the new concept.}
}
@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},
pages = {117-125},
address = {INRIA Rocquencourt, France},
month = {March},
abstract = {Processing visual data is an important ability of interactive systems
to act in dynamically changing environments. Looking at the human
visual and cognitive system this requires efficient mechanisms for
data processing and storage as well as intelligent strategies for
data acquisition. In this paper we present a visual memory supporting
efficient representation of image sequences of active cameras in
an online fashion. The memory is based on mosaic images extending
the field of view of a camera in space and time. As one prototypical
field of application for the memory active scene exploration is discussed.
The temporally and spatially integrated data of the memory combined
with additional feature maps serves as an ideal starting point for
the selection of focus points. Hence the memory demonstrates the
combination of efficient acquisition and storage of visual data and
helps to provide interactive systems with high flexibility to operate
in dynamically changing environments.}
}
@inproceedings{Moeller05_IROS,
author = {B. M{\"o}ller and S. Posch and A. Haasch and J. Fritsch and G. Sagerer},
title = {Interactive Object Learning for Robot Companions using Mosaic Images},
booktitle = {Proc. IEEE/RSJ Int. Conf. on Intelligent Robots and Systems},
year = {2005},
pages = {2650 - 2655},
address = {Edmonton, Alberta, Canada},
month = {August},
abstract = {Natural human-robot interaction (HRI) is a key feature of mobile robot
companions collaborating with humans. To achieve natural HRI, multiple
communication modalities like vision, speech, and gestures have to
be utilized. Besides, capabilities to emulate cognitive processes,
e.g., object learning and object recognition, are essential. In this
work we present a new approach to interactive object learning enabling
multi-view object representation. To overcome a robot's limitation
of having only one view point, we make use of an iconic memory consisting
of previously acquired images. As the relevant scene area is unknown
during construction of the iconic memory, a representation in the
form of mosaic images is applied. The relevant image patches describing
an object referenced by the user are selected through an object attention
mechanism. The resulting multi-view object representations improve
the flexibility of our interactive approach for object learning.},
url = {http://ieeexplore.ieee.org/iel5/10375/32977/01545009.pdf?isnumber=&arnumber=1545009}
}
@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},
address = {Istanbul, Turkey},
month = {August},
publisher = {IEEE},
abstract = {Cell tissue in microscope images is often grained and its intensities
do not well agree with Gaussian distribution assumptions widely used
in many segmentation approaches. We present a new cascaded segmentation
scheme for inhomogeneous cell tissue based on active contour models.
Cell regions are iteratively expanded from initial nuclei regions
applying a data-dependent number of optimization levels. Experimental
results on a set of microscope images from a human hepatoma cell
line prove high quality of the results with regard to the cell segmentation
task and biomedical investigations.},
url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5597237}
}
@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},
editor = {B. Michaelis and G. Krell},
series = {LNCS 2781},
pages = {386-393},
address = {Magdeburg, Germany},
month = {September},
publisher = {Springer},
abstract = {Mosaicing is a technique to efficiently condense the static information
of an image sequence within one extended mosaic image. The core of
mosaicing is to estimate a global transformation between images due
to the global camera motion. This is usually accomplished by either
matching segmented image features or exploiting all iconic image
data directly within a featureless approach. In this paper we propose
to combine aspects from both techniques where we abandon to segment
features, however select pixels to be used for parameter estimation
based on structural image data and information about independently
moving scene parts. While this results in a speed up of the estimation
process the main focus is to improve robustness with respect to ambiguities
arising from homogeneous image regions and to motion in the scene.},
url = {http://www.springerlink.com/content/81w82twx323pvtm0/fulltext.pdf}
}
@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, Spec. Issue},
year = {2004},
volume = {14(2)},
pages = {262-266},
abstract = {Interactive systems using active cameras produce a large amount of
image data to be processed. The task of a visual memory is to represent
this data in an efficient way and thus assisting subsequent image
analysis algorithms. In this paper we extent our mosaic based approach
to large scenes where distortions occur if the camera rotation covers
a wide angle. This problem can be solved by using a spherical mosaic
surface. However, since most vision algorithms are created for planar
images we propose to tile the sphere with planar patches resulting
in a mosaic polytope we call multi-mosaic. A more spacious scene
can be represented by a number of such multi-mosaics taken from different
spatial positions. If a mobile robot is used for image acquisition
the path in between can additionally be represented by manifold mosaics
to connect the positions.}
}
@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},
pages = {108-111},
address = {Katun Village, Altai Region, Russian Federation},
month = {25.-30. August},
abstract = {Interactive systems using active cameras produce a big amount of image
data to be processed. The task of a visual memory is to represent
this data in an efficient way and thus assisting subsequent image
analysis algorithms. In this paper we extent our mosaic based approach
to large scenes where distortions occure if the camera rotation covers
a wide angle. This problem can be solved by using a spherical mosaic
surface. However, since most vision algorithms are created for planar
images we propose to tile the sphere with planar patches resulting
in a mosaic polytope we call multi-mosaic. A more spacious scene
can be represented by a number of such multi-mosaics taken from different
spatial positions. If a mobile robot is used for image acquisition
the path in between can additionally be represented (by manifold
mosaics) to connect the positions.}
}
@inproceedings{Posch12_IJ,
author = {S. Posch and B. M{\"o}ller},
title = {Automatic Generation of Processing Histories using Alida},
booktitle = {Proc. of ImageJ User \& Developer Conference},
year = {2012},
pages = {218-221},
address = {Mondorf-les-Bains, Luxembourg},
month = {October},
abstract = {Analysis of data is subject of many fields of applications. Besides
the results per se, the documentation of analysis processes is important
for later verification, reconstruction, or publication. As manual documentation
is tedious and error prone the Java library Alida provides fully automatic
extraction of processing histories.
As applications we present our own image processing toolbox MiToBo
based on ImageJ and demonstrate the integration of Alida into ImageJ 2.0.},
comment = {ISBN 2-919941-18-6},
keywords = {Processing History, Process Documentation, Processing Graph, XML,
Alida, ImageJ}
}
@inproceedings{Posch12_ISBI_WS,
author = {S. Posch and B. M{\"o}ller},
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},
note = {Poster presentation},
abstract = {Analysis of biomedical data may be interpreted as a flow of objects
through an analysis pipeline. The Java framework Alida (http://www.informatik.uni-halle.de/alida)
defines the concept of operators as the single places of these manipulations.
Typically, operators may be invoked sequentially or in parallel,
and often also nested. Besides invocation on the programming level
their functionality should also be available directly to users, including
developers of algorithms and non-experts. This calls for graphical
as well as command line interfaces. Eliminating the need to explicitly
code these interfaces, Alida features fully automated generation
of graphical and command line user interfaces for each operator implemented
in the Alida framework.
The basis is a formalism for an operator to define all input and
output data objects and parameters to control processing. Automatic
generation of interfaces is based on the model view presenter design
pattern to achieve maximal independence between the operators, interfaces,
and I/O of data objects. For implementation Java's annotation mechanism
is used. The programmer is only required to properly annotate classes
and member variables. Out of the box this facilitates I/O for a wide
variety of Java objects including primitive data types, enumerations,
arrays, and collections. In a generic way Alida handles also operators
as parameters of other operators and inheritance. Only specialized
classes like images require additional data providers to be implemented.
While Alida is devised for data processing in general, it is used
in our image analysis toolbox MiToBo (http://www.informatik.uni-halle.de/mitobo)
for biomedical image analysis which is based on ImageJ and compatible
to it.}
}
@inproceedings{Moeller03_CISST,
author = {Denis Williams and Birgit M{\"o}ller and Stefan Posch},
title = {Integrated System for a Visual Memory Based on Mosaics},
booktitle = {Proceedings of International Conference on Imaging Science, Systems,
and Technology (CISST'03)},
year = {2003},
editor = {H.R. Arabnia and Youngsong Mun},
pages = {II: 633-639},
address = {Monte Carlo Resort, Las Vegas, Nevada, USA},
month = {23.-26. June},
publisher = {CSREA Press},
abstract = {Exploring a scene with an active camera yields an image sequence containing
implicit information of the environment, but also a considerable
amount of redundancies. In this paper the system AViSMo is described
to explicitly represent the information about the scene in a visual
memory. It is based on the construction of a mosaic image containing
non-redundantly iconic data of static scene parts. This mosaic is
augmented with trajectories of moving objects, activities detected
from image data in a bottom-up fashion, and external high-level data.
AViSMo is a highly modular and extendable system, capable of communicating
with external components using a variety of transport mechanisms.
As an example of such an external component it comprises a GUI to
control and visualize the mosaicing process. Thus, it is ideally
suited to supply interactive systems with a visual scene memory.}
}
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